151
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Newman R, McHugh J, Turner M. RNA binding proteins as regulators of immune cell biology. Clin Exp Immunol 2015. [PMID: 26201441 DOI: 10.1111/cei.12684] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Sequence-specific RNA binding proteins (RBP) are important regulators of the immune response. RBP modulate gene expression by regulating splicing, polyadenylation, localization, translation and decay of target mRNAs. Increasing evidence suggests that RBP play critical roles in the development, activation and function of lymphocyte populations in the immune system. This review will discuss the post-transcriptional regulation of gene expression by RBP during lymphocyte development, with particular focus on the Tristetraprolin family of RBP.
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Affiliation(s)
- R Newman
- Babraham Institute, Cambridge, UK
| | - J McHugh
- Babraham Institute, Cambridge, UK
| | - M Turner
- Babraham Institute, Cambridge, UK
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152
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Abstract
Messenger ribonucleoprotein (mRNP) granules are dynamic, self-assembling structures that harbor non-translating mRNAs bound by various proteins that regulate mRNA translation, localization, and turnover. Their importance in gene expression regulation is far reaching, ranging from precise spatial-temporal control of mRNAs that drive developmental programs in oocytes and embryos, to similarly exquisite control of mRNAs in neurons that underpin synaptic plasticity, and thus, memory formation. Analysis of mRNP granules in their various contexts has revealed common themes of assembly, disassembly, and modes of mRNA regulation, yet new studies continue to reveal unexpected and important findings, such as links between aberrant mRNP granule assembly and neurodegenerative disease. Continued study of these enigmatic structures thus promises fascinating new insights into cellular function, and may also suggest novel therapeutic strategies in various disease states.
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Affiliation(s)
- J Ross Buchan
- a Department of Molecular and Cellular Biology ; University of Arizona ; Tucson , AZ USA
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153
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Mikhed Y, Görlach A, Knaus UG, Daiber A. Redox regulation of genome stability by effects on gene expression, epigenetic pathways and DNA damage/repair. Redox Biol 2015; 5:275-289. [PMID: 26079210 PMCID: PMC4475862 DOI: 10.1016/j.redox.2015.05.008] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 05/28/2015] [Accepted: 05/29/2015] [Indexed: 02/07/2023] Open
Abstract
Reactive oxygen and nitrogen species (e.g. H2O2, nitric oxide) confer redox regulation of essential cellular signaling pathways such as cell differentiation, proliferation, migration and apoptosis. In addition, classical regulation of gene expression or activity, including gene transcription to RNA followed by translation to the protein level, by transcription factors (e.g. NF-κB, HIF-1α) and mRNA binding proteins (e.g. GAPDH, HuR) is subject to redox regulation. This review will give an update of recent discoveries in this field, and specifically highlight the impact of reactive oxygen and nitrogen species on DNA repair systems that contribute to genomic stability. Emphasis will be placed on the emerging role of redox mechanisms regulating epigenetic pathways (e.g. miRNA, DNA methylation and histone modifications). By providing clinical correlations we discuss how oxidative stress can impact on gene regulation/activity and vise versa, how epigenetic processes, other gene regulatory mechanisms and DNA repair can influence the cellular redox state and contribute or prevent development or progression of disease.
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Affiliation(s)
- Yuliya Mikhed
- 2nd Medical Clinic, Department of Cardiology, Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Agnes Görlach
- German Heart Center Munich at the Technical University Munich, DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
| | - Ulla G Knaus
- Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland
| | - Andreas Daiber
- 2nd Medical Clinic, Department of Cardiology, Medical Center of the Johannes Gutenberg University, Mainz, Germany.
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154
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Kratochvill F, Gratz N, Qualls JE, Van De Velde LA, Chi H, Kovarik P, Murray PJ. Tristetraprolin Limits Inflammatory Cytokine Production in Tumor-Associated Macrophages in an mRNA Decay-Independent Manner. Cancer Res 2015; 75:3054-64. [PMID: 26183929 DOI: 10.1158/0008-5472.can-15-0205] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 05/08/2015] [Indexed: 12/14/2022]
Abstract
Tristetraprolin (TTP) is an inducible zinc finger AU-rich RNA-binding protein essential for enforcing degradation of mRNAs encoding inflammatory chemokines and cytokines. Most studies on TTP center on the connection between mRNA half-life and inflammatory output, because loss of TTP amplifies inflammation by increasing the stability of AU-rich mRNAs. Here, we focused on how TTP controls cytokine and chemokine production in the nonresolving inflammation of cancer using tissue-specific approaches. In contrast with model in vitro macrophage systems, we found constitutive TTP expression in late-stage tumor-associated macrophages (TAM). However, TTP's effects on AU-rich mRNA stability were negligible and limited by constitutive p38α MAPK activity, which was the main driver of proinflammatory cytokine production in TAMs at the posttranscriptional level. Instead, elimination of TTP caused excessive protein production of inflammatory mediators, suggesting TTP-dependent translational suppression of AU-rich mRNAs. Manipulation of the p38α-TTP axis in macrophages has significant effects on the growth of tumors and therefore represents a means to manipulate inflammation in the tumor microenvironment.
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Affiliation(s)
- Franz Kratochvill
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee. Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Nina Gratz
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Joseph E Qualls
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee. Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Lee-Ann Van De Velde
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee. Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Hongbo Chi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Pavel Kovarik
- Max F. Perutz Laboratories, Center for Molecular Biology, University of Vienna, Vienna, Austria
| | - Peter J Murray
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee. Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee.
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155
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An interplay between the p38 MAPK pathway and AUBPs regulates c-fos mRNA stability during mitogenic stimulation. Biochem J 2015; 467:77-90. [PMID: 25588078 DOI: 10.1042/bj20141100] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Mitogen-activated protein kinase (MAPK) pathways constitute key regulatory elements linking extracellular stimuli to nuclear gene expression. Immediate-early responsive genes (IEGs) of the activator protein 1 (AP-1) family, such as fos, achieve peak expression levels shortly after cells are stimulated with growth factors and sharply decrease thereafter. Several AU-rich binding proteins (AUBPs), including HuR (Hu-antigen R, Elav-like protein 1, ELAVL1) and KSRP (far upstream element-binding protein 2, KHSRP) bind to a fos AU-rich element (ARE) present in the 3'-UTR (untranslated region) of fos mRNA regulating its stability by a still poorly defined mechanism. We show in the present study that, whereas HuR binds and stabilizes transcribed reporter mRNAs bearing the fos 3'-UTR, KSRP counteracts this effect. Furthermore, we found that fos mRNA stability and HuR phosphorylation status are dependent on the activity of p38 MAPK in both epithelial cells and fibroblasts upon proliferative stimulation. Analysing PPI (protein-protein interaction) networks, we performed a thorough query of interacting proteins for p38 MAPKs, HuR and other AUBPs upon growth factor stimulation. This revealed novel HuR interactors including inhibitors of protein phosphatase 2 (PP2A) activity. Over-expression of two of these interactors, pp32 and APRIL (acidic leucine-rich nuclear phosphoprotein 32 family member B, ANP32B) and pharmacological inhibition of PP2A stabilized a fos reporter mRNA. Our results indicate that p38 MAPK regulates fos mRNA decay by affecting the state of phosphorylation of HuR while controlling yet to be fully elucidated PP regulatory networks.
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156
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Boucas J, Fritz C, Schmitt A, Riabinska A, Thelen L, Peifer M, Leeser U, Nuernberg P, Altmueller J, Gaestel M, Dieterich C, Reinhardt HC. Label-Free Protein-RNA Interactome Analysis Identifies Khsrp Signaling Downstream of the p38/Mk2 Kinase Complex as a Critical Modulator of Cell Cycle Progression. PLoS One 2015; 10:e0125745. [PMID: 25993413 PMCID: PMC4439058 DOI: 10.1371/journal.pone.0125745] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 03/26/2015] [Indexed: 12/11/2022] Open
Abstract
Growing evidence suggests a key role for RNA binding proteins (RBPs) in genome stability programs. Additionally, recent developments in RNA sequencing technologies, as well as mass-spectrometry techniques, have greatly expanded our knowledge on protein-RNA interactions. We here use full transcriptome sequencing and label-free LC/MS/MS to identify global changes in protein-RNA interactions in response to etoposide-induced genotoxic stress. We show that RBPs have distinct binding patterns in response to genotoxic stress and that inactivation of the RBP regulator module, p38/MK2, can affect the entire spectrum of protein-RNA interactions that take place in response to stress. In addition to validating the role of known RBPs like Srsf1, Srsf2, Elavl1 in the genotoxic stress response, we add a new collection of RBPs to the DNA damage response. We identify Khsrp as a highly regulated RBP in response to genotoxic stress and further validate its role as a driver of the G(1/)S transition through the suppression of Cdkn1a(P21) transcripts. Finally, we identify KHSRP as an indicator of overall survival, as well as disease free survival in glioblastoma multiforme.
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Affiliation(s)
- Jorge Boucas
- Department I of Internal Medicine, University Hospital of Cologne, Weyertal 115B, 50931, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of Cologne, Weyertal 115B, 50931, Cologne, Germany
| | - Christian Fritz
- Department I of Internal Medicine, University Hospital of Cologne, Weyertal 115B, 50931, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of Cologne, Weyertal 115B, 50931, Cologne, Germany
| | - Anna Schmitt
- Department I of Internal Medicine, University Hospital of Cologne, Weyertal 115B, 50931, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of Cologne, Weyertal 115B, 50931, Cologne, Germany
| | - Arina Riabinska
- Department I of Internal Medicine, University Hospital of Cologne, Weyertal 115B, 50931, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of Cologne, Weyertal 115B, 50931, Cologne, Germany
| | - Lisa Thelen
- Department I of Internal Medicine, University Hospital of Cologne, Weyertal 115B, 50931, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of Cologne, Weyertal 115B, 50931, Cologne, Germany
| | - Martin Peifer
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Department of Translational Genomics, University of Cologne, Cologne, Germany
| | - Uschi Leeser
- Department I of Internal Medicine, University Hospital of Cologne, Weyertal 115B, 50931, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of Cologne, Weyertal 115B, 50931, Cologne, Germany
| | - Peter Nuernberg
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of Cologne, Weyertal 115B, 50931, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Janine Altmueller
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Matthias Gaestel
- Institute of Biochemistry, Hannover Medical School, Hannover, Germany
| | - Christoph Dieterich
- Computational RNA Biology and Ageing, Max Planck Institute for Biology of Ageing, Joseph-Stelzmann Straße 9b, 50913, Cologne, Germany
| | - H. Christian Reinhardt
- Department I of Internal Medicine, University Hospital of Cologne, Weyertal 115B, 50931, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of Cologne, Weyertal 115B, 50931, Cologne, Germany
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157
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Panas MD, Kedersha N, McInerney GM. Methods for the characterization of stress granules in virus infected cells. Methods 2015; 90:57-64. [PMID: 25896634 PMCID: PMC7128402 DOI: 10.1016/j.ymeth.2015.04.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 04/08/2015] [Accepted: 04/09/2015] [Indexed: 12/25/2022] Open
Abstract
Stress granules are induced as a cellular defence against virus infection. We discuss methods for the detection of viral and cellular proteins and RNA in SGs. In addition, we describe a surrogate in vitro assay for SG formation.
Stress granules are induced in many different viral infections, and in turn are inhibited by the expression of viral proteins or RNAs. It is therefore evident that these bodies are not compatible with efficient viral replication, but the mechanism by which they act to restrict viral gene expression or genome replication is not yet understood. This article discusses a number of methods that can be employed to gain a more complete understanding of the relationship between cellular SGs and viral RNA and protein synthesis in cells infected with diverse viruses.
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Affiliation(s)
- Marc D Panas
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Nancy Kedersha
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA, USA
| | - Gerald M McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
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158
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Shen ZJ, Malter JS. Regulation of AU-Rich Element RNA Binding Proteins by Phosphorylation and the Prolyl Isomerase Pin1. Biomolecules 2015; 5:412-34. [PMID: 25874604 PMCID: PMC4496679 DOI: 10.3390/biom5020412] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 03/23/2015] [Accepted: 03/31/2015] [Indexed: 01/19/2023] Open
Abstract
The accumulation of 3' untranslated region (3'-UTR), AU-rich element (ARE) containing mRNAs, are predominantly controlled at the post-transcriptional level. Regulation appears to rely on a variable and dynamic interaction between mRNA target and ARE-specific binding proteins (AUBPs). The AUBP-ARE mRNA recognition is directed by multiple intracellular signals that are predominantly targeted at the AUBPs. These include (but are unlikely limited to) methylation, acetylation, phosphorylation, ubiquitination and isomerization. These regulatory events ultimately affect ARE mRNA location, abundance, translation and stability. In this review, we describe recent advances in our understanding of phosphorylation and its impact on conformation of the AUBPs, interaction with ARE mRNAs and highlight the role of Pin1 mediated prolyl cis-trans isomerization in these biological process.
