51
|
Gao P, Li N, Ji K, Wang Y, Xu C, Liu Y, Wang Q, Wang J, He N, Sun Z, Du L, Liu Q. Resveratrol targets TyrRS acetylation to protect against radiation-induced damage. FASEB J 2019; 33:8083-8093. [PMID: 30939244 DOI: 10.1096/fj.201802474rr] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Resveratrol (RSV) has broad prospective applications as a radiation protection drug, but its mechanism of action is not yet clear. Here, we found that 5 μM RSV can effectively reduce the cell death caused by irradiation. Irradiation leads to G2/M phase arrest in the cell cycle, whereas RSV treatment increases S-phase cell cycle arrest, which is associated with sirtuin 1 (SIRT1) regulation. Meanwhile, RSV promotes DNA damage repair, mainly by accelerating the efficiency of homologous recombination repair. Under oxidative stress, tyrosyl-tRNA synthetase (TyrRS) is transported to the nucleus to protect against DNA damage. RSV can promote TyrRS acetylation, thus promoting TyrRS to enter the nucleus, where it regulates the relevant signaling proteins and reduces apoptosis and DNA damage. SIRT1 is a deacetylase, and SIRT1 knockdown or inhibition can increase TyrRS acetylation levels, further reducing radiation-induced apoptosis after RSV treatment. Our study revealed a new radiation protection mechanism for RSV, in which the acetylation of TyrRS and its translocation into the nucleus is promoted, and this mechanism may also represent a novel protective target against irradiation.-Gao, P., Li, N., Ji, K., Wang, Y., Xu, C., Liu, Y., Wang, Q., Wang, J., He, N., Sun, Z., Du, L., Liu, Q. Resveratrol targets TyrRS acetylation to protect against radiation-induced damage.
Collapse
Affiliation(s)
- Piaoyang Gao
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences-Peking Union Medical College, Tianjin, China
| | - Na Li
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences-Peking Union Medical College, Tianjin, China
| | - Kaihua Ji
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences-Peking Union Medical College, Tianjin, China
| | - Yan Wang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences-Peking Union Medical College, Tianjin, China
| | - Chang Xu
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences-Peking Union Medical College, Tianjin, China
| | - Yang Liu
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences-Peking Union Medical College, Tianjin, China
| | - Qin Wang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences-Peking Union Medical College, Tianjin, China
| | - Jihan Wang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences-Peking Union Medical College, Tianjin, China
| | - Ningning He
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences-Peking Union Medical College, Tianjin, China
| | - Zhijuan Sun
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences-Peking Union Medical College, Tianjin, China
| | - Liqing Du
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences-Peking Union Medical College, Tianjin, China
| | - Qiang Liu
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences-Peking Union Medical College, Tianjin, China
| |
Collapse
|
52
|
Abstract
Serum lactate levels are traditionally interpreted as a marker of tissue hypoxia and often used clinically as an indicator of severity and outcome of sepsis/septic shock. Interestingly, recent studies involving the effects of tumor-derived lactate suggest that lactate itself may have an immunosuppressive effect in its local environment. This finding adds to the recent advances in immunometabolism that shed light on the importance of metabolism and metabolic intermediates in the regulation of innate immune and inflammatory responses in sepsis. In this article, we summarize recent studies, showing that the activation of immune cells requires aerobic glycolytic metabolism and that lactate produced by aerobic glycolysis may play an immunosuppressive role in sepsis.
Collapse
|
53
|
Wei N, Zhang Q, Yang XL. Neurodegenerative Charcot-Marie-Tooth disease as a case study to decipher novel functions of aminoacyl-tRNA synthetases. J Biol Chem 2019; 294:5321-5339. [PMID: 30643024 DOI: 10.1074/jbc.rev118.002955] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are essential enzymes that catalyze the first reaction in protein biosynthesis, namely the charging of transfer RNAs (tRNAs) with their cognate amino acids. aaRSs have been increasingly implicated in dominantly and recessively inherited human diseases. The most common aaRS-associated monogenic disorder is the incurable neurodegenerative disease Charcot-Marie-Tooth neuropathy (CMT), caused by dominant mono-allelic mutations in aaRSs. With six currently known members (GlyRS, TyrRS, AlaRS, HisRS, TrpRS, and MetRS), aaRSs represent the largest protein family implicated in CMT etiology. After the initial discovery linking aaRSs to CMT, the field has progressed from understanding whether impaired tRNA charging is a critical component of this disease to elucidating the specific pathways affected by CMT-causing mutations in aaRSs. Although many aaRS CMT mutants result in loss of tRNA aminoacylation function, animal genetics studies demonstrated that dominant mutations in GlyRS cause CMT through toxic gain-of-function effects, which also may apply to other aaRS-linked CMT subtypes. The CMT-causing mechanism is likely to be multifactorial and involves multiple cellular compartments, including the nucleus and the extracellular space, where the normal WT enzymes also appear. Thus, the association of aaRSs with neuropathy is relevant to discoveries indicating that aaRSs also have nonenzymatic regulatory functions that coordinate protein synthesis with other biological processes. Through genetic, functional, and structural analyses, commonalities among different mutations and different aaRS-linked CMT subtypes have begun to emerge, providing insights into the nonenzymatic functions of aaRSs and the pathogenesis of aaRS-linked CMT to guide therapeutic development to treat this disease.
Collapse
Affiliation(s)
- Na Wei
- From the Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037
| | - Qian Zhang
- From the Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037
| | - Xiang-Lei Yang
- From the Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037
| |
Collapse
|
54
|
Amorim IS, Lach G, Gkogkas CG. The Role of the Eukaryotic Translation Initiation Factor 4E (eIF4E) in Neuropsychiatric Disorders. Front Genet 2018; 9:561. [PMID: 30532767 PMCID: PMC6265315 DOI: 10.3389/fgene.2018.00561] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 11/06/2018] [Indexed: 12/24/2022] Open
Abstract
Protein synthesis in eukaryotic cells is a complex, multi-step and tightly regulated process. Translation initiation, the rate limiting step in protein synthesis, is dependent on the activity of eukaryotic translation Initiation Factor 4E (eIF4E). eIF4E is the cap-binding protein which, in synergy with proteins such as the helicase eIF4A and the scaffolding protein eIF4G, binds to mRNA, allowing the recruitment of ribosomes and translation initiation. The function of eIF4E is tightly regulated in cells under normal physiological conditions and can be controlled by post-translational modifications, such as phosphorylation, and by the binding of inhibitory proteins, including eIF4E binding proteins (4E-BPs) and CYFIP1. Recent studies have highlighted the importance of eIF4E in normal or aberrant function of the nervous system. In this mini-review, we will highlight the role of eIF4E function and regulation in the pathophysiology of neurodevelopmental and neuropsychiatric disorders.