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Affiliation(s)
- Zhong-Jian Shen
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390-8548, USA.
| | - James S Malter
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390-8548, USA.
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159
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Hausburg MA, Doles JD, Clement SL, Cadwallader AB, Hall MN, Blackshear PJ, Lykke-Andersen J, Olwin BB. Post-transcriptional regulation of satellite cell quiescence by TTP-mediated mRNA decay. eLife 2015; 4:e03390. [PMID: 25815583 PMCID: PMC4415119 DOI: 10.7554/elife.03390] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 03/26/2015] [Indexed: 12/20/2022] Open
Abstract
Skeletal muscle satellite cells in their niche are quiescent and upon muscle injury, exit quiescence, proliferate to repair muscle tissue, and self-renew to replenish the satellite cell population. To understand the mechanisms involved in maintaining satellite cell quiescence, we identified gene transcripts that were differentially expressed during satellite cell activation following muscle injury. Transcripts encoding RNA binding proteins were among the most significantly changed and included the mRNA decay factor Tristetraprolin. Tristetraprolin promotes the decay of MyoD mRNA, which encodes a transcriptional regulator of myogenic commitment, via binding to the MyoD mRNA 3′ untranslated region. Upon satellite cell activation, p38α/β MAPK phosphorylates MAPKAP2 and inactivates Tristetraprolin, stabilizing MyoD mRNA. Satellite cell specific knockdown of Tristetraprolin precociously activates satellite cells in vivo, enabling MyoD accumulation, differentiation and cell fusion into myofibers. Regulation of mRNAs by Tristetraprolin appears to function as one of several critical post-transcriptional regulatory mechanisms controlling satellite cell homeostasis. DOI:http://dx.doi.org/10.7554/eLife.03390.001 When muscles are damaged, they can repair themselves to some extent by making new muscle cells. These develop from groups of cells called satellite cells, which are found near the surface of muscle fibers. Once the muscle is injured, the satellite cells are activated and can divide to form two cells with different properties. One remains a satellite cell, while the other forms a ‘myoblast’ that eventually fuses into a mature muscle fiber. Under normal conditions the satellite cells remain in a dormant state and do not divide, but it is not clear how they maintain this dormant state. To create a protein, the gene that encodes it is first ‘transcribed’ to produce a molecule called mRNA, which is then used as a template to build the protein. A protein called Tristetraprolin (TTP) can bind to mRNA molecules and cause them to break down or decay, and so TTP can prevent the mRNA from being used to make a protein. Hausburg, Doles et al. analyzed satellite cells from uninjured muscle and compared them with those from injured tissue. This revealed that when injured, the satellite cells reduced the abundance of several mRNAs, including TTP. Further investigation found that in satellite cells from uninjured tissue, TTP causes the decay of mRNA molecules that are used to produce a protein called MyoD. As MyoD helps the satellite cells to specialize, this decay therefore prevents the formation of myoblasts and keeps the satellite cells in a dormant state. In contrast, damage to the muscle tissue activates a signaling pathway that ultimately inactivates TTP. This enables more of the MyoD protein to be made and the myoblast population to expand. When Hausburg, Doles et al. experimentally reduced the levels of TTP inside satellite cells, the cells developed into myoblasts even when the tissue was uninjured. Thus, TTP is an important regulator that allows satellite cells to remain in a dormant state. In dormant adult stem cells, regulation of protein availability by RNA binding proteins, such as TTP, may co-ordinate rapid changes in metabolic state to promptly repair injured tissue. A major challenge will be to identify the group of proteins involved and determine the precise mechanisms involved in regulating their availability. DOI:http://dx.doi.org/10.7554/eLife.03390.002
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Affiliation(s)
- Melissa A Hausburg
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, United States
| | - Jason D Doles
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, United States
| | - Sandra L Clement
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, United States
| | - Adam B Cadwallader
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, United States
| | - Monica N Hall
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, United States
| | - Perry J Blackshear
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, United States
| | - Jens Lykke-Andersen
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, United States
| | - Bradley B Olwin
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, United States
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160
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Staudacher JJ, Naarmann-de Vries IS, Ujvari SJ, Klinger B, Kasim M, Benko E, Ostareck-Lederer A, Ostareck DH, Bondke Persson A, Lorenzen S, Meier JC, Blüthgen N, Persson PB, Henrion-Caude A, Mrowka R, Fähling M. Hypoxia-induced gene expression results from selective mRNA partitioning to the endoplasmic reticulum. Nucleic Acids Res 2015; 43:3219-36. [PMID: 25753659 PMCID: PMC4381074 DOI: 10.1093/nar/gkv167] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 02/21/2015] [Indexed: 01/01/2023] Open
Abstract
Protein synthesis is a primary energy-consuming process in the cell. Therefore, under hypoxic conditions, rapid inhibition of global mRNA translation represents a major protective strategy to maintain energy metabolism. How some mRNAs, especially those that encode crucial survival factors, continue to be efficiently translated in hypoxia is not completely understood. By comparing specific transcript levels in ribonucleoprotein complexes, cytoplasmic polysomes and endoplasmic reticulum (ER)-bound ribosomes, we show that the synthesis of proteins encoded by hypoxia marker genes is favoured at the ER in hypoxia. Gene expression profiling revealed that transcripts particularly increased by the HIF-1 transcription factor network show hypoxia-induced enrichment at the ER. We found that mRNAs favourably translated at the ER have higher conservation scores for both the 5'- and 3'-untranslated regions (UTRs) and contain less upstream initiation codons (uAUGs), indicating the significance of these sequence elements for sustained mRNA translation under hypoxic conditions. Furthermore, we found enrichment of specific cis-elements in mRNA 5'- as well as 3'-UTRs that mediate transcript localization to the ER in hypoxia. We conclude that transcriptome partitioning between the cytoplasm and the ER permits selective mRNA translation under conditions of energy shortage.
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Affiliation(s)
- Jonas J Staudacher
- Charité - Universitätsmedizin Berlin, Institut für Vegetative Physiologie, Charitéplatz 1, D-10117 Berlin, Germany
| | - Isabel S Naarmann-de Vries
- University Hospital Aachen, RWTH Aachen University, Department of Intensive and Intermediate Care, Experimental Research Unit, D-52074 Aachen, Germany
| | - Stefanie J Ujvari
- Charité - Universitätsmedizin Berlin, Institut für Vegetative Physiologie, Charitéplatz 1, D-10117 Berlin, Germany
| | - Bertram Klinger
- Humboldt Universität zu Berlin, Institut für Theoretische Biologie, D-10115 Berlin, Germany Charité - Universitätsmedizin Berlin, Institut für Pathologie, D-10117 Berlin, Germany
| | - Mumtaz Kasim
- Charité - Universitätsmedizin Berlin, Institut für Vegetative Physiologie, Charitéplatz 1, D-10117 Berlin, Germany
| | - Edgar Benko
- Charité - Universitätsmedizin Berlin, Institut für Vegetative Physiologie, Charitéplatz 1, D-10117 Berlin, Germany
| | - Antje Ostareck-Lederer
- University Hospital Aachen, RWTH Aachen University, Department of Intensive and Intermediate Care, Experimental Research Unit, D-52074 Aachen, Germany
| | - Dirk H Ostareck
- University Hospital Aachen, RWTH Aachen University, Department of Intensive and Intermediate Care, Experimental Research Unit, D-52074 Aachen, Germany
| | - Anja Bondke Persson
- Charité - Universitätsmedizin Berlin, Institut für Vegetative Physiologie, Charitéplatz 1, D-10117 Berlin, Germany
| | - Stephan Lorenzen
- Universitätsklinikum Jena, Klinik für Innere Medizin III, AG Experimentelle Nephrologie, D-07743 Jena, Germany
| | - Jochen C Meier
- Max Delbrück Center for Molecular Medicine, RNA Editing and Hyperexcitability Disorders Helmholtz Group, D-13125 Berlin, Germany TU Braunschweig, Zoological Institute, Division of Cell Physiology, D-38106 Braunschweig, Germany
| | - Nils Blüthgen
- Humboldt Universität zu Berlin, Institut für Theoretische Biologie, D-10115 Berlin, Germany Charité - Universitätsmedizin Berlin, Institut für Pathologie, D-10117 Berlin, Germany
| | - Pontus B Persson
- Charité - Universitätsmedizin Berlin, Institut für Vegetative Physiologie, Charitéplatz 1, D-10117 Berlin, Germany
| | - Alexandra Henrion-Caude
- Hôpital Necker-Enfants Malades, Université Paris Descartes, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR1163 and Imagine Foundation, 75015 Paris, France
| | - Ralf Mrowka
- Universitätsklinikum Jena, Klinik für Innere Medizin III, AG Experimentelle Nephrologie, D-07743 Jena, Germany
| | - Michael Fähling
- Charité - Universitätsmedizin Berlin, Institut für Vegetative Physiologie, Charitéplatz 1, D-10117 Berlin, Germany
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161
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Aditi, Folkmann AW, Wente SR. Cytoplasmic hGle1A regulates stress granules by modulation of translation. Mol Biol Cell 2015; 26:1476-90. [PMID: 25694449 PMCID: PMC4395128 DOI: 10.1091/mbc.e14-11-1523] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 02/11/2015] [Indexed: 12/21/2022] Open
Abstract
When eukaryotic cells respond to stress, gene expression pathways change to selectively export and translate subsets of mRNAs. Translationally repressed mRNAs accumulate in cytoplasmic foci known as stress granules (SGs). SGs are in dynamic equilibrium with the translational machinery, but mechanisms controlling this are unclear. Gle1 is required for DEAD-box protein function during mRNA export and translation. We document that human Gle1 (hGle1) is a critical regulator of translation during stress. hGle1 is recruited to SGs, and hGLE1 small interfering RNA-mediated knockdown perturbs SG assembly, resulting in increased numbers of smaller SGs. The rate of SG disassembly is also delayed. Furthermore, SG hGle1-depletion defects correlate with translation perturbations, and the hGle1 role in SGs is independent of mRNA export. Interestingly, we observe isoform-specific roles for hGle1 in which SG function requires hGle1A, whereas mRNA export requires hGle1B. We find that the SG defects in hGle1-depleted cells are rescued by puromycin or DDX3 expression. Together with recent links of hGLE1 mutations in amyotrophic lateral sclerosis patients, these results uncover a paradigm for hGle1A modulating the balance between translation and SGs during stress and disease.
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Affiliation(s)
- Aditi
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Andrew W Folkmann
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Susan R Wente
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
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162
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Tiedje C, Lubas M, Tehrani M, Menon MB, Ronkina N, Rousseau S, Cohen P, Kotlyarov A, Gaestel M. p38MAPK/MK2-mediated phosphorylation of RBM7 regulates the human nuclear exosome targeting complex. RNA (NEW YORK, N.Y.) 2015; 21:262-278. [PMID: 25525152 PMCID: PMC4338353 DOI: 10.1261/rna.048090.114] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 11/19/2014] [Indexed: 06/04/2023]
Abstract
The nuclear exosome targeting complex (NEXT) directs a major 3'-5' exonuclease, the RNA exosome, for degradation of nuclear noncoding (nc) RNAs. We identified the RNA-binding component of the NEXT complex, RBM7, as a substrate of p38(MAPK)/MK2-mediated phosphorylation at residue S136. As a result of this phosphorylation, RBM7 displays a strongly decreased RNA-binding capacity, while inhibition of p38(MAPK) or mutation of S136A in RBM7 increases its RNA association. Interestingly, promoter-upstream transcripts (PROMPTs), such as proRBM39, proEXT1, proDNAJB4, accumulated upon stress stimulation in a p38(MAPK)/MK2-dependent manner, a process inhibited by overexpression of RBM7(S136A). While there are no stress-dependent changes in RNA-polymerase II (RNAPII) occupation of PROMPT regions representing unchanged transcription, stability of PROMPTs is increased. Hence, we propose that phosphorylation of RBM7 by the p38(MAPK)/MK2 axis increases nuclear ncRNA stability by blocking their RBM7-binding and subsequent RNA exosome targeting to allow stress-dependent modulations of the noncoding transcriptome.
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Affiliation(s)
- Christopher Tiedje
- Institute of Physiological Chemistry, Hannover Medical School, 30625 Hannover, Germany
| | - Michal Lubas
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Mohammad Tehrani
- Institute of Physiological Chemistry, Hannover Medical School, 30625 Hannover, Germany
| | - Manoj B Menon
- Institute of Physiological Chemistry, Hannover Medical School, 30625 Hannover, Germany
| | - Natalia Ronkina
- Institute of Physiological Chemistry, Hannover Medical School, 30625 Hannover, Germany
| | - Simon Rousseau
- MRC Phosphorylation und Ubiquitylation Unit (MRC-PPU), Dundee, Scotland DD1 5EH, United Kingdom
| | - Philip Cohen
- MRC Phosphorylation und Ubiquitylation Unit (MRC-PPU), Dundee, Scotland DD1 5EH, United Kingdom
| | - Alexey Kotlyarov
- Institute of Physiological Chemistry, Hannover Medical School, 30625 Hannover, Germany
| | - Matthias Gaestel
- Institute of Physiological Chemistry, Hannover Medical School, 30625 Hannover, Germany
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163
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Corcoran JA, Johnston BP, McCormick C. Viral activation of MK2-hsp27-p115RhoGEF-RhoA signaling axis causes cytoskeletal rearrangements, p-body disruption and ARE-mRNA stabilization. PLoS Pathog 2015; 11:e1004597. [PMID: 25569678 PMCID: PMC4287613 DOI: 10.1371/journal.ppat.1004597] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 12/02/2014] [Indexed: 11/30/2022] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) is the infectious cause of several AIDS-related cancers, including the endothelial cell (EC) neoplasm Kaposi's sarcoma (KS). KSHV-infected ECs secrete abundant host-derived pro-inflammatory molecules and angiogenic factors that contribute to tumorigenesis. The precise contributions of viral gene products to this secretory phenotype remain to be elucidated, but there is emerging evidence for post-transcriptional regulation. The Kaposin B (KapB) protein is thought to contribute to the secretory phenotype in infected cells by binding and activating the stress-responsive kinase MK2, thereby selectively blocking decay of AU-rich mRNAs (ARE-mRNAs) encoding pro-inflammatory cytokines and angiogenic factors. Processing bodies (PBs) are cytoplasmic ribonucleoprotein foci in which ARE-mRNAs normally undergo rapid 5′ to 3′ decay. Here, we demonstrate that PB dispersion is a feature of latent KSHV infection, which is dependent on kaposin protein expression. KapB is sufficient to disperse PBs, and KapB-mediated ARE-mRNA stabilization could be partially reversed by treatments that restore PBs. Using a combination of genetic and chemical approaches we provide evidence that KapB-mediated PB dispersion is dependent on activation of a non-canonical Rho-GTPase signaling axis involving MK2, hsp27, p115RhoGEF and RhoA. PB dispersion in latently infected cells is likewise dependent on p115RhoGEF. In addition to PB dispersion, KapB-mediated RhoA activation in primary ECs caused actin stress fiber formation, increased cell motility and angiogenesis; these effects were dependent on the activity of the RhoA substrate kinases ROCK1/2. By contrast, KapB-mediated PB dispersion occurred in a ROCK1/2-independent manner. Taken together, these observations position KapB as a key contributor to viral reprogramming of ECs, capable of eliciting many of the phenotypes characteristic of KS tumor cells, and strongly contributing to the post-transcriptional control of EC gene expression and secretion. We have only scratched the surface in understanding how viruses control host gene expression. Several viruses disrupt important sites of post-transcriptional control of gene expression known as processing bodies (PBs), but underlying regulatory mechanisms and biological relevance remain poorly understood in most cases. Our study shows that the Kaposin B (KapB) protein of Kaposi's sarcoma (KS)-associated herpesvirus, known to block the degradation of a class of labile host mRNAs, does so by constitutively activating a signaling axis involving MK2, hsp27, p115RhoGEF and RhoA, thereby dispersing PBs. Thus, PB disruption may support the secretion of host pro-inflammatory cytokines and angiogenic factors that underlies KS tumor formation. Furthermore, by activating RhoA, KapB also causes cytoskeletal rearrangements, accelerated cell migration and angiogenesis in an endothelial cell model. Our findings position KapB as a key contributor to viral reprogramming of endothelial cells.
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Affiliation(s)
- Jennifer A. Corcoran
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, Nova Scotia, Canada
| | - Benjamin P. Johnston
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, Nova Scotia, Canada
| | - Craig McCormick
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, Nova Scotia, Canada
- * E-mail:
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164
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Jiang P, Coller H. Functional interactions between microRNAs and RNA binding proteins. Microrna 2014; 1:70-9. [PMID: 25048093 DOI: 10.2174/2211536611201010070] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Revised: 10/11/2011] [Accepted: 11/05/2011] [Indexed: 01/19/2023]
Abstract
Ensuring the appropriate spatial-temporal control of protein abundance requires careful control of transcript levels. This process is regulated at many steps, including the rate at which transcripts decay. microRNAs (miRNAs) and RNA Binding Proteins (RBPs) represent two important regulators of transcript degradation. We review here recent literature that suggests these two regulators of transcript decay may functionally interact. Some studies have reported an excess of miRNA binding sites surrounding the positions at which RBPs bind. Experimental reports focusing on a particular transcript have identified instances in which RBPs and miRNAs compete for the same target sites, and instances in which the binding of a RBP makes a miRNA recognition site more accessible to the RISC complex. Further, miRNAs and RBPs use similar enzymes for degradation of target transcripts and the degradation of the target transcripts occurs in similar subcellular compartments. In addition to miRNA-RBP interactions involving transcript decay, RBPs have also been reported to facilitate the processing of pri-miRNAs to their final form. We summarize here several possible mechanisms through which miRNA-RBP interactions may occur.
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Affiliation(s)
| | - Hilary Coller
- Department of Molecular Biology, Lewis Thomas Laboratory, Room 140, Princeton University Princeton, NJ 08544
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165
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Anderson P, Kedersha N, Ivanov P. Stress granules, P-bodies and cancer. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1849:861-70. [PMID: 25482014 DOI: 10.1016/j.bbagrm.2014.11.009] [Citation(s) in RCA: 272] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 11/21/2014] [Accepted: 11/26/2014] [Indexed: 12/27/2022]
Abstract
Cancer cells are exposed to adverse conditions in the tumor microenvironment, and utilize post-transcriptional control mechanisms to re-program gene expression in ways that enhance cell survival. Stress granules and processing bodies are RNA-containing granules that contribute to this process by modulating cellular signaling pathways, metabolic machinery, and stress response programs. This review examines evidence implicating RNA granules in the pathogenesis of cancer and discusses their potential as targets for anticancer therapies. This article is part of a Special Issue entitled: Translation and Cancer.
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Affiliation(s)
- Paul Anderson
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
| | - Nancy Kedersha
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Pavel Ivanov
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
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166
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Prabhala P, Ammit AJ. Tristetraprolin and its role in regulation of airway inflammation. Mol Pharmacol 2014; 87:629-38. [PMID: 25429052 DOI: 10.1124/mol.114.095984] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Chronic inflammatory diseases, such as asthma and chronic obstructive pulmonary disease (COPD), are clinically and socioeconomically important diseases globally. Currently the mainstay of anti-inflammatory therapy in respiratory diseases is corticosteroids. Although corticosteroids have proven clinical efficacy in asthma, many asthmatic inflammatory conditions (e.g., infection, exacerbation, and severe asthma) are not responsive to corticosteroids. Moreover, despite an understanding that COPD progression is driven by inflammation, we currently do not have effective anti-inflammatory strategies to combat this disease. Hence, alternative anti-inflammatory strategies are required. p38 mitogen-activated protein kinase (MAPK) has emerged as an important signaling molecule driving airway inflammation, and pharmacological inhibitors against p38 MAPK may provide potential therapies for chronic respiratory disease. In this review, we discuss some of the recent in vitro and in vivo studies targeting p38 MAPK, but suggest that p38 MAPK inhibitors may prove less effective than originally considered because they may block anti-inflammatory molecules along with proinflammatory responses. We propose that an alternative strategy may be to target an anti-inflammatory molecule farther downstream of p38 MAPK, i.e., tristetraprolin (TTP). TTP is an mRNA-destabilizing, RNA-binding protein that enhances the decay of mRNAs, including those encoding proteins implicated in chronic respiratory diseases. We suggest that understanding the molecular mechanism of TTP expression and its temporal regulation will guide future development of novel anti-inflammatory pharmacotherapeutic approaches to combat respiratory disease.
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Affiliation(s)
- Pavan Prabhala
- Faculty of Pharmacy, University of Sydney, Sydney, New South Wales, Australia
| | - Alaina J Ammit
- Faculty of Pharmacy, University of Sydney, Sydney, New South Wales, Australia
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167
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Caldwell AB, Cheng Z, Vargas JD, Birnbaum HA, Hoffmann A. Network dynamics determine the autocrine and paracrine signaling functions of TNF. Genes Dev 2014; 28:2120-33. [PMID: 25274725 PMCID: PMC4180974 DOI: 10.1101/gad.244749.114] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
A hallmark of the inflammatory response to pathogen exposure is the production of tumor necrosis factor (TNF) that coordinates innate and adaptive immune responses by functioning in an autocrine or paracrine manner. Numerous molecular mechanisms contributing to TNF production have been identified, but how they function together in macrophages remains unclear. Here, we pursued an iterative systems biology approach to develop a quantitative understanding of the regulatory modules that control TNF mRNA synthesis and processing, mRNA half-life and translation, and protein processing and secretion. By linking the resulting model of TNF production to models of the TLR-, the TNFR-, and the NFκB signaling modules, we were able to study TNF's functions during the inflammatory response to diverse TLR agonists. Contrary to expectation, we predicted and then experimentally confirmed that in response to lipopolysaccaride, TNF does not have an autocrine function in amplifying the NFκB response, although it plays a potent paracrine role in neighboring cells. However, in response to CpG DNA, autocrine TNF extends the duration of NFκB activity and shapes CpG-induced gene expression programs. Our systems biology approach revealed that network dynamics of MyD88 and TRIF signaling and of cytokine production and response govern the stimulus-specific autocrine and paracrine functions of TNF.
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Affiliation(s)
- Andrew B Caldwell
- Signaling Systems Laboratory, Department of Chemistry and Biochemistry, and San Diego Center for Systems Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Zhang Cheng
- Signaling Systems Laboratory, Department of Chemistry and Biochemistry, and San Diego Center for Systems Biology, University of California at San Diego, La Jolla, California 92093, USA; Institute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California 90025, USA
| | - Jesse D Vargas
- Signaling Systems Laboratory, Department of Chemistry and Biochemistry, and San Diego Center for Systems Biology, University of California at San Diego, La Jolla, California 92093, USA; Institute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California 90025, USA
| | - Harry A Birnbaum
- Signaling Systems Laboratory, Department of Chemistry and Biochemistry, and San Diego Center for Systems Biology, University of California at San Diego, La Jolla, California 92093, USA; Institute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California 90025, USA
| | - Alexander Hoffmann
- Signaling Systems Laboratory, Department of Chemistry and Biochemistry, and San Diego Center for Systems Biology, University of California at San Diego, La Jolla, California 92093, USA; Institute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California 90025, USA
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168
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Zinoviev A, Manor S, Shapira M. Nutritional stress affects an atypical cap-binding protein in Leishmania. RNA Biol 2014; 9:1450-60. [DOI: 10.4161/rna.22709] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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169
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Hodge DL, Berthet C, Coppola V, Kastenmüller W, Buschman MD, Schaughency PM, Shirota H, Scarzello AJ, Subleski JJ, Anver MR, Ortaldo JR, Lin F, Reynolds DA, Sanford ME, Kaldis P, Tessarollo L, Klinman DM, Young HA. IFN-gamma AU-rich element removal promotes chronic IFN-gamma expression and autoimmunity in mice. J Autoimmun 2014; 53:33-45. [PMID: 24583068 PMCID: PMC4148478 DOI: 10.1016/j.jaut.2014.02.003] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 01/17/2014] [Accepted: 02/05/2014] [Indexed: 12/31/2022]
Abstract
We generated a mouse model with a 162 nt AU-rich element (ARE) region deletion in the 3' untranslated region (3'UTR) of the interferon-gamma (IFN-γ) gene that results in chronic circulating serum IFN-γ levels. Mice homozygous for the ARE deletion (ARE-Del) (-/-) present both serologic and cellular abnormalities typical of patients with systemic lupus erythematosus (SLE). ARE-Del(-/-) mice display increased numbers of pDCs in bone marrow and spleen. Addition of IFN-γ to Flt3-ligand (Flt3L) treated in vitro bone marrow cultures results in a 2-fold increase in pDCs with concurrent increases in IRF8 expression. Marginal zone B (MZB) cells and marginal zone macrophages (MZMs) are absent in ARE-Del(-/-) mice. ARE-Del(+/-) mice retain both MZB cells and MZMs and develop no or mild autoimmunity. However, low dose clodronate treatment in ARE-Del(+/-) mice specifically eliminates MZMs and promotes anti-DNA antibody development and glomerulonephritis. Our findings demonstrate the consequences of a chronic IFN-γ milieu on B220(+) cell types and in particular the impact of MZB cell loss on MZM function in autoimmunity. Furthermore, similarities between disease states in ARE-Del(-/-) mice and SLE patients suggest that IFN-γ may not only be a product of SLE but may be critical for disease onset and progression.