Collapse
Affiliation(s)
- Inês S Amorim
- Centre for Discovery Brain Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Gilliard Lach
- Centre for Discovery Brain Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Christos G Gkogkas
- Centre for Discovery Brain Sciences, The University of Edinburgh, Edinburgh, United Kingdom.,The Patrick Wild Centre, The University of Edinburgh, Edinburgh, United Kingdom
| |
Collapse
|
55
|
Molavi G, Samadi N, Hosseingholi EZ. The roles of moonlight ribosomal proteins in the development of human cancers. J Cell Physiol 2018; 234:8327-8341. [PMID: 30417503 DOI: 10.1002/jcp.27722] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 09/23/2018] [Indexed: 12/13/2022]
Abstract
"Moonlighting protein" is a term used to define a single protein with multiple functions and different activities that are not derived from gene fusions, multiple RNA splicing, or the proteolytic activity of promiscuous enzymes. Different proteinous constituents of ribosomes have been shown to have important moonlighting extra-ribosomal functions. In this review, we introduce the impact of key moonlight ribosomal proteins and dependent signal transduction in the initiation and progression of various cancers. As a future perspective, the potential role of these moonlight ribosomal proteins in the diagnosis, prognosis, and development of novel strategies to improve the efficacy of therapies for human cancers has been suggested.
Collapse
Affiliation(s)
- Ghader Molavi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nasser Samadi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Biochemistry, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | | |
Collapse
|
56
|
Eswarappa SM, Potdar AA, Sahoo S, Sankar S, Fox PL. Metabolic origin of the fused aminoacyl-tRNA synthetase, glutamyl-prolyl-tRNA synthetase. J Biol Chem 2018; 293:19148-19156. [PMID: 30309984 DOI: 10.1074/jbc.ra118.004276] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/03/2018] [Indexed: 11/06/2022] Open
Abstract
About 1 billion years ago, in a single-celled holozoan ancestor of all animals, a gene fusion of two tRNA synthetases formed the bifunctional enzyme, glutamyl-prolyl-tRNA synthetase (EPRS). We propose here that a confluence of metabolic, biochemical, and environmental factors contributed to the specific fusion of glutamyl- (ERS) and prolyl- (PRS) tRNA synthetases. To test this idea, we developed a mathematical model that centers on the precursor-product relationship of glutamic acid and proline, as well as metabolic constraints on free glutamic acid availability near the time of the fusion event. Our findings indicate that proline content increased in the proteome during the emergence of animals, thereby increasing demand for free proline. Together, these constraints contributed to a marked cellular depletion of glutamic acid and its products, with potentially catastrophic consequences. In response, an ancient organism invented an elegant solution in which genes encoding ERS and PRS fused to form EPRS, forcing coexpression of the two enzymes and preventing lethal dysregulation. The substantial evolutionary advantage of this coregulatory mechanism is evidenced by the persistence of EPRS in nearly all extant animals.
Collapse
Affiliation(s)
- Sandeep M Eswarappa
- From the Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, India,
| | - Alka A Potdar
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, and
| | - Sarthak Sahoo
- From the Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, India
| | - Santhosh Sankar
- From the Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, India
| | - Paul L Fox
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195
| |
Collapse
|
57
|
Park HY, Kang HS, Im SS. Recent insight into the correlation of SREBP-mediated lipid metabolism and innate immune response. J Mol Endocrinol 2018; 61:R123-R131. [PMID: 30307160 DOI: 10.1530/jme-17-0289] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Fatty acids are essential nutrients that contribute to several intracellular functions. Fatty acid synthesis and oxidation are known to be regulated by sterol regulatory element-binding proteins (SREBPs), which play a pivotal role in the regulation of cellular triglyceride synthesis and cholesterol biogenesis. Recent studies point to a multifunctional role of SREBPs in the pathogenesis of metabolic diseases, such as obesity, type II diabetes and cancer as well as in immune responses. Notably, fatty acid metabolic intermediates are involved in energy homeostasis and pathophysiological conditions. In particular, intracellular fatty acid metabolism affects an inflammatory response, thereby influencing metabolic diseases. The objective of this review is to summarize the recent advances in our understanding of the dual role of SREBPs in both lipid metabolism and inflammation-mediated metabolic diseases.
Collapse
Affiliation(s)
- Hyeon Young Park
- Department of Physiology, Keimyung University School of Medicine, Daegu, South Korea
| | - Hye Suk Kang
- Department of Physiology, Keimyung University School of Medicine, Daegu, South Korea
| | - Seung-Soon Im
- Department of Physiology, Keimyung University School of Medicine, Daegu, South Korea
| |
Collapse
|
58
|
Tyrosyl-tRNA synthetase stimulates thrombopoietin-independent hematopoiesis accelerating recovery from thrombocytopenia. Proc Natl Acad Sci U S A 2018; 115:E8228-E8235. [PMID: 30104364 PMCID: PMC6126720 DOI: 10.1073/pnas.1807000115] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) catalyze aminoacylation of tRNAs in the first step of protein synthesis in the cytoplasm. However, in higher eukaryotes, they acquired additional functions beyond translation. In the present study, we show that an activated form of tyrosyl-tRNA synthetase (YRSACT) functions to enhance megakaryopoiesis and platelet production in vitro and in vivo. These findings were confirmed with human megakaryocytes differentiated from peripheral blood CD34+ hematopoietic stem cells and with human induced pluripotent stem (iPS) cells. The activity of YRSACT is independent of thrombopoietin (TPO), as evidenced by expansion of the megakaryocytes from iPS cell-derived hematopoietic stem cells from a patient deficient in TPO signaling. These findings demonstrate a previously unrecognized function of an aaRS which may have implications for therapeutic interventions. New mechanisms behind blood cell formation continue to be uncovered, with therapeutic approaches for hematological diseases being of great interest. Here we report an enzyme in protein synthesis, known for cell-based activities beyond translation, is a factor inducing megakaryocyte-biased hematopoiesis, most likely under stress conditions. We show an activated form of tyrosyl-tRNA synthetase (YRSACT), prepared either by rationally designed mutagenesis or alternative splicing, induces expansion of a previously unrecognized high-ploidy Sca-1+ megakaryocyte population capable of accelerating platelet replenishment after depletion. Moreover, YRSACT targets monocytic cells to induce secretion of transacting cytokines that enhance megakaryocyte expansion stimulating the Toll-like receptor/MyD88 pathway. Platelet replenishment by YRSACT is independent of thrombopoietin (TPO), as evidenced by expansion of the megakaryocytes from induced pluripotent stem cell-derived hematopoietic stem cells from a patient deficient in TPO signaling. We suggest megakaryocyte-biased hematopoiesis induced by YRSACT offers new approaches for treating thrombocytopenia, boosting yields from cell-culture production of platelet concentrates for transfusion, and bridging therapy for hematopoietic stem cell transplantation.