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Affiliation(s)
- Deborah L Hodge
- Laboratory of Experimental Immunology, Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute-Frederick, MD 21702, USA.
| | - Cyril Berthet
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD 21702, USA; Oncodesign, 20 Rue Jean Mazen, Dijon 21076, France.
| | - Vincenzo Coppola
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD 21702, USA; Department of Molecular Virology, Immunology and Medical Genetics at The Ohio State University, 460 W. 12th Street, Columbus, OH 43210, USA.
| | - Wolfgang Kastenmüller
- Lymphocyte Biology Section, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Cellular Interactions and Immunimaging Institutes of Molecular Medicine and Experimental Immunology (IMMEI), University of Bonn, Sigmund-Freud Str. 25, Bonn 53105, Germany.
| | - Matthew D Buschman
- Laboratory of Experimental Immunology, Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute-Frederick, MD 21702, USA; Division of Endocrinology and Metabolism, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
| | - Paul M Schaughency
- Laboratory of Experimental Immunology, Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute-Frederick, MD 21702, USA; Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Hidekazu Shirota
- Laboratory of Experimental Immunology, Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute-Frederick, MD 21702, USA; Department of Clinical Oncology, Tohoku University Hospital, 1-1 Seiryo-machi, Aoba-ku, Sendai 980-8574, Japan.
| | - Anthony J Scarzello
- Laboratory of Experimental Immunology, Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute-Frederick, MD 21702, USA.
| | - Jeff J Subleski
- Laboratory of Experimental Immunology, Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute-Frederick, MD 21702, USA.
| | - Miriam R Anver
- Laboratory Animal Science Program (LASP), Science Applications International Corporation (SAIC), National Cancer Institute, Frederick, MD 21702, USA.
| | - John R Ortaldo
- Laboratory of Experimental Immunology, Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute-Frederick, MD 21702, USA.
| | - Fanching Lin
- Laboratory of Experimental Immunology, Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute-Frederick, MD 21702, USA.
| | - Della A Reynolds
- Laboratory of Experimental Immunology, Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute-Frederick, MD 21702, USA.
| | - Michael E Sanford
- Laboratory of Experimental Immunology, Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute-Frederick, MD 21702, USA.
| | - Philipp Kaldis
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD 21702, USA; Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Proteos, 61 Biopolis Drive, Singapore 138673, Republic of Singapore.
| | - Lino Tessarollo
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD 21702, USA.
| | - Dennis M Klinman
- Laboratory of Experimental Immunology, Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute-Frederick, MD 21702, USA.
| | - Howard A Young
- Laboratory of Experimental Immunology, Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute-Frederick, MD 21702, USA.
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170
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Shi JX, Li JS, Hu R, Shi Y, Su X, Guo XJ, Li XM. Tristetraprolin is involved in the glucocorticoid-mediated interleukin 8 repression. Int Immunopharmacol 2014; 22:480-5. [PMID: 25111853 DOI: 10.1016/j.intimp.2014.07.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 07/20/2014] [Accepted: 07/27/2014] [Indexed: 11/29/2022]
Abstract
Glucocorticoids have been widely used in various inflammatory disorders, and the transcriptional repression of inflammatory mediators has been considered to be the main mechanism of action. However, a previous study showed that dexamethasone inhibited interleukin 8 (IL-8) expression by promoting IL-8 mRNA decay, which implies a posttranscriptional regulation. Nevertheless, by which mechanism dexamethasone destabilized IL-8 mRNA was unclear. Another study indicated that an RNA-binding protein, tristetraprolin (TTP), could be induced by dexamethasone. TTP can bind to AU-rich elements (ARE) in the 3'-untranslated region of target mRNAs and promotes mRNA degradation. So, we speculated that dexamethasone destabilized IL-8 mRNA by upregulating TTP expression. Here, we report that dexamethasone reduced IL-8 expression through destabilizing IL-8 mRNA in human pulmonary microvascular endothelial cells (HPMECs). Dexamethasone stimulation increased TTP mRNA and protein levels. TTP silencing led to mRNA stabilization and protein upregulation of IL-8. These results provide the evidence that the glucocorticoid, in HPMECs, inhibits IL-8 expression through TTP at the posttranscriptional level.
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Affiliation(s)
- Jia-Xin Shi
- Department of Respiratory Medicine, Lianyungang First People's Hospital, Affiliated Hospital of Xuzhou Medical College, Clinical Medical School of Nanjing Medical University, Lianyungang 222002, China.
| | - Jia-Shu Li
- Department of Respiratory Medicine, Lianyungang First People's Hospital, Affiliated Hospital of Xuzhou Medical College, Clinical Medical School of Nanjing Medical University, Lianyungang 222002, China.
| | - Rong Hu
- Department of Respiratory Medicine, Lianyungang First People's Hospital, Affiliated Hospital of Xuzhou Medical College, Clinical Medical School of Nanjing Medical University, Lianyungang 222002, China
| | - Yi Shi
- Department of Respiratory and Critical Care Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing 210002, China.
| | - Xin Su
- Department of Respiratory and Critical Care Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing 210002, China
| | - Xiang-Jun Guo
- Department of Respiratory Medicine, Lianyungang First People's Hospital, Affiliated Hospital of Xuzhou Medical College, Clinical Medical School of Nanjing Medical University, Lianyungang 222002, China
| | - Xiao-Mei Li
- Department of Respiratory Medicine, Lianyungang First People's Hospital, Affiliated Hospital of Xuzhou Medical College, Clinical Medical School of Nanjing Medical University, Lianyungang 222002, China
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171
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Carpenter S, Ricci EP, Mercier BC, Moore MJ, Fitzgerald KA. Post-transcriptional regulation of gene expression in innate immunity. Nat Rev Immunol 2014; 14:361-76. [PMID: 24854588 DOI: 10.1038/nri3682] [Citation(s) in RCA: 275] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Innate immune responses combat infectious microorganisms by inducing inflammatory responses, antimicrobial pathways and adaptive immunity. Multiple genes within each of these functional categories are coordinately and temporally regulated in response to distinct external stimuli. The substantial potential of these responses to drive pathological inflammation and tissue damage highlights the need for rigorous control of these responses. Although transcriptional control of inflammatory gene expression has been studied extensively, the importance of post-transcriptional regulation of these processes is less well defined. In this Review, we discuss the regulatory mechanisms that occur at the level of mRNA splicing, mRNA polyadenylation, mRNA stability and protein translation, and that have instrumental roles in controlling both the magnitude and duration of the inflammatory response.
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Affiliation(s)
- Susan Carpenter
- 1] Program in Innate Immunity, Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA. [2]
| | - Emiliano P Ricci
- 1] Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA. [2]
| | - Blandine C Mercier
- 1] Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA. [2]
| | - Melissa J Moore
- Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Katherine A Fitzgerald
- 1] Program in Innate Immunity, Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA. [2] Centre of Molecular Inflammation Research, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, 7491 Trondheim, Norway
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172
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Cao H, Deterding LJ, Blackshear PJ. Identification of a major phosphopeptide in human tristetraprolin by phosphopeptide mapping and mass spectrometry. PLoS One 2014; 9:e100977. [PMID: 25010646 PMCID: PMC4091943 DOI: 10.1371/journal.pone.0100977] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 06/02/2014] [Indexed: 11/18/2022] Open
Abstract
Tristetraprolin/zinc finger protein 36 (TTP/ZFP36) binds and destabilizes some pro-inflammatory cytokine mRNAs. TTP-deficient mice develop a profound inflammatory syndrome due to excessive production of pro-inflammatory cytokines. TTP expression is induced by various factors including insulin and extracts from cinnamon and green tea. TTP is highly phosphorylated in vivo and is a substrate for several protein kinases. Multiple phosphorylation sites are identified in human TTP, but it is difficult to assign major vs. minor phosphorylation sites. This study aimed to generate additional information on TTP phosphorylation using phosphopeptide mapping and mass spectrometry (MS). Wild-type and site-directed mutant TTP proteins were expressed in transfected human cells followed by in vivo radiolabeling with [32P]-orthophosphate. Histidine-tagged TTP proteins were purified with Ni-NTA affinity beads and digested with trypsin and lysyl endopeptidase. The digested peptides were separated by C18 column with high performance liquid chromatography. Wild-type and all mutant TTP proteins were localized in the cytosol, phosphorylated extensively in vivo and capable of binding to ARE-containing RNA probes. Mutant TTP with S90 and S93 mutations resulted in the disappearance of a major phosphopeptide peak. Mutant TTP with an S197 mutation resulted in another major phosphopeptide peak being eluted earlier than the wild-type. Additional mutations at S186, S296 and T271 exhibited little effect on phosphopeptide profiles. MS analysis identified the peptide that was missing in the S90 and S93 mutant protein as LGPELSPSPTSPTATSTTPSR (corresponding to amino acid residues 83–103 of human TTP). MS also identified a major phosphopeptide associated with the first zinc-finger region. These analyses suggest that the tryptic peptide containing S90 and S93 is a major phosphopeptide in human TTP.
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Affiliation(s)
- Heping Cao
- U. S. Department of Agriculture, Agricultural Research Service, Southern Regional Research Center, New Orleans, Louisiana, United States of America
- * E-mail:
| | - Leesa J. Deterding
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, United States of America
| | - Perry J. Blackshear
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, United States of America and Departments of Biochemistry and Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
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173
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Translational regulation of specific mRNAs controls feedback inhibition and survival during macrophage activation. PLoS Genet 2014; 10:e1004368. [PMID: 24945926 PMCID: PMC4063670 DOI: 10.1371/journal.pgen.1004368] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 03/24/2014] [Indexed: 01/10/2023] Open
Abstract
For a rapid induction and efficient resolution of the inflammatory response, gene expression in cells of the immune system is tightly regulated at the transcriptional and post-transcriptional level. The control of mRNA translation has emerged as an important determinant of protein levels, yet its role in macrophage activation is not well understood. We systematically analyzed the contribution of translational regulation to the early phase of the macrophage response by polysome fractionation from mouse macrophages stimulated with lipopolysaccharide (LPS). Individual mRNAs whose translation is specifically regulated during macrophage activation were identified by microarray analysis. Stimulation with LPS for 1 h caused translational activation of many feedback inhibitors of the inflammatory response including NF-κB inhibitors (Nfkbid, Nfkbiz, Nr4a1, Ier3), a p38 MAPK antagonist (Dusp1) and post-transcriptional suppressors of cytokine expression (Zfp36 and Zc3h12a). Our analysis showed that their translation is repressed in resting and de-repressed in activated macrophages. Quantification of mRNA levels at a high temporal resolution by RNASeq allowed us to define groups with different expression patterns. Thereby, we were able to distinguish mRNAs whose translation is actively regulated from mRNAs whose polysomal shifts are due to changes in mRNA levels. Active up-regulation of translation was associated with a higher content in AU-rich elements (AREs). For one example, Ier3 mRNA, we show that repression in resting cells as well as de-repression after stimulation depends on the ARE. Bone-marrow derived macrophages from Ier3 knockout mice showed reduced survival upon activation, indicating that IER3 induction protects macrophages from LPS-induced cell death. Taken together, our analysis reveals that translational control during macrophage activation is important for cellular survival as well as the expression of anti-inflammatory feedback inhibitors that promote the resolution of inflammation. When macrophages encounter pathogens, they initiate inflammation by secreting pro-inflammatory factors such as the cytokine TNF. Because a prolonged or overshooting release of these factors is harmful for the organism, their production needs to be tightly controlled and shut off in due time. To ensure a rapid but transient inflammatory response, gene expression is regulated at multiple levels, including transcription, stability and translation of mRNAs. While control of transcription and mRNA stability has been studied extensively, little is known about translational regulation in macrophages. In this study, we measured the translation of all mRNAs expressed in mouse macrophages. Upon activation of macrophages with the bacterial cell wall component lipopolysaccharide, we found that many feedback inhibitors, which are important for dampening the inflammatory response, are translationally up-regulated. Translation of these mRNAs is repressed in resting cells and de-repressed after stimulation. In contrast to feedback inhibitors, most cytokines are primarily regulated by changes in mRNA abundance. Furthermore, we could show that one of the feedback inhibitors, IER3, protects macrophages from cell death during activation. Therefore, regulation at the level of translation is important for the induction of negative feedback loops and cellular survival.
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Adjibade P, Mazroui R. Control of mRNA turnover: implication of cytoplasmic RNA granules. Semin Cell Dev Biol 2014; 34:15-23. [PMID: 24946962 DOI: 10.1016/j.semcdb.2014.05.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 05/21/2014] [Indexed: 12/15/2022]
Abstract
The control of mRNA turnover is essential for the cell to rationalize its mRNA content both under physiological conditions and upon stress. Several mechanisms involved in the control of mRNA turnover have been elucidated. These include surveillance mechanisms such as nonsense-mediated decay, non-stop mediated decay and non-go-mediated decay that eliminate aberrant mRNAs, and regulatory mechanisms including AU-mediated decay, GU-mediated decay, and CDE-mediated decay that ensure mRNA plasticity. In general, the mechanisms of RNA decay rely on interactions between specific cis-acting RNA elements and selected RNA-binding proteins that either prevent the degradation of mRNA targets or induce the recruitment of decaying effectors leading to mRNA degradation. Formation of cytoplasmic RNA granules including processing bodies, stress granules, UV granules, and exosome granules have recently emerged as an additional mechanism that control mRNA turnover of selected mRNAs. Here we will review briefly review the main mechanisms that control mRNA decay and highlight possible implication of RNA granules in such mechanisms.
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Affiliation(s)
- Pauline Adjibade
- Centre de recherche du CHU de Québec, Département de biologie moléculaire, biochimie médicale et pathologie, Université Laval, Québec, PQ, Canada
| | - Rachid Mazroui
- Centre de recherche du CHU de Québec, Département de biologie moléculaire, biochimie médicale et pathologie, Université Laval, Québec, PQ, Canada.
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175
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176
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Hahn RT, Hoppstädter J, Hirschfelder K, Hachenthal N, Diesel B, Kessler SM, Huwer H, Kiemer AK. Downregulation of the glucocorticoid-induced leucine zipper (GILZ) promotes vascular inflammation. Atherosclerosis 2014; 234:391-400. [PMID: 24747114 DOI: 10.1016/j.atherosclerosis.2014.03.028] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 02/28/2014] [Accepted: 03/23/2014] [Indexed: 12/27/2022]
Abstract
OBJECTIVE Glucocorticoid-induced leucine zipper (GILZ) represents an anti-inflammatory mediator, whose downregulation has been described in various inflammatory processes. Aim of our study was to decipher the regulation of GILZ in vascular inflammation. APPROACH AND RESULTS Degenerated aortocoronary saphenous vein bypass grafts (n = 15), which exhibited inflammatory cell activation as determined by enhanced monocyte chemoattractrant protein 1 (MCP-1, CCL2) and Toll-like receptor 2 (TLR2) expression, showed significantly diminished GILZ protein and mRNA levels compared to healthy veins (n = 23). GILZ was also downregulated in human umbilical vein endothelial cells (HUVEC) and macrophages upon treatment with the inflammatory cytokine TNF-α in a tristetraprolin (ZFP36, TTP)- and p38 MAPK-dependent manner. To assess the functional implications of decreased GILZ expression, we determined NF-κB activation after GILZ knockdown by siRNA and found that NF-κB activity and inflammatory gene expression were significantly enhanced. Importantly, ZFP36 is induced in TNF-α-activated HUVEC as well as in degenerated vein bypasses. When atheroprotective laminar shear stress was employed, GILZ levels in HUVEC increased on mRNA and protein level. Laminar flow also counteracted TNF-α-induced ZFP36 expression and GILZ downregulation. MAP kinase phosphatase 1 (MKP-1, DUSP1), a negative regulator of ZFP36 expression, was distinctly upregulated under laminar shear stress conditions and downregulated in degenerated vein bypasses. CONCLUSION Our data show a diminished expression of the anti-inflammatory mediator GILZ in the inflamed vasculature and indicate that GILZ downregulation requires the mRNA binding protein ZFP36. We suggest that reduced GILZ levels play a role in cardiovascular disease.
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Affiliation(s)
- Rebecca T Hahn
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Saarbruecken, Germany
| | - Jessica Hoppstädter
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Saarbruecken, Germany
| | - Kerstin Hirschfelder
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Saarbruecken, Germany
| | - Nina Hachenthal
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Saarbruecken, Germany
| | - Britta Diesel
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Saarbruecken, Germany
| | - Sonja M Kessler
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Saarbruecken, Germany
| | - Hanno Huwer
- Department of Cardiothoracic Surgery, Völklingen Heart Centre, Völklingen, Germany
| | - Alexandra K Kiemer
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Saarbruecken, Germany.
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177
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Xiao J, Gao H, Jin Y, Zhao Z, Guo J, Liu Z, Zhao Z. The abnormal expressions of tristetraprolin and the VEGF family in uraemic rats with peritoneal dialysis. Mol Cell Biochem 2014; 392:229-38. [PMID: 24696420 DOI: 10.1007/s11010-014-2033-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 03/14/2014] [Indexed: 01/01/2023]
Abstract
The effect of peritoneal dialysis (PD) with high-glucose dialysis fluid on the VEGF family, tristetraprolin (TTP), angiogenesis and lymphangiogenesis was investigated. Forty male SD rats were randomised into five groups: normal group, sham operation group, uraemia group, PD 2-week group and PD4-week group. After 4 weeks of PD, microvessel density (MVD) and lymphatic vessel density (LVD) were measured. The expressions of both the VEGF family and TTP were detected. Compared with the normal group, the mRNA expression levels of the VEGF family were significantly increased in the uraemia group (P < 0.05), and also in the PD 2-week group and PD4-week group (P < 0.05) compared with uraemia group. The mRNAs of VEGF-A and VEGF-C in 4-week PD group likewise were significantly increased compared with the 2-week PD group. However, the mRNA expression of TTP was significantly decreased in the uraemia group compared with the normal group (P < 0.05), and also in the PD group compared with the uraemia group (P < 0.05). Compared with the normal group, the protein expressions of TTP were significantly decreased in the uraemia group (P < 0.05), and also in the PD group compared with the uraemia group (P < 0.05). Compared with the normal group, the MVD and LVD counts were gradually increased in the PD group, which was associated with PD time. In addition, the expression of TTP gradually decreased over PD time. High-glucose PD fluid and uraemic circumstance resulted in the abnormal expression of TTP and the VEGF family in a PD time-dependent manner; this may lead to UFF through angiogenesis and lymphangiogenesis.
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Affiliation(s)
- Jing Xiao
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, No.1 Eastern Jianshe Road, Zhengzhou, 450052, Henan, China
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Gaestel M. What goes up must come down: molecular basis of MAPKAP kinase 2/3-dependent regulation of the inflammatory response and its inhibition. Biol Chem 2014; 394:1301-15. [PMID: 23832958 DOI: 10.1515/hsz-2013-0197] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 07/01/2013] [Indexed: 12/21/2022]
Abstract
Inflammation is normally a fast and transient response to microbial invaders or sterile damage and has to be stringently controlled. The closely-related mitogen-activated protein kinase-activated protein kinases MK2 and MK3 are involved in both up- and down-regulation of inflammation in mammals and govern the inflammatory response at different regulatory levels of gene expression and with different kinetics. In conjunction with their activator MAP kinase p38, MK2 and MK3 stimulate the transcription of immediate-early genes including that of the mRNA-binding protein tristetraprolin (TTP). TTP competes with the constitutively expressed protein human antigen R in binding to the mRNA destabilizing adenylate-uridylate -rich element. MK2 and MK3 also regulate the activity of TTP by direct phosphorylation, determine stability and stimulate the translation of cytokine mRNAs. In addition, TTP controls its own re-synthesis via stability and translation of its mRNA in a phosphorylation-dependent manner. This results in a complex scenario of gene expression and guarantees fast up-regulation and intrinsic feedback control of the inflammatory response of macrophages. Inhibition of MK2/3 by small-molecule pharmaceutical inhibitors is an emerging strategy to manipulate the inflammatory response as a therapeutic option. This strategy could display advantages over the direct inhibition of MAP kinase p38.
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179
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Bann DV, Beyer AR, Parent LJ. A murine retrovirus co-Opts YB-1, a translational regulator and stress granule-associated protein, to facilitate virus assembly. J Virol 2014; 88:4434-50. [PMID: 24501406 PMCID: PMC3993753 DOI: 10.1128/jvi.02607-13] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 01/28/2014] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The Gag protein of the murine retrovirus mouse mammary tumor virus (MMTV) orchestrates the assembly of immature virus particles in the cytoplasm which are subsequently transported to the plasma membrane for release from the cell. The morphogenetic pathway of MMTV assembly is similar to that of Saccharomyces cerevisiae retrotransposons Ty1 and Ty3, which assemble virus-like particles (VLPs) in intracytoplasmic ribonucleoprotein (RNP) complexes. Assembly of Ty1 and Ty3 VLPs depends upon cellular mRNA processing factors, prompting us to examine whether MMTV utilizes a similar set of host proteins to facilitate viral capsid assembly. Our data revealed that MMTV Gag colocalized with YB-1, a translational regulator found in stress granules and P bodies, in intracytoplasmic foci. The association of MMTV Gag and YB-1 in cytoplasmic granules was not disrupted by cycloheximide treatment, suggesting that these sites were not typical stress granules. However, the association of MMTV Gag and YB-1 was RNA dependent, and an MMTV RNA reporter construct colocalized with Gag and YB-1 in cytoplasmic RNP complexes. Knockdown of YB-1 resulted in a significant decrease in MMTV particle production, indicating that YB-1 plays a role in MMTV capsid formation. Analysis by live-cell imaging with fluorescence recovery after photobleaching (FRAP) revealed that the population of Gag proteins localized within YB-1 complexes was relatively immobile, suggesting that Gag forms stable complexes in association with YB-1. Together, our data imply that the formation of intracytoplasmic Gag-RNA complexes is facilitated by YB-1, which promotes MMTV virus assembly. IMPORTANCE Cellular mRNA processing factors regulate the posttranscriptional fates of mRNAs, affecting localization and utilization of mRNAs under normal conditions and in response to stress. RNA viruses such as retroviruses interact with cellular mRNA processing factors that accumulate in ribonucleoprotein complexes known as P bodies and stress granules. This report shows for the first time that mouse mammary tumor virus (MMTV), a mammalian retrovirus that assembles intracytoplasmic virus particles, commandeers the cellular factor YB-1, a key regulator of translation involved in the cellular stress response. YB-1 is essential for the efficient production of MMTV particles, a process directed by the viral Gag protein. We found that Gag and YB-1 localize together in cytoplasmic granules. Functional studies of Gag/YB-1 granules suggest that they may be sites where virus particles assemble. These studies provide significant insights into the interplay between mRNA processing factors and retroviruses.