Collapse
|
59
|
Garcia-Moreno M, Järvelin AI, Castello A. Unconventional RNA-binding proteins step into the virus-host battlefront. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1498. [PMID: 30091184 PMCID: PMC7169762 DOI: 10.1002/wrna.1498] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 06/01/2018] [Accepted: 06/05/2018] [Indexed: 12/15/2022]
Abstract
The crucial participation of cellular RNA‐binding proteins (RBPs) in virtually all steps of virus infection has been known for decades. However, most of the studies characterizing this phenomenon have focused on well‐established RBPs harboring classical RNA‐binding domains (RBDs). Recent proteome‐wide approaches have greatly expanded the census of RBPs, discovering hundreds of proteins that interact with RNA through unconventional RBDs. These domains include protein–protein interaction platforms, enzymatic cores, and intrinsically disordered regions. Here, we compared the experimentally determined census of RBPs to gene ontology terms and literature, finding that 472 proteins have previous links with viruses. We discuss what these proteins are and what their roles in infection might be. We also review some of the pioneering examples of unorthodox RBPs whose RNA‐binding activity has been shown to be critical for virus infection. Finally, we highlight the potential of these proteins for host‐based therapies against viruses. This article is categorized under:
RNA Interactions with Proteins and Other Molecules > Protein–RNA Interactions: Functional Implications RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > RNA–Protein Complexes
Collapse
Affiliation(s)
| | - Aino I Järvelin
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | |
Collapse
|
60
|
Almamy A, Schwerk C, Schroten H, Ishikawa H, Asif AR, Reuss B. Interactions of antisera to different Chlamydia and Chlamydophila species with the ribosomal protein RPS27a correlate with impaired protein synthesis in a human choroid plexus papilloma cell line. Immunol Res 2018; 65:1110-1123. [PMID: 28913776 DOI: 10.1007/s12026-017-8952-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Chlamydia trachomatis (CT) and the Chlamydophila species (CS) Chlamydophila pneumoniae (CPn), and Chlamydophila psittaci (CPs) are suggested to induce autoantibodies causative of several human autoimmune disorders like rheumatoid arthritis and systemic lupus erythematosus (SLE). The aim of the present study was therefore to identify cellular protein interaction partners with antisera to CT (α-CT) or CS (α-CS) and to identify functional consequences of such interaction in vitro. As detected with a commercial first trimester human prenatal brain multiprotein array (hEXselect, Engine, Germany), the most frequent interaction partner with both α-CT and α-CS was the ribosomal small subunit protein RPS27a. This could be confirmed by Western blot analysis with a recombinant RPS27a sample. In addition, immunocytochemistry with both antisera in the human choroid plexus papilloma cell line HIBCPP revealed a granular cytoplasmic staining, and Western blot analysis with whole-cell protein samples of HIBCPP cells revealed both antisera to label protein bands of different molecular weights and intensity. By 2D Western blot analysis and mass spectrometry, one of the protein spots interacting with α-CT could be identified as the RPS27a. Finally, two different methods for the detection of protein synthesis activity, the SUnSET technique and an HPG fluorescence assay revealed both antisera to cause reduced translational activity in HIBCPP cells. Together with previous findings of RPS27a as an autoimmune target in a mouse model of systemic lupus erythematosus (SLE), these results suggest that infections with CT and/or CS could induce SLE-associated immune modifications. However, direct evidence for a pathogenic role of these interactions for SLE demands further investigations.
Collapse
Affiliation(s)
- Abdullah Almamy
- Neuroanatomy, University Medical Center Göttingen, Göttingen, Germany
| | - Christian Schwerk
- Pediatric Infectious Diseases, University Children's Hospital Mannheim, Heidelberg University, Heidelberg, Germany
| | - Horst Schroten
- Pediatric Infectious Diseases, University Children's Hospital Mannheim, Heidelberg University, Heidelberg, Germany
| | | | - Abdul Rahman Asif
- Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Bernhard Reuss
- Neuroanatomy, University Medical Center Göttingen, Göttingen, Germany. .,Institute for Neuroanatomy, University Medical Center Göttingen, Kreuzbergring 36, 37075, Göttingen, Federal Republic of Germany.
| |
Collapse
|
61
|
Ito N, Anam MB, Ahmad SAI, Ohta K. Transdifferentiation of human somatic cells by ribosome. Dev Growth Differ 2018; 60:241-247. [PMID: 29845598 DOI: 10.1111/dgd.12538] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 04/18/2018] [Accepted: 04/18/2018] [Indexed: 01/19/2023]
Abstract
Ribosomes are intracellular organelles ubiquitous in all organisms, which translate information from mRNAs to synthesize proteins. They are complex macromolecules composed of dozens of proteins and ribosomal RNAs. Other than translation, some ribosomal proteins also have side-jobs called "Moonlighting" function. The majority of these moonlighting functions influence cancer progression, early development and differentiation. Recently, we discovered that ribosome is involved in the regulation of cellular transdifferentiation of human dermal fibroblasts (HDFs). In vitro incorporation of ribosomes into HDFs arrests cell proliferation and induces the formation of cell clusters, that differentiate into three germ layer derived cells upon induction by differentiation mediums. The discovery of ribosome induced transdifferentiation, that is not based on genetic modification, find new possibilities for the treatment of cancer and congenital diseases, as well as to understand early development and cellular lineage differentiation.
Collapse
Affiliation(s)
- Naofumi Ito
- Department of Developmental Neurobiology, Graduate School of Life Sciences, Kumamoto University, Kumamoto, Japan.,International Research Core for Stem Cell-based Developmental Medicine, Kumamoto University, Kumamoto, Japan.,Program for Leading Graduate Schools "HIGO Program", Kumamoto University, Kumamoto, Japan
| | - Mohammad Badrul Anam
- Department of Developmental Neurobiology, Graduate School of Life Sciences, Kumamoto University, Kumamoto, Japan.,International Research Core for Stem Cell-based Developmental Medicine, Kumamoto University, Kumamoto, Japan.,Program for Leading Graduate Schools "HIGO Program", Kumamoto University, Kumamoto, Japan
| | - Shah Adil Ishtiyaq Ahmad
- Department of Developmental Neurobiology, Graduate School of Life Sciences, Kumamoto University, Kumamoto, Japan.,International Research Core for Stem Cell-based Developmental Medicine, Kumamoto University, Kumamoto, Japan.,Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Kunimasa Ohta
- Department of Developmental Neurobiology, Graduate School of Life Sciences, Kumamoto University, Kumamoto, Japan.,International Research Core for Stem Cell-based Developmental Medicine, Kumamoto University, Kumamoto, Japan.,Program for Leading Graduate Schools "HIGO Program", Kumamoto University, Kumamoto, Japan.,Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
| |
Collapse
|
62
|
Halawani D, Gogonea V, DiDonato JA, Pipich V, Yao P, China A, Topbas C, Vasu K, Arif A, Hazen SL, Fox PL. Structural control of caspase-generated glutamyl-tRNA synthetase by appended noncatalytic WHEP domains. J Biol Chem 2018; 293:8843-8860. [PMID: 29643180 DOI: 10.1074/jbc.m117.807503] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 03/26/2018] [Indexed: 02/02/2023] Open
Abstract
Aminoacyl-tRNA synthetases are ubiquitous, evolutionarily conserved enzymes catalyzing the conjugation of amino acids onto cognate tRNAs. During eukaryotic evolution, tRNA synthetases have been the targets of persistent structural modifications. These modifications can be additive, as in the evolutionary acquisition of noncatalytic domains, or subtractive, as in the generation of truncated variants through regulated mechanisms such as proteolytic processing, alternative splicing, or coding region polyadenylation. A unique variant is the human glutamyl-prolyl-tRNA synthetase (EPRS) consisting of two fused synthetases joined by a linker containing three copies of the WHEP domain (termed by its presence in tryptophanyl-, histidyl-, and glutamyl-prolyl-tRNA synthetases). Here, we identify site-selective proteolysis as a mechanism that severs the linkage between the EPRS synthetases in vitro and in vivo Caspase action targeted Asp-929 in the third WHEP domain, thereby separating the two synthetases. Using a neoepitope antibody directed against the newly exposed C terminus, we demonstrate EPRS cleavage at Asp-929 in vitro and in vivo Biochemical and biophysical characterizations of the N-terminally generated EPRS proteoform containing the glutamyl-tRNA synthetase and most of the linker, including two WHEP domains, combined with structural analysis by small-angle neutron scattering, revealed a role for the WHEP domains in modulating conformations of the catalytic core and GSH-S-transferase-C-terminal-like (GST-C) domain. WHEP-driven conformational rearrangement altered GST-C domain interactions and conferred distinct oligomeric states in solution. Collectively, our results reveal long-range conformational changes imposed by the WHEP domains and illustrate how noncatalytic domains can modulate the global structure of tRNA synthetases in complex eukaryotic systems.
Collapse
Affiliation(s)
- Dalia Halawani
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and
| | - Valentin Gogonea
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and .,the Department of Chemistry, Cleveland State University, Cleveland, Ohio 44115
| | - Joseph A DiDonato
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and
| | - Vitaliy Pipich
- the Jülich Center for Neutron Science, Outstation at Maier-Leibnitz Zentrum, Forschungszentrum Jülich, GmbH, Lichtenbergstrasse 1, 85747 Garching, Germany, and
| | - Peng Yao
- the Department of Medicine, Aab Cardiovascular Research Institute, University of Rochester, Rochester, New York 14642
| | - Arnab China
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and
| | - Celalettin Topbas
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and.,the Department of Chemistry, Cleveland State University, Cleveland, Ohio 44115
| | - Kommireddy Vasu
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and
| | - Abul Arif
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and
| | - Stanley L Hazen
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and.,Center for Cardiovascular Diagnostics and Prevention, and Department of Cardiovascular Medicine, Cleveland Clinic Foundation, Cleveland, Ohio 44195
| | - Paul L Fox
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and
| |
Collapse
|
63
|
Battu S, Afroz S, Giddaluru J, Naz S, Huang W, Khumukcham SS, Khan RA, Bhat SY, Qureshi IA, Manavathi B, Khan AA, August A, Hasnain SE, Khan N. Amino acid starvation sensing dampens IL-1β production by activating riboclustering and autophagy. PLoS Biol 2018; 16:e2005317. [PMID: 29621237 PMCID: PMC5903674 DOI: 10.1371/journal.pbio.2005317] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 04/17/2018] [Accepted: 03/05/2018] [Indexed: 11/22/2022] Open
Abstract
Activation of the amino acid starvation response (AAR) increases lifespan and acute stress resistance as well as regulates inflammation. However, the underlying mechanisms remain unclear. Here, we show that activation of AAR pharmacologically by Halofuginone (HF) significantly inhibits production of the proinflammatory cytokine interleukin 1β (IL-1β) and provides protection from intestinal inflammation in mice. HF inhibits IL-1β through general control nonderepressible 2 kinase (GCN2)–dependent activation of the cytoprotective integrated stress response (ISR) pathway, resulting in rerouting of IL-1β mRNA from translationally active polysomes to inactive ribocluster complexes—such as stress granules (SGs)—via recruitment of RNA-binding proteins (RBPs) T cell–restricted intracellular antigen-1(TIA-1)/TIA-1–related (TIAR), which are further cleared through induction of autophagy. GCN2 ablation resulted in reduced autophagy and SG formation, which is inversely correlated with IL-1β production. Furthermore, HF diminishes inflammasome activation through suppression of reactive oxygen species (ROS) production. Our study unveils a novel mechanism by which IL-1β is regulated by AAR and further suggests that administration of HF might offer an effective therapeutic intervention against inflammatory diseases. Reduced intake of food (also known as dietary restriction) without malnutrition has been shown to benefit health in humans and animals, including an increase in life expectancy, metabolic fitness, and resistance to acute stress. Recent studies have attributed the benefits associated with dietary restriction to the reduced intake of amino acids. However, the underlying mechanisms through which amino acid restriction regulates various homeostatic processes are poorly defined. Here, we show that activation of amino acid starvation response (AAR) by the small molecule Halofuginone (HF) results in a significant inhibition of production of interleukin 1β (IL-1β), a proinflammatory mediator. We find that AAR provides protection from intestinal inflammation–associated pathology in a mouse model of colitis through a novel mechanism involving the formation of riboclusters (groups of RNA-binding proteins (RBPs) and stalled mRNA complexes) and autophagy. We further show that HF-mediated inhibition in IL-1β production is dependent on general control nonderepressible 2 kinase (GCN2), an amino acid deprivation sensor. This study provides the mechanisms regulating AAR-induced benefits in the context of inflammation and further suggests that the administration of HF might offer an effective therapeutic intervention against inflammatory diseases in mammals.