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Affiliation(s)
- Darrin V. Bann
- Department of Medicine, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Andrea R. Beyer
- Department of Microbiology and Immunology, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Leslie J. Parent
- Department of Medicine, Penn State College of Medicine, Hershey, Pennsylvania, USA
- Department of Microbiology and Immunology, Penn State College of Medicine, Hershey, Pennsylvania, USA
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Abstract
The binding of tumour necrosis factor α (TNFα) to cell surface receptors engages multiple signal transduction pathways, including three groups of mitogen-activated protein (MAP) kinases: extracellular-signal-regulated kinases (ERKs); the cJun NH2-terminal kinases (JNKs); and the p38 MAP kinases. These MAP kinase signalling pathways induce a secondary response by increasing the expression of several inflammatory cytokines (including TNFα) that contribute to the biological activity of TNFα. MAP kinases therefore function both upstream and down-stream of signalling by TNFα receptors. Here we review mechanisms that mediate these actions of MAP kinases during the response to TNFα.
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Affiliation(s)
- Guadalupe Sabio
- Department of Vascular Biology and Inflammation, Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III, 28029 Madrid, Spain
| | - Roger J Davis
- Howard Hughes Medical Institute and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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181
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Droppelmann CA, Campos-Melo D, Ishtiaq M, Volkening K, Strong MJ. RNA metabolism in ALS: When normal processes become pathological. Amyotroph Lateral Scler Frontotemporal Degener 2014; 15:321-36. [DOI: 10.3109/21678421.2014.881377] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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182
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Mukherjee N, Jacobs NC, Hafner M, Kennington EA, Nusbaum JD, Tuschl T, Blackshear PJ, Ohler U. Global target mRNA specification and regulation by the RNA-binding protein ZFP36. Genome Biol 2014; 15:R12. [PMID: 24401661 PMCID: PMC4053807 DOI: 10.1186/gb-2014-15-1-r12] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 01/08/2013] [Indexed: 02/05/2023] Open
Abstract
Background ZFP36, also known as tristetraprolin or TTP, and ELAVL1, also known as HuR, are two disease-relevant RNA-binding proteins (RBPs) that both interact with AU-rich sequences but have antagonistic roles. While ELAVL1 binding has been profiled in several studies, the precise in vivo binding specificity of ZFP36 has not been investigated on a global scale. We determined ZFP36 binding preferences using cross-linking and immunoprecipitation in human embryonic kidney cells, and examined the combinatorial regulation of AU-rich elements by ZFP36 and ELAVL1. Results Targets bound and negatively regulated by ZFP36 include transcripts encoding proteins necessary for immune function and cancer, and transcripts encoding other RBPs. Using partial correlation analysis, we were able to quantify the association between ZFP36 binding sites and differential target RNA abundance upon ZFP36 overexpression independent of effects from confounding features. Genes with increased mRNA half-lives in ZFP36 knockout versus wild-type mouse cells were significantly enriched for our human ZFP36 targets. We identified thousands of overlapping ZFP36 and ELAVL1 binding sites, in 1,313 genes, and found that ZFP36 degrades transcripts through specific AU-rich sequences, representing a subset of the U-rich sequences ELAVL1 interacts with to stabilize transcripts. Conclusions ZFP36-RNA target specificities in vivo are quantitatively similar to previously reported in vitro binding affinities. ZFP36 and ELAVL1 bind an overlapping spectrum of RNA sequences, yet with differential relative preferences that dictate combinatorial regulatory potential. Our findings and methodology delineate an approach to unravel in vivo combinatorial regulation by RNA-binding proteins.
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183
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Gabryšová L, Howes A, Saraiva M, O'Garra A. The regulation of IL-10 expression. Curr Top Microbiol Immunol 2014; 380:157-90. [PMID: 25004818 DOI: 10.1007/978-3-662-43492-5_8] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Interleukin (IL)-10 is an important immunoregulatory cytokine and an understanding of how IL-10 expression is controlled is critical in the design of immune intervention strategies. IL-10 is produced by almost all cell types within the innate (including macrophages, monocytes, dendritic cells (DCs), mast cells, neutrophils, eosinophils and natural killer cells) and adaptive (including CD4(+) T cells, CD8(+) T cells and B cells) immune systems. The mechanisms of IL-10 regulation operate at several stages including chromatin remodelling at the Il10 locus, transcriptional regulation of Il10 expression and post-transcriptional regulation of Il10 mRNA. In addition, whereas some aspects of Il10 gene regulation are conserved between different immune cell types, several are cell type- or stimulus-specific. Here, we outline the complexity of IL-10 production by discussing what is known about its regulation in macrophages, monocytes, DCs and CD4(+) T helper cells.
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Affiliation(s)
- Leona Gabryšová
- Division of Immunoregulation, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, UK
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184
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Gurgis FMS, Ziaziaris W, Munoz L. Mitogen-Activated Protein Kinase–Activated Protein Kinase 2 in Neuroinflammation, Heat Shock Protein 27 Phosphorylation, and Cell Cycle: Role and Targeting. Mol Pharmacol 2013; 85:345-56. [DOI: 10.1124/mol.113.090365] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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185
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Lee HH, Yang SS, Vo MT, Cho WJ, Lee BJ, Leem SH, Lee SH, Cha HJ, Park JW. Tristetraprolin down-regulates IL-23 expression in colon cancer cells. Mol Cells 2013; 36:571-6. [PMID: 24292977 PMCID: PMC3887959 DOI: 10.1007/s10059-013-0268-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 10/25/2013] [Accepted: 10/31/2013] [Indexed: 12/13/2022] Open
Abstract
Interleukin 23 (IL-23) is an inflammatory cytokine that plays an important role in tumor promotion. Expression of IL-23 is increased in cancer cells and correlates with tumor progression. However, the mechanisms regulating IL-23 expression in cancer cells are still unclear. Here we report that tristetraprolin (TTP), an AU-rich element (ARE)-binding protein, inhibits IL-23 production in CT26 mouse colon cancer cells. Overexpression of TTP decreased the stability of IL-23 mRNA and the expression level of IL-23 in CT26 cells. Conversely, inhibition of TTP by siRNA increased IL-23 production. TTP destabilized a luciferase mRNA reporter containing the IL-23 mRNA 3'UTR, which contains five AREs. Analyses of deletion and point mutants of the IL-23 mRNA 3'UTR demonstrated that the ARE cluster between the third and fifth AREs was responsible for TTP-mediated destabilization of IL-23 mRNA. A RNA electrophoretic mobility shift assay confirmed that TTP binds to this ARE cluster. Taken together, these results demonstrate that TTP acts as a negative regulator of IL-23 gene expression in mouse colon cancer cells and suggest its potential application as a novel therapeutic target to control IL-23-mediated tumor promotion.
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Affiliation(s)
- Hyun Hee Lee
- Department of Biological Sciences, University of Ulsan, Ulsan 680-749,
Korea
- Department of Biological Sciences, Dong-A University, Busan 604-714,
Korea
| | - Song Soo Yang
- Department of Surgery, Ulsan University Hospital, University of Ulsan College of Medicine, Ulsan 682-060,
Korea
| | - Mai-Tram Vo
- Department of Biological Sciences, University of Ulsan, Ulsan 680-749,
Korea
| | - Wha Ja Cho
- Biomedical Research Center, Ulsan University Hospital, University of Ulsan College of Medicine, Ulsan 682-060,
Korea
| | - Byung Ju Lee
- Department of Biological Sciences, University of Ulsan, Ulsan 680-749,
Korea
| | - Sun-Hee Leem
- Department of Biological Sciences, Dong-A University, Busan 604-714,
Korea
| | - Sang-Hyun Lee
- Department of Anesthesiology and Pain Medicine, Ulsan University Hospital, University of Ulsan College of Medicine, Ulsan 682-060,
Korea
| | - Hee Jeong Cha
- Department of Pathology, Ulsan University Hospital, University of Ulsan College of Medicine, Ulsan 682-060,
Korea
| | - Jeong Woo Park
- Department of Biological Sciences, University of Ulsan, Ulsan 680-749,
Korea
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186
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Dai XY, Cai Y, Sun W, Ding Y, Wang W, Kong W, Tang C, Zhu Y, Xu MJ, Wang X. Intermedin inhibits macrophage foam-cell formation via tristetraprolin-mediated decay of CD36 mRNA. Cardiovasc Res 2013; 101:297-305. [PMID: 24253523 DOI: 10.1093/cvr/cvt254] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
AIMS CD36-mediated uptake of oxidized low-density lipoprotein (oxLDL) plays a pivotal role in macrophage foam-cell formation and atherogenesis. Previously we reported on intermedin (IMD), a novel member of the calcitonin gene-related peptide family, in atherosclerotic plaque reducing atherogenesis in apolipoprotein E-deficient (apoE(-/-)) mice. Here, we studied the role of IMD in CD36-mediated macrophage foam-cell formation. METHODS AND RESULTS In apoE(-/-) mice, 6-week IMD infusion reduced oxLDL uptake, intracellular cholesterol content, and foam-cell formation in peritoneal macrophages and reduced protein and mRNA levels of CD36. These in vivo results agreed with in vitro observations in primary peritoneal macrophages. Reduced CD36 protein and mRNA levels were due to an IMD-accelerated decay of CD36 mRNA. Tristetraprolin (TTP), which binds to AU-rich elements in the 3' untranslated regions (UTRs) of mRNA and promotes its degradation, mediated CD36 mRNA destabilization. TTP knockdown by short-hairpin RNA increased and TTP overexpression reduced CD36 expression, and TTP knockdown rescued IMD-reduced CD36 expression. Moreover, IMD repressed TTP phosphorylation, thereby activating TTP, for increased TTP binding to the 3'-UTR of CD36 mRNA. CONCLUSION Thus, IMD attenuates macrophage foam-cell formation via TTP-mediated degradation of CD36 mRNA. Our findings reveal a new mechanism of the anti-atherogenic role of IMD and a novel pattern for regulation of CD36 expression in macrophages.
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Affiliation(s)
- Xiao-Yan Dai
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University Health Science Center, Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing 100191, P. R. China
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187
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Leppek K, Stoecklin G. An optimized streptavidin-binding RNA aptamer for purification of ribonucleoprotein complexes identifies novel ARE-binding proteins. Nucleic Acids Res 2013; 42:e13. [PMID: 24157833 PMCID: PMC3902943 DOI: 10.1093/nar/gkt956] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Determining the composition of messenger ribonucleoprotein (mRNP) particles is essential for a comprehensive understanding of the complex mechanisms underlying mRNA regulation, but is technically challenging. Here we present an RNA-based method to identify RNP components using a modified streptavidin (SA)-binding RNA aptamer termed S1m. By optimizing the RNA aptamer S1 in structure and repeat conformation, we improved its affinity for SA and found a 4-fold repeat of S1m (4×S1m) to be more efficient than the established MS2 and PP7 systems from bacteriophages. We then attached the AU-rich element (ARE) of tumor necrosis factor alpha (TNFα), a well-known RNA motif that induces mRNA degradation, via 4×S1m to a SA matrix, and used the resulting RNA affinity column to purify ARE-binding proteins (BPs) from cellular extracts. By quantitative mass spectrometry using differential dimethyl labeling, we identified the majority of established ARE-BPs and detected several RNA-BPs that had previously not been associated with AREs. For two of these proteins, Rbms1 and Roxan, we confirmed specific binding to the TNFα ARE. The optimized 4×S1m aptamer, therefore, provides a powerful tool for the discovery of mRNP components in a single affinity purification step.
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Affiliation(s)
- Kathrin Leppek
- Helmholtz Junior Research Group Posttranscriptional Control of Gene Expression, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany, Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Im Neuenheimer Feld 282, 69120 Heidelberg, Germany and DKFZ-ZMBH Alliance
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188
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Yoon JH, Abdelmohsen K, Srikantan S, Guo R, Yang X, Martindale JL, Gorospe M. Tyrosine phosphorylation of HuR by JAK3 triggers dissociation and degradation of HuR target mRNAs. Nucleic Acids Res 2013; 42:1196-208. [PMID: 24106086 PMCID: PMC3902907 DOI: 10.1093/nar/gkt903] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In response to stress conditions, many mammalian mRNAs accumulate in stress granules (SGs) together with numerous RNA-binding proteins that control mRNA turnover and translation. However, the signaling cascades that modulate the presence of ribonucleoprotein (RNP) complexes in SGs are poorly understood. Here, we investigated the localization of human antigen R (HuR), an mRNA-stabilizing RNA-binding protein, in SGs following exposure to the stress agent arsenite. Unexpectedly, the mobilization of HuR to SGs was prevented through the activation of Janus kinase 3 (JAK3) by the vitamin K3 analog menadione. JAK3 phosphorylated HuR at tyrosine 200, in turn inhibiting HuR localization in SGs, reducing HuR interaction with targets SIRT1 and VHL mRNAs, and accelerating target mRNA decay. Our findings indicate that HuR is tyrosine-phosphorylated by JAK3, and link this modification to HuR subcytoplasmic localization and to the fate of HuR target mRNAs.