Collapse
Affiliation(s)
- Srikanth Battu
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Sumbul Afroz
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Jeevan Giddaluru
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Saima Naz
- Centre for Liver Research and Diagnostics, Central Laboratory for Stem Cell Research and Translational Medicine, Deccan College of Medical Sciences, Kanchanbagh, Hyderabad, Telangana, India
| | - Weishan Huang
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | | | - Rafiq Ahmad Khan
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Saleem Yousuf Bhat
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Insaf Ahmed Qureshi
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Bramanandam Manavathi
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Aleem Ahmed Khan
- Centre for Liver Research and Diagnostics, Central Laboratory for Stem Cell Research and Translational Medicine, Deccan College of Medical Sciences, Kanchanbagh, Hyderabad, Telangana, India
| | - Avery August
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Seyed Ehtesham Hasnain
- JH-Institute of Molecular Medicine, Jamia Hamdard University, Hamdard Nagar, New Delhi, India
- Molecular Infection and Functional Biology Laboratory, Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi, India
- Dr Reddy’s Institute of Life Sciences, University of Hyderabad Campus, Hyderabad, Telangana, India
| | - Nooruddin Khan
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
- * E-mail:
| |
Collapse
|
64
|
Regulation of Immune Cell Functions by Metabolic Reprogramming. J Immunol Res 2018; 2018:8605471. [PMID: 29651445 PMCID: PMC5831954 DOI: 10.1155/2018/8605471] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 01/14/2018] [Indexed: 02/07/2023] Open
Abstract
Recent findings show that the metabolic status of immune cells can determine immune responses. Metabolic reprogramming between aerobic glycolysis and oxidative phosphorylation, previously speculated as exclusively observable in cancer cells, exists in various types of immune and stromal cells in many different pathological conditions other than cancer. The microenvironments of cancer, obese adipose, and wound-repairing tissues share common features of inflammatory reactions. In addition, the metabolic changes in macrophages and T cells are now regarded as crucial for the functional plasticity of the immune cells and responsible for the progression and regression of many pathological processes, notably cancer. It is possible that metabolic changes in the microenvironment induced by other cellular components are responsible for the functional plasticity of immune cells. This review explores the molecular mechanisms responsible for metabolic reprogramming in macrophages and T cells and also provides a summary of recent updates with regard to the functional modulation of the immune cells by metabolic changes in the microenvironment, notably the tumor microenvironment.
Collapse
|
65
|
Katsyv I, Wang M, Song WM, Zhou X, Zhao Y, Park S, Zhu J, Zhang B, Irie HY. EPRS is a critical regulator of cell proliferation and estrogen signaling in ER+ breast cancer. Oncotarget 2018; 7:69592-69605. [PMID: 27612429 PMCID: PMC5342500 DOI: 10.18632/oncotarget.11870] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 08/25/2016] [Indexed: 02/06/2023] Open
Abstract
Aminoacyl tRNA synthetases (ARSs) are a class of enzymes with well-conserved housekeeping functions in cellular translation. Recent evidence suggests that ARS genes may participate in a wide array of cellular processes, and may contribute to the pathology of autoimmune disease, cancer, and other diseases. Several studies have suggested a role for the glutamyl prolyl tRNA synthetase (EPRS) in breast cancers, although none has identified any underlying mechanism about how EPRS contributes to carcinogenesis. In this study, we identified EPRS as upregulated in estrogen receptor positive (ER+) human breast tumors in the TCGA and METABRIC cohorts, with copy number gains in nearly 50% of samples in both datasets. EPRS expression is associated with reduced overall survival in patients with ER+ tumors in TCGA and METABRIC datasets. EPRS expression was also associated with reduced distant relapse-free survival in patients treated with adjuvant tamoxifen monotherapy for five years, and EPRS-correlated genes were highly enriched for genes predictive of a poor response to tamoxifen. We demonstrated the necessity of EPRS for proliferation of tamoxifen-resistant ER+ breast cancer, but not ER- breast cancer cells. Transcriptomic profiling showed that EPRS regulated cell cycle and estrogen response genes. Finally, we constructed a causal gene network based on over 2500 ER+ breast tumor samples to build up an EPRS-estrogen signaling pathway. EPRS and its regulated estrogenic gene network may offer a promising alternative approach to target ER+ breast cancers that are refractory to current anti-estrogens.
Collapse
Affiliation(s)
- Igor Katsyv
- Medical Scientist Training Program, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Minghui Wang
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Won Min Song
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Xianxiao Zhou
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yongzhong Zhao
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sun Park
- Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jun Zhu
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Bin Zhang
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hanna Y Irie
- Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| |
Collapse
|
66
|
Loss of eIF4E Phosphorylation Engenders Depression-like Behaviors via Selective mRNA Translation. J Neurosci 2018; 38:2118-2133. [PMID: 29367404 PMCID: PMC5824745 DOI: 10.1523/jneurosci.2673-17.2018] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 12/03/2017] [Accepted: 01/08/2018] [Indexed: 12/23/2022] Open
Abstract
The MAPK/ERK (mitogen-activated protein kinases/extracellular signal-regulated kinase) pathway is a cardinal regulator of synaptic plasticity, learning, and memory in the hippocampus. One of major endpoints of this signaling cascade is the 5′ mRNA cap binding protein eIF4E (eukaryotic Initiation Factor 4E), which is phosphorylated on Ser 209 by MNK (MAPK-interacting protein kinases) and controls mRNA translation. The precise role of phospho-eIF4E in the brain is yet to be determined. Herein, we demonstrate that ablation of eIF4E phosphorylation in male mice (4Eki mice) does not impair long-term spatial or contextual fear memory, or the late phase of LTP. Using unbiased translational profiling in mouse brain, we show that phospho-eIF4E differentially regulates the translation of a subset of mRNAs linked to inflammation, the extracellular matrix, pituitary hormones, and the serotonin pathway. Consequently, 4Eki male mice display exaggerated inflammatory responses and reduced levels of serotonin, concomitant with depression and anxiety-like behaviors. Remarkably, eIF4E phosphorylation is required for the chronic antidepressant action of the selective serotonin reuptake inhibitor fluoxetine. Finally, we propose a novel phospho-eIF4E-dependent translational control mechanism in the brain, via the GAIT complex (gamma IFN activated inhibitor of translation). In summary, our work proposes a novel translational control mechanism involved in the regulation of inflammation and depression, which could be exploited to design novel therapeutics. SIGNIFICANCE STATEMENT We demonstrate that downstream of the MAPK (mitogen-activated protein kinase) pathway, eukaryotic Initiation Factor 4E (eIF4E) Ser209 phosphorylation is not required for classical forms of hippocampal LTP and memory. We reveal a novel role for eIF4E phosphorylation in inflammatory responses and depression-like behaviors. eIF4E phosphorylation is required for the chronic action of antidepressants, such as fluoxetine in mice. These phenotypes are accompanied by selective translation of extracellular matrix, pituitary hormones, and serotonin pathway genes, in eIF4E phospho-mutant mice. We also describe a previously unidentified translational control mechanism in the brain, whereby eIF4E phosphorylation is required for inhibiting the translation of gamma IFN activated inhibitor of translation element-containing mRNAs. These findings can be used to design novel therapeutics for depression.
Collapse
|
67
|
Yamashita A, Takeuchi O. Translational control of mRNAs by 3'-Untranslated region binding proteins. BMB Rep 2018; 50:194-200. [PMID: 28287067 PMCID: PMC5437963 DOI: 10.5483/bmbrep.2017.50.4.040] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Indexed: 12/31/2022] Open
Abstract
Eukaryotic gene expression is precisely regulated at all points between transcription and translation. In this review, we focus on translational control mediated by the 3′-untranslated regions (UTRs) of mRNAs. mRNA 3′-UTRs contain cis-acting elements that function in the regulation of protein translation or mRNA decay. Each RNA binding protein that binds to these cis-acting elements regulates mRNA translation via various mechanisms targeting the mRNA cap structure, the eukaryotic initiation factor 4E (eIF4E)-eIF4G complex, ribosomes, and the poly (A) tail. We also discuss translation-mediated regulation of mRNA fate.
Collapse
Affiliation(s)
- Akio Yamashita
- Department of Molecular Biology, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
| | - Osamu Takeuchi
- Laboratory of Infection and Prevention, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| |
Collapse
|
68
|
Accornero F, Schips TG, Petrosino JM, Gu SQ, Kanisicak O, van Berlo JH, Molkentin JD. BEX1 is an RNA-dependent mediator of cardiomyopathy. Nat Commun 2017; 8:1875. [PMID: 29192139 PMCID: PMC5709413 DOI: 10.1038/s41467-017-02005-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 11/01/2017] [Indexed: 01/29/2023] Open
Abstract
Regulation of mRNA splicing, processing and stability is increasingly recognized as a critical control point in dynamically altering gene expression during stress or disease. Very little is understood of this process in heart failure. Here, we show that BEX1 is a heart failure-induced gene functioning as an mRNA-associated protein that enhances expression of a subset of cardiac disease-promoting genes. Modeling the increase in BEX1 that occurs in disease, cardiac-specific BEX1 transgenic mice show worse cardiac disease with stress stimulation, whereas Bex1 gene-deleted mice are protected from heart failure-promoting insults. Proteomic and interactive screening assays show that BEX1 is part of a large ribonucleoprotein processing complex involved in regulating proinflammatory mRNA expression in the heart. Specifically, induction of BEX1 augments the stability and expression of AU-rich element containing mRNAs typically found within proinflammatory genes. Thus, BEX1 functions as an mRNA-dependent effector that augments pathology-promoting gene expression during heart failure. Little is known about the changes in mRNA splicing, processing and stability that can alter gene expression during heart failure. Here, the authors show that BEX1 is induced during heart failure and is part of a ribonucleoprotein complex enhancing the expression and stability of proinflammatory genes.
Collapse
Affiliation(s)
- Federica Accornero
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA. .,Dorothy M. Davis Heart and Lung Research Institute, Department of Physiology and Cell Biology, Ohio State University, Columbus, OH, 43210, USA.
| | - Tobias G Schips
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Jennifer M Petrosino
- Dorothy M. Davis Heart and Lung Research Institute, Department of Physiology and Cell Biology, Ohio State University, Columbus, OH, 43210, USA
| | - Shan-Qing Gu
- Dorothy M. Davis Heart and Lung Research Institute, Department of Physiology and Cell Biology, Ohio State University, Columbus, OH, 43210, USA
| | - Onur Kanisicak
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Jop H van Berlo
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.,Department of Medicine, Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Jeffery D Molkentin
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA. .,Howard Hughes Medical Institute, Cincinnati, OH, 45229, USA.
| |
Collapse
|
69
|
Bisogno LS, Keene JD. RNA regulons in cancer and inflammation. Curr Opin Genet Dev 2017; 48:97-103. [PMID: 29175729 DOI: 10.1016/j.gde.2017.11.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 11/07/2017] [Accepted: 11/10/2017] [Indexed: 01/05/2023]
Abstract
Gene expression is the fundamental driving force that coordinates normal cellular processes and adapts to dysfunctional conditions such as oncogenic development and progression. While transcription is the basal process of gene expression, RNA transcripts are both the templates that encode proteins as well as perform functions that directly regulate diverse cellular processes. All levels of gene expression require coordination to optimize available resources, but how global gene expression drives cancers or responds to disrupting oncogenic mutations is not understood. Post-transcriptional coordination is controlled by RNA regulons that are governed by RNA-binding proteins (RBPs) and noncoding RNAs (ncRNAs) that bind and regulate multiple overlapping groups of functionally related RNAs. RNA regulons have been demonstrated to affect many biological functions and diseases, and many examples are known to regulate protein production in cancer and immune cells. In this review, we discuss RNA regulons demonstrated to coordinate global post-transcriptional mechanisms in carcinogenesis and inflammation.
Collapse
Affiliation(s)
- Laura Simone Bisogno
- Department of Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC 27710, United States
| | - Jack Donald Keene
- Department of Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC 27710, United States.
| |
Collapse
|
70
|
Arif A, Yao P, Terenzi F, Jia J, Ray PS, Fox PL. The GAIT translational control system. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 9. [PMID: 29152905 PMCID: PMC5815886 DOI: 10.1002/wrna.1441] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 07/12/2017] [Accepted: 07/31/2017] [Indexed: 01/19/2023]
Abstract
The interferon (IFN)‐γ‐activated inhibitor of translation (GAIT) system directs transcript‐selective translational control of functionally related genes. In myeloid cells, IFN‐γ induces formation of a multiprotein GAIT complex that binds structural GAIT elements in the 3′‐untranslated regions (UTRs) of multiple inflammation‐related mRNAs, including ceruloplasmin and VEGF‐A, and represses their translation. The human GAIT complex is a heterotetramer containing glutamyl‐prolyl tRNA synthetase (EPRS), NS1‐associated protein 1 (NSAP1), ribosomal protein L13a (L13a), and glyceraldehyde‐3‐phosphate dehydrogenase (GAPDH). A network of IFN‐γ‐stimulated kinases regulates recruitment and assembly of GAIT complex constituents. Activation of cyclin‐dependent kinase 5 (Cdk5), mammalian target of rapamycin complex 1 (mTORC1), and S6K1 kinases induces EPRS release from its parental multiaminoacyl tRNA synthetase complex to join NSAP1 in a ‘pre‐GAIT’ complex. Subsequently, the DAPK‐ZIPK kinase axis phosphorylates L13a, inducing release from the 60S ribosomal subunit and binding to GAPDH. The subcomplexes join to form the functional GAIT complex. Each constituent has a distinct role in the GAIT system. EPRS binds the GAIT element in target mRNAs, NSAP1 negatively regulates mRNA binding, L13a binds eIF4G to block ribosome recruitment, and GAPDH shields L13a from proteasomal degradation. The GAIT system is susceptible to genetic and condition‐specific regulation. An N‐terminus EPRS truncate is a dominant‐negative inhibitor ensuring a ‘translational trickle’ of target transcripts. Also, hypoxia and oxidatively modified lipoproteins regulate GAIT activity. Mouse models exhibiting absent or genetically modified GAIT complex constituents are beginning to elucidate the physiological role of the GAIT system, particularly in the resolution of chronic inflammation. Finally, GAIT‐like systems in proto‐chordates suggests an evolutionarily conserved role of the pathway in innate immunity. WIREs RNA 2018, 9:e1441. doi: 10.1002/wrna.1441 This article is categorized under:
Translation > Translation Regulation RNA Interactions with Proteins and Other Molecules > RNA–Protein Complexes Regulatory RNAs/RNAi/Riboswitches > Riboswitches
Collapse
Affiliation(s)
- Abul Arif
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Peng Yao
- Aab Cardiovascular Research Institute, University of Rochester School of Medicine & Dentistry, Rochester, NY, USA
| | - Fulvia Terenzi
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Jie Jia
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Partho Sarothi Ray
- Department of Biological Sciences, Indian Institute of Science Education and Research, Kolkata, India
| | - Paul L Fox
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| |
Collapse
|
71
|
Abstract
Cardiovascular diseases (CVDs) are the commonest cause of global mortality and morbidity. Atherosclerosis, the fundamental pathological manifestation of CVDs, is a complex process and is poorly managed both in terms of preventive and therapeutic intervention. Aberrant lipid metabolism and chronic inflammation play critical roles in the development of atherosclerosis. These processes can be targeted for effective management of the disease. Although managing lipid metabolism is in the forefront of current therapeutic approaches, controlling inflammation may also prove to be crucial for an efficient treatment regimen of the disease. Flavonoids, the plant-derived polyphenols, are known for their antiinflammatory properties. This review discusses the possible antiatherogenic role of 3 flavonoids, namely, chrysin, quercetin, and luteolin primarily known for their antiinflammatory properties.