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Affiliation(s)
- Je-Hyun Yoon
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH, Baltimore, MD 21224, USA
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189
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Lachance C, Wojewodka G, Skinner TAA, Guilbault C, De Sanctis JB, Radzioch D. Fenretinide corrects the imbalance between omega-6 to omega-3 polyunsaturated fatty acids and inhibits macrophage inflammatory mediators via the ERK pathway. PLoS One 2013; 8:e74875. [PMID: 24069363 PMCID: PMC3771966 DOI: 10.1371/journal.pone.0074875] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 08/09/2013] [Indexed: 12/24/2022] Open
Abstract
We previously identified Fragile X-related protein 1 (FXR1) as an RNA-binding protein involved in the post-transcriptional control of TNF and other cytokines in macrophages. Macrophages derived from FXR1-KO mice overexpress several inflammatory cytokines including TNF. Recently, we showed that fenretinide (4HPR) is able to inhibit several inflammatory cytokines in the lungs of cystic fibrosis mice, which also have abnormal immune responses. Therefore, we hypothesized that 4HPR might also be able to downregulate excessive inflammation even in macrophages with ablated FXR1. Indeed, our results demonstrate that 4HPR inhibited the excessive production of inflammatory mediators, including TNF, IL-6, CCL2 and CCL-5 in LPS-stimulated FXR1-KO macrophages, by selectively inhibiting phosphorylation of ERK1/2, which is naturally more phosphorylated in FXR1-KO cells. We also found that LPS stimulation of FXR1-KO macrophages led to significantly higher ratio of arachidonic acid/docosahexaenoic acid than observed in FXR1-WT macrophages. Interestingly, treatment with 4HPR was associated with the normalization of arachidonic acid/docosahexaenoic acid ratio in macrophages, which we found to impact phosphorylation of ERK1/2. Overall, this study shows for the first time that 4HPR modulates inflammatory cytokine expression in macrophages by correcting a phospholipid-bound fatty acid imbalance that impacts the phosphorylation of ERK1/2.
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Affiliation(s)
- Claude Lachance
- McGill University, Department of Medicine and Department of Human Genetics, McGill University Health Center Research Institute, Montreal, Quebec, Canada
| | - Gabriella Wojewodka
- McGill University, Department of Medicine and Department of Human Genetics, McGill University Health Center Research Institute, Montreal, Quebec, Canada
| | - Tom A. A. Skinner
- McGill University, Department of Medicine and Department of Human Genetics, McGill University Health Center Research Institute, Montreal, Quebec, Canada
| | - Claudine Guilbault
- McGill University, Department of Medicine and Department of Human Genetics, McGill University Health Center Research Institute, Montreal, Quebec, Canada
| | - Juan B. De Sanctis
- Central University of Venezuela, Institute of Immunology, Caracas, Venezuela
| | - Danuta Radzioch
- McGill University, Department of Medicine and Department of Human Genetics, McGill University Health Center Research Institute, Montreal, Quebec, Canada
- * E-mail:
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190
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Kedersha N, Ivanov P, Anderson P. Stress granules and cell signaling: more than just a passing phase? Trends Biochem Sci 2013; 38:494-506. [PMID: 24029419 DOI: 10.1016/j.tibs.2013.07.004] [Citation(s) in RCA: 454] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 07/23/2013] [Accepted: 07/29/2013] [Indexed: 12/27/2022]
Abstract
Stress granules (SGs) contain translationally-stalled mRNAs, associated preinitiation factors, and specific RNA-binding proteins. In addition, many signaling proteins are recruited to SGs and/or influence their assembly, which is transient, lasting only until the cells adapt to stress or die. Beyond their role as mRNA triage centers, we posit that SGs constitute RNA-centric signaling hubs analogous to classical multiprotein signaling domains such as transmembrane receptor complexes. As signaling centers, SG formation communicates a 'state of emergency', and their transient existence alters multiple signaling pathways by intercepting and sequestering signaling components. SG assembly and downstream signaling functions may require a cytosolic phase transition facilitated by intrinsically disordered, aggregation-prone protein regions shared by RNA-binding and signaling proteins.
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Affiliation(s)
- Nancy Kedersha
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Smith 652, One Jimmy Fund Way, Boston, MA 02115, USA
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191
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Read GS. Virus-encoded endonucleases: expected and novel functions. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 4:693-708. [PMID: 23900973 DOI: 10.1002/wrna.1188] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 06/21/2013] [Accepted: 06/24/2013] [Indexed: 12/21/2022]
Abstract
Endonucleases catalyze critical steps in the processing, function, and turnover of many cellular RNAs. It is, therefore, not surprising that a number of viruses encode endonucleases that play important roles in viral gene expression. The virion host shutoff (Vhs) endonuclease of herpes simplex virus, the SOX protein of Kaposi Sarcoma Herpesvirus (KSHV), and the influenza virus PB1 endonuclease have well-characterized functions that stem from their abilities to cleave RNA. Vhs accelerates turnover of many cellular and viral mRNAs, redirecting the cell from host to viral gene expression, counteracting key elements of the innate immune response, and facilitating sequential expression of different classes of viral genes. SOX reduces synthesis of many host proteins during the lytic phase of KSHV infections. PB1 is a component of the influenza RNA polymerase that snatches capped oligonucleotides from cellular pre-mRNAs to serve as primers during viral mRNA synthesis. However, all three proteins have important second functions. Vhs stimulates translation of the 3' cistron of bicistronic mRNAs that have selected cellular internal ribosome entry sites, and stimulates polysome loading and translation of selected viral mRNAs at late times during productive infections. SOX has an alkaline exonuclease activity that is important for processing and maturation of newly synthesized copies of the KSHV genome. The influenza RNA polymerase binds the cap and 5' region of viral mRNAs and recruits eIF4G and other factors to viral mRNAs, allowing them to be translated under conditions of reduced eIF4E functionality. This review will discuss the novel and expected functions of these viral endonucleases.
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Affiliation(s)
- G Sullivan Read
- Division of Cell Biology and Biophysics, University of Missouri, Kansas City, Kansas City, MO, USA
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192
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Kaposi's sarcoma-associated herpesvirus kaposin B induces unique monophosphorylation of STAT3 at serine 727 and MK2-mediated inactivation of the STAT3 transcriptional repressor TRIM28. J Virol 2013; 87:8779-91. [PMID: 23740979 DOI: 10.1128/jvi.02976-12] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) is the etiologic agent of primary effusion lymphoma (PEL), multicentric Castleman's disease (MCD), and the inflammation-driven neoplasm Kaposi's sarcoma (KS). A triad of processes, including abnormal proliferation of endothelial cells, aberrant angiogenesis, and chronic inflammation, characterize KS lesions. STAT3 is a key transcription factor governing these processes, and deregulation of STAT3 activity is linked to a wide range of cancers, including PEL and KS. Using primary human endothelial cells (ECs), I demonstrate that KSHV infection modulated STAT3 activation in two ways: (i) KSHV induced uncoupling of canonical tyrosine (Y) and serine (S) phosphorylation events while (ii) concomitantly inducing the phosphorylation and inactivation of TRIM28 (also known as KAP-1 or TIF-1β), a newly identified negative regulator of STAT3 activity. KSHV infection of primary ECs induced chronic STAT3 activation characterized by a shift from the canonical dual P-STAT3 Y705 S727 form to a mono P-STAT3 S727 form. Expression of the latent protein kaposin B promoted the unique phosphorylation of STAT3 at S727, in the absence of Y705, activated the host kinase mitogen-activated protein kinase-activated protein (MAPKAP) kinase 2 (MK2), and stimulated increased expression of STAT3-dependent genes, including CCL5, in ECs. TRIM28-mediated repression of STAT3 is relieved by phosphorylation of S473, and in vitro kinase assays identified TRIM28 S473 as a bona fide target of MK2. Together, these data suggest that kaposin B significantly contributes to the chronic inflammatory environment that is a hallmark of KS by unique activation of the proto-oncogene STAT3, coupled with MK2-mediated inactivation of the STAT3 transcriptional repressor TRIM28.
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193
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Fabian MR, Frank F, Rouya C, Siddiqui N, Lai WS, Karetnikov A, Blackshear PJ, Nagar B, Sonenberg N. Structural basis for the recruitment of the human CCR4-NOT deadenylase complex by tristetraprolin. Nat Struct Mol Biol 2013; 20:735-9. [PMID: 23644599 PMCID: PMC4811204 DOI: 10.1038/nsmb.2572] [Citation(s) in RCA: 196] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 03/19/2013] [Indexed: 12/27/2022]
Abstract
Tristetraprolin (TTP) is an RNA-binding protein that controls the inflammatory response by limiting the expression of several proinflammatory cytokines. TTP post-transcriptionally represses gene expression by interacting with AU-rich elements (AREs) in 3' untranslated regions of target mRNAs and subsequently engenders their deadenylation and decay. TTP accomplishes these tasks, at least in part, by recruiting the multisubunit CCR4-NOT deadenylase complex to the mRNA. Here we identify an evolutionarily conserved C-terminal motif in human TTP that directly binds a central domain of CNOT1, a core subunit of the CCR4-NOT complex. A high-resolution crystal structure of the TTP-CNOT1 complex was determined, providing the first structural insight, to our knowledge, into an ARE-binding protein bound to the CCR4-NOT complex. Mutations at the CNOT1-TTP interface impair TTP-mediated deadenylation, demonstrating the significance of this interaction in TTP-mediated gene silencing.
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MESH Headings
- Binding Sites
- Crystallography, X-Ray
- Humans
- Models, Biological
- Models, Molecular
- Mutagenesis, Site-Directed
- Mutant Proteins/chemistry
- Mutant Proteins/metabolism
- Nuclear Receptor Subfamily 4, Group A, Member 2/chemistry
- Nuclear Receptor Subfamily 4, Group A, Member 2/metabolism
- Protein Binding
- Protein Conformation
- Receptors, CCR4/chemistry
- Receptors, CCR4/metabolism
- Ribonucleases/chemistry
- Ribonucleases/metabolism
- Tristetraprolin/chemistry
- Tristetraprolin/metabolism
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Affiliation(s)
- Marc R. Fabian
- Lady Davis Institute for Medical Research, SMBD-Jewish General Hospital. Montréal, Quebec, Canada
- Department of Oncology, McGill University, Montreal, Quebec, Canada
| | - Filipp Frank
- Department of Biochemistry and Goodman Cancer Centre, McGill University, Montreal, Quebec, Canada
| | - Christopher Rouya
- Department of Biochemistry and Goodman Cancer Centre, McGill University, Montreal, Quebec, Canada
| | - Nadeem Siddiqui
- Department of Biochemistry and Goodman Cancer Centre, McGill University, Montreal, Quebec, Canada
| | - Wi S. Lai
- Laboratory of Signal Transduction, National Institute of Environmental Health Science,, NC, USA
| | - Alexey Karetnikov
- Department of Biochemistry and Goodman Cancer Centre, McGill University, Montreal, Quebec, Canada
| | - Perry J. Blackshear
- Laboratory of Signal Transduction, National Institute of Environmental Health Science,, NC, USA
| | - Bhushan Nagar
- Department of Biochemistry and Goodman Cancer Centre, McGill University, Montreal, Quebec, Canada
| | - Nahum Sonenberg
- Department of Biochemistry and Goodman Cancer Centre, McGill University, Montreal, Quebec, Canada
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194
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Ciais D, Cherradi N, Feige JJ. Multiple functions of tristetraprolin/TIS11 RNA-binding proteins in the regulation of mRNA biogenesis and degradation. Cell Mol Life Sci 2013; 70:2031-44. [PMID: 22968342 PMCID: PMC11113850 DOI: 10.1007/s00018-012-1150-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 08/27/2012] [Accepted: 08/28/2012] [Indexed: 02/06/2023]
Abstract
Members of the tristetraprolin (TTP/TIS11) family are important RNA-binding proteins initially characterized as mediators of mRNA degradation. They act via their interaction with AU-rich elements present in the 3'UTR of regulated transcripts. However, it is progressively appearing that the different steps of mRNA processing and fate including transcription, splicing, polyadenylation, translation, and degradation are coordinately regulated by multifunctional integrator proteins that possess a larger panel of functions than originally anticipated. Tristetraprolin and related proteins are very good examples of such integrators. This review gathers the present knowledge on the functions of this family of RNA-binding proteins, including their role in AU-rich element-mediated mRNA decay and focuses on recent advances that support the concept of their broader involvement in distinct steps of mRNA biogenesis and degradation.