Collapse
|
72
|
Condensin II and GAIT complexes cooperate to restrict LINE-1 retrotransposition in epithelial cells. PLoS Genet 2017; 13:e1007051. [PMID: 29028794 PMCID: PMC5656329 DOI: 10.1371/journal.pgen.1007051] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 10/25/2017] [Accepted: 10/03/2017] [Indexed: 12/15/2022] Open
Abstract
LINE-1 (L1) retrotransposons can mobilize (retrotranspose) within the human genome, and mutagenic de novo L1 insertions can lead to human diseases, including cancers. As a result, cells are actively engaged in preventing L1 retrotransposition. This work reveals that the human Condensin II complex restricts L1 retrotransposition in both non-transformed and transformed cell lines through inhibition of L1 transcription and translation. Condensin II subunits, CAP-D3 and CAP-H2, interact with members of the Gamma-Interferon Activated Inhibitor of Translation (GAIT) complex including the glutamyl-prolyl-tRNA synthetase (EPRS), the ribosomal protein L13a, Glyceraldehyde 3-phosphate dehydrogenase (GAPDH), and NS1 associated protein 1 (NSAP1). GAIT has been shown to inhibit translation of mRNAs encoding inflammatory proteins in myeloid cells by preventing the binding of the translation initiation complex, in response to Interferon gamma (IFN-γ). Excitingly, our data show that Condensin II promotes complexation of GAIT subunits. Furthermore, RNA-Immunoprecipitation experiments in epithelial cells demonstrate that Condensin II and GAIT subunits associate with L1 RNA in a co-dependent manner, independent of IFN-γ. These findings suggest that cooperation between the Condensin II and GAIT complexes may facilitate a novel mechanism of L1 repression, thus contributing to the maintenance of genome stability in somatic cells.
Collapse
|
73
|
Gardiner CM, Finlay DK. What Fuels Natural Killers? Metabolism and NK Cell Responses. Front Immunol 2017; 8:367. [PMID: 28421073 PMCID: PMC5376555 DOI: 10.3389/fimmu.2017.00367] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 03/14/2017] [Indexed: 01/05/2023] Open
Abstract
There is a growing appreciation that cellular metabolism is important in determining the course of lymphocyte responses. Additionally, changes in metabolic processes have been linked to dysfunctional lymphocyte functions in a number of different diseases. While most early studies of metabolic regulation of lymphocyte function focused on T lymphocytes, an understanding of how metabolic pathways impact upon natural killer (NK) cell responses is now starting to emerge. In this review article, we will discuss how cellular metabolism influences lymphocyte function with a particular focus upon NK cells.
Collapse
Affiliation(s)
- Clair M Gardiner
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - David K Finlay
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland.,School of Pharmacy and Pharmaceutical Sciences, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| |
Collapse
|
74
|
Abstract
Alterations in regulatory networks contribute to evolutionary change. Transcriptional networks are reconfigured by changes in the binding specificity of transcription factors and their cognate sites. The evolution of RNA-protein regulatory networks is far less understood. The PUF (Pumilio and FBF) family of RNA regulatory proteins controls the translation, stability, and movements of hundreds of mRNAs in a single species. We probe the evolution of PUF-RNA networks by direct identification of the mRNAs bound to PUF proteins in budding and filamentous fungi and by computational analyses of orthologous RNAs from 62 fungal species. Our findings reveal that PUF proteins gain and lose mRNAs with related and emergent biological functions during evolution. We demonstrate at least two independent rewiring events for PUF3 orthologs, independent but convergent evolution of PUF4/5 binding specificity and the rewiring of the PUF4/5 regulons in different fungal lineages. These findings demonstrate plasticity in RNA regulatory networks and suggest ways in which their rewiring occurs.
Collapse
|
75
|
Schmoch T, Uhle F, Siegler BH, Fleming T, Morgenstern J, Nawroth PP, Weigand MA, Brenner T. The Glyoxalase System and Methylglyoxal-Derived Carbonyl Stress in Sepsis: Glycotoxic Aspects of Sepsis Pathophysiology. Int J Mol Sci 2017; 18:E657. [PMID: 28304355 PMCID: PMC5372669 DOI: 10.3390/ijms18030657] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Revised: 03/08/2017] [Accepted: 03/14/2017] [Indexed: 01/08/2023] Open
Abstract
Sepsis remains one of the leading causes of death in intensive care units. Although sepsis is caused by a viral, fungal or bacterial infection, it is the dysregulated generalized host response that ultimately leads to severe dysfunction of multiple organs and death. The concomitant profound metabolic changes are characterized by hyperglycemia, insulin resistance, and profound transformations of the intracellular energy supply in both peripheral and immune cells. A further hallmark of the early phases of sepsis is a massive formation of reactive oxygen (ROS; e.g., superoxide) as well as nitrogen (RNS; e.g., nitric oxide) species. Reactive carbonyl species (RCS) form a third crucial group of highly reactive metabolites, which until today have been not the focus of interest in sepsis. However, we previously showed in a prospective observational clinical trial that patients suffering from septic shock are characterized by significant methylglyoxal (MG)-derived carbonyl stress, with the glyoxalase system being downregulated in peripheral blood mononuclear cells. In this review, we give a detailed insight into the current state of research regarding the metabolic changes that entail an increased MG-production in septicemia. Thus, we point out the special role of the glyoxalase system in the context of sepsis.