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Affiliation(s)
- Delphine Ciais
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1036, 17 rue des Martyrs, 38054 Grenoble Cedex 9, France
- Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV)/Biologie du Cancer et de l’Infection (BCI), 38054 Grenoble, France
- Université Joseph Fourier-Grenoble 1, 38041 Grenoble, France
| | - Nadia Cherradi
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1036, 17 rue des Martyrs, 38054 Grenoble Cedex 9, France
- Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV)/Biologie du Cancer et de l’Infection (BCI), 38054 Grenoble, France
- Université Joseph Fourier-Grenoble 1, 38041 Grenoble, France
| | - Jean-Jacques Feige
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1036, 17 rue des Martyrs, 38054 Grenoble Cedex 9, France
- Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV)/Biologie du Cancer et de l’Infection (BCI), 38054 Grenoble, France
- Université Joseph Fourier-Grenoble 1, 38041 Grenoble, France
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195
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Mahboubi H, Kodiha M, Stochaj U. Automated detection and quantification of granular cell compartments. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2013; 19:617-628. [PMID: 23552615 DOI: 10.1017/s1431927613000159] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Many cellular processes are organized in a compartmentalized and dynamic fashion to ensure effective adaptation to physiological changes. Thus, in response to stress and disease, cells initiate protective mechanisms to restore homeostasis. Among these mechanisms are the arrest of translation and remodeling of ribonucleoprotein complexes into granular compartments in the cytoplasm, known as stress granules (SGs). To date, the analysis of SGs has relied on the manual demarcation and measurement of the compartment, making quantitative studies time-consuming, while preventing the efficient use of high-throughput technology. We developed the first fully automated, computer-based procedures that measure the association of fluorescent molecules with granular compartments. Our methods quantify automatically multiple granule parameters and generate data at the level of single cells or individual SGs. These techniques detect simultaneously in an automated fashion proteins and RNAs located in SGs. The effectiveness of our protocols is demonstrated by studies that reveal several of the unique biological and structural characteristics of SGs. In particular, we show that the type of stress determines granule size and composition, as illustrated by the concentration of poly(A)-RNA and a specific SG marker protein. Furthermore, we took advantage of the computer-based and automated methods to design assays suitable for high-throughput screening.
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Affiliation(s)
- Hicham Mahboubi
- Department of Physiology, McGill University, Montreal H3G 1Y6, Quebec, Canada
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196
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Brooks SA, Blackshear PJ. Tristetraprolin (TTP): interactions with mRNA and proteins, and current thoughts on mechanisms of action. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1829:666-79. [PMID: 23428348 PMCID: PMC3752887 DOI: 10.1016/j.bbagrm.2013.02.003] [Citation(s) in RCA: 296] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 01/25/2013] [Accepted: 02/04/2013] [Indexed: 12/14/2022]
Abstract
Changes in mRNA stability and translation are critical control points in the regulation of gene expression, particularly genes encoding growth factors, inflammatory mediators, and proto-oncogenes. Adenosine and uridine (AU)-rich elements (ARE), often located in the 3' untranslated regions (3'UTR) of mRNAs, are known to target transcripts for rapid decay. They are also involved in the regulation of mRNA stability and translation in response to extracellular cues. This review focuses on one of the best characterized ARE binding proteins, tristetraprolin (TTP), the founding member of a small family of CCCH tandem zinc finger proteins. In this survey, we have reviewed the current status of TTP interactions with mRNA and proteins, and discussed current thinking about TTP's mechanism of action to promote mRNA decay. We also review the proposed regulation of TTP's functions by phosphorylation. Finally, we have discussed emerging evidence for TTP operating as a translational regulator. This article is part of a Special Issue entitled: RNA Decay mechanisms.
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Affiliation(s)
- Seth A. Brooks
- Veterans Affairs Medical Center, White River Junction, Vermont, USA
- Department of Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
| | - Perry J. Blackshear
- The Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
- Departments of Medicine and Biochemistry, Duke University Medical Center, Durham, North Carolina USA
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197
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Droll D, Minia I, Fadda A, Singh A, Stewart M, Queiroz R, Clayton C. Post-transcriptional regulation of the trypanosome heat shock response by a zinc finger protein. PLoS Pathog 2013; 9:e1003286. [PMID: 23592996 PMCID: PMC3616968 DOI: 10.1371/journal.ppat.1003286] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 02/19/2013] [Indexed: 12/30/2022] Open
Abstract
In most organisms, the heat-shock response involves increased heat-shock gene transcription. In Kinetoplastid protists, however, virtually all control of gene expression is post-transcriptional. Correspondingly, Trypanosoma brucei heat-shock protein 70 (HSP70) synthesis after heat shock depends on regulation of HSP70 mRNA turnover. We here show that the T. brucei CCCH zinc finger protein ZC3H11 is a post-transcriptional regulator of trypanosome chaperone mRNAs. ZC3H11 is essential in bloodstream-form trypanosomes and for recovery of insect-form trypanosomes from heat shock. ZC3H11 binds to mRNAs encoding heat-shock protein homologues, with clear specificity for the subset of trypanosome chaperones that is required for protein refolding. In procyclic forms, ZC3H11 was required for stabilisation of target chaperone-encoding mRNAs after heat shock, and the HSP70 mRNA was also decreased upon ZC3H11 depletion in bloodstream forms. Many mRNAs bound to ZC3H11 have a consensus AUU repeat motif in the 3'-untranslated region. ZC3H11 bound preferentially to AUU repeats in vitro, and ZC3H11 regulation of HSP70 mRNA in bloodstream forms depended on its AUU repeat region. Tethering of ZC3H11 to a reporter mRNA increased reporter expression, showing that it is capable of actively stabilizing an mRNA. These results show that expression of trypanosome heat-shock genes is controlled by a specific RNA-protein interaction. They also show that heat-shock-induced chaperone expression in procyclic trypanosome enhances parasite survival at elevated temperatures.
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Affiliation(s)
- Dorothea Droll
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Igor Minia
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Abeer Fadda
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Aditi Singh
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Mhairi Stewart
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Rafael Queiroz
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Christine Clayton
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
- * E-mail:
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198
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Moens U, Kostenko S, Sveinbjørnsson B. The Role of Mitogen-Activated Protein Kinase-Activated Protein Kinases (MAPKAPKs) in Inflammation. Genes (Basel) 2013; 4:101-33. [PMID: 24705157 PMCID: PMC3899974 DOI: 10.3390/genes4020101] [Citation(s) in RCA: 142] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 03/18/2013] [Accepted: 03/20/2013] [Indexed: 01/18/2023] Open
Abstract
Mitogen-activated protein kinase (MAPK) pathways are implicated in several cellular processes including proliferation, differentiation, apoptosis, cell survival, cell motility, metabolism, stress response and inflammation. MAPK pathways transmit and convert a plethora of extracellular signals by three consecutive phosphorylation events involving a MAPK kinase kinase, a MAPK kinase, and a MAPK. In turn MAPKs phosphorylate substrates, including other protein kinases referred to as MAPK-activated protein kinases (MAPKAPKs). Eleven mammalian MAPKAPKs have been identified: ribosomal-S6-kinases (RSK1-4), mitogen- and stress-activated kinases (MSK1-2), MAPK-interacting kinases (MNK1-2), MAPKAPK-2 (MK2), MAPKAPK-3 (MK3), and MAPKAPK-5 (MK5). The role of these MAPKAPKs in inflammation will be reviewed.
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Affiliation(s)
- Ugo Moens
- Molecular Inflammation Research Group, Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, NO-9037 Tromsø, Norway.
| | - Sergiy Kostenko
- Molecular Inflammation Research Group, Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, NO-9037 Tromsø, Norway.
| | - Baldur Sveinbjørnsson
- Molecular Inflammation Research Group, Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, NO-9037 Tromsø, Norway.
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199
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Higashi S, Kabuta T, Nagai Y, Tsuchiya Y, Akiyama H, Wada K. TDP-43 associates with stalled ribosomes and contributes to cell survival during cellular stress. J Neurochem 2013; 126:288-300. [PMID: 23398327 DOI: 10.1111/jnc.12194] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 02/05/2013] [Accepted: 02/06/2013] [Indexed: 12/11/2022]
Abstract
TAR DNA-binding protein 43 (TDP-43) has emerged as an important contributor to amyotrophic lateral sclerosis and frontotemporal lobar degeneration. To understand the physiological roles of TDP-43 in the complex translational regulation mechanisms, we exposed cultured cells to oxidative stress induced by sodium arsenite (ARS) for different periods of time, leading to non-lethal or sublethal injury. Polysome profile analysis revealed that ARS-induced stress caused the association of TDP-43 with stalled ribosomes via binding to mRNA, which was not found under the steady-state condition. When the cells were exposed to short-term/non-lethal stress, TDP-43 associating with ribosomes localized to stress granules (SGs); this association was transient because it was immediately dissolved by the removal of the stress. In contrast, when the cells were exposed to long-term/sublethal stress, TDP-43 was excluded from SGs and shifted to the heavy fractions independent of any binding to mRNA. In these severely stressed cells, biochemical alterations of TDP-43, such as increased insolubility and disulfide bond formation, were irreversible. TDP-43 was finally phosphorylated via the ARS-induced c-jun N-terminal kinase pathway. In TDP-43-silenced cells, stalled mRNA and poly (A)(+) RNA stability was disturbed and cytotoxicity increased under sublethal stress. Thus, TDP-43 associates with stalled ribosomes and contributes to cell survival during cellular stress.
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Affiliation(s)
- Shinji Higashi
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan.
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200
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Ray D, Shukla S, Allam US, Helman A, Ramanand SG, Tran L, Bassetti M, Krishnamurthy PM, Rumschlag M, Paulsen M, Sun L, Shanley TP, Ljungman M, Nyati MK, Zhang M, Lawrence TS. Tristetraprolin mediates radiation-induced TNF-α production in lung macrophages. PLoS One 2013; 8:e57290. [PMID: 23468959 PMCID: PMC3585360 DOI: 10.1371/journal.pone.0057290] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 01/20/2013] [Indexed: 12/26/2022] Open
Abstract
The efficacy of radiation therapy for lung cancer is limited by radiation-induced lung toxicity (RILT). Although tumor necrosis factor-alpha (TNF-α) signaling plays a critical role in RILT, the molecular regulators of radiation-induced TNF-α production remain unknown. We investigated the role of a major TNF-α regulator, Tristetraprolin (TTP), in radiation-induced TNF-α production by macrophages. For in vitro studies we irradiated (4 Gy) either a mouse lung macrophage cell line, MH-S or macrophages isolated from TTP knockout mice, and studied the effects of radiation on TTP and TNF-α levels. To study the in vivo relevance, mouse lungs were irradiated with a single dose (15 Gy) and assessed at varying times for TTP alterations. Irradiation of MH-S cells caused TTP to undergo an inhibitory phosphorylation at Ser-178 and proteasome-mediated degradation, which resulted in increased TNF-α mRNA stabilization and secretion. Similarly, MH-S cells treated with TTP siRNA or macrophages isolated from ttp (−/−) mice had higher basal levels of TNF-α, which was increased minimally after irradiation. Conversely, cells overexpressing TTP mutants defective in undergoing phosphorylation released significantly lower levels of TNF-α. Inhibition of p38, a known kinase for TTP, by either siRNA or a small molecule inhibitor abrogated radiation-induced TNF-α release by MH-S cells. Lung irradiation induced TTPSer178 phosphorylation and protein degradation and a simultaneous increase in TNF-α production in C57BL/6 mice starting 24 h post-radiation. In conclusion, irradiation of lung macrophages causes TTP inactivation via p38-mediated phosphorylation and proteasome-mediated degradation, leading to TNF-α production. These findings suggest that agents capable of blocking TTP phosphorylation or stabilizing TTP after irradiation could decrease RILT.
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Affiliation(s)
- Dipankar Ray
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, United States of America.
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