Collapse
Affiliation(s)
- Thomas Schmoch
- Department of Anesthesiology, Heidelberg University Hospital, 69120 Heidelberg, Germany.
| | - Florian Uhle
- Department of Anesthesiology, Heidelberg University Hospital, 69120 Heidelberg, Germany.
| | - Benedikt H Siegler
- Department of Anesthesiology, Heidelberg University Hospital, 69120 Heidelberg, Germany.
| | - Thomas Fleming
- Department of Medicine I and Clinical Chemistry, Heidelberg University Hospital, 69120 Heidelberg, Germany.
| | - Jakob Morgenstern
- Department of Medicine I and Clinical Chemistry, Heidelberg University Hospital, 69120 Heidelberg, Germany.
| | - Peter P Nawroth
- Department of Medicine I and Clinical Chemistry, Heidelberg University Hospital, 69120 Heidelberg, Germany.
| | - Markus A Weigand
- Department of Anesthesiology, Heidelberg University Hospital, 69120 Heidelberg, Germany.
| | - Thorsten Brenner
- Department of Anesthesiology, Heidelberg University Hospital, 69120 Heidelberg, Germany.
| |
Collapse
|
76
|
Intersections of post-transcriptional gene regulatory mechanisms with intermediary metabolism. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:349-362. [PMID: 28088440 DOI: 10.1016/j.bbagrm.2017.01.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 01/09/2017] [Accepted: 01/09/2017] [Indexed: 12/16/2022]
Abstract
Intermediary metabolism studies have typically concentrated on four major regulatory mechanisms-substrate availability, allosteric enzyme regulation, post-translational enzyme modification, and regulated enzyme synthesis. Although transcriptional control has been a big focus, it is becoming increasingly evident that many post-transcriptional events are deeply embedded within the core regulatory circuits of enzyme synthesis/breakdown that maintain metabolic homeostasis. The prominent post-transcriptional mechanisms affecting intermediary metabolism include alternative pre-mRNA processing, mRNA stability and translation control, and the more recently discovered regulation by noncoding RNAs. In this review, we discuss the latest advances in our understanding of these diverse mechanisms at the cell-, tissue- and organismal-level. We also highlight the dynamics, complexity and non-linear nature of their regulatory roles in metabolic decision making, and deliberate some of the outstanding questions and challenges in this rapidly expanding field.
Collapse
|
77
|
Radhakrishnan VM, Gilpatrick MM, Parsa NA, Kiela PR, Ghishan FK. Expression of Cav1.3 calcium channel in the human and mouse colon: posttranscriptional inhibition by IFNγ. Am J Physiol Gastrointest Liver Physiol 2017; 312:G77-G84. [PMID: 27932504 PMCID: PMC5283901 DOI: 10.1152/ajpgi.00394.2016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 12/05/2016] [Accepted: 12/06/2016] [Indexed: 01/31/2023]
Abstract
It has been hypothesized that apically expressed L-type Ca2+ channel Cav1.3 (encoded by CACNA1D gene) contributes toward an alternative TRPV6-independent route of intestinal epithelial Ca2+ absorption, especially during digestion when high luminal concentration of Ca2+ and other nutrients limit TRPV6 contribution. We and others have implicated altered expression and activity of key mediators of intestinal and renal Ca2+ (re)absorption as contributors to negative systemic Ca2+ balance and bone loss in intestinal inflammation. Here, we investigated the effects of experimental colitis and related inflammatory mediators on colonic Cav1.3 expression. We confirmed Cav1.3 expression within the segments of the mouse and human gastrointestinal tract. Consistent with available microarray data (GEO database) from inflammatory bowel disease (IBD) patients, mouse colonic expression of Cav1.3 was significantly reduced in trinitrobenzene sulfonic acid (TNBS) colitis. In vitro, IFNγ most potently reduced Cav1.3 expression. We reproduced these findings in vivo with wild-type and Stat1-/- mice injected with IFNγ. The observed effect in Stat1-/- suggested a noncanonical transcriptional repression or a posttranscriptional mechanism. In support of the latter, we observed no effect on the cloned Cav1.3 gene promoter activity and accelerated Cav1.3 mRNA decay rate in IFNγ-treated HCT116 cells. While the relative contribution of Cav1.3 to intestinal Ca2+ absorption and its value as a therapeutic target remain to be established, we postulate that Cav1.3 downregulation in IBD may contribute to the negative systemic Ca2+ balance, to increased bone resorption, and to reduced bone mineral density in IBD patients.
Collapse
Affiliation(s)
| | | | - Nour Alhoda Parsa
- 1Department of Pediatrics, The University of Arizona, Tucson, Arizona; and
| | - Pawel R. Kiela
- 1Department of Pediatrics, The University of Arizona, Tucson, Arizona; and ,2Department of Immunobiology, The University of Arizona, Tucson, Arizona
| | - Fayez K. Ghishan
- 1Department of Pediatrics, The University of Arizona, Tucson, Arizona; and
| |
Collapse
|
78
|
Hellwig B, Madjar K, Edlund K, Marchan R, Cadenas C, Heimes AS, Almstedt K, Lebrecht A, Sicking I, Battista MJ, Micke P, Schmidt M, Hengstler JG, Rahnenführer J. Epsin Family Member 3 and Ribosome-Related Genes Are Associated with Late Metastasis in Estrogen Receptor-Positive Breast Cancer and Long-Term Survival in Non-Small Cell Lung Cancer Using a Genome-Wide Identification and Validation Strategy. PLoS One 2016; 11:e0167585. [PMID: 27926932 PMCID: PMC5142791 DOI: 10.1371/journal.pone.0167585] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 11/16/2016] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND In breast cancer, gene signatures that predict the risk of metastasis after surgical tumor resection are mainly indicative of early events. The purpose of this study was to identify genes linked to metastatic recurrence more than three years after surgery. METHODS Affymetrix HG U133A and Plus 2.0 array datasets with information on metastasis-free, disease-free or overall survival were accessed via public repositories. Time restricted Cox regression models were used to identify genes associated with metastasis during or after the first three years post-surgery (early- and late-type genes). A sequential validation study design, with two non-adjuvantly treated discovery cohorts (n = 409) and one validation cohort (n = 169) was applied and identified genes were further evaluated in tamoxifen-treated breast cancer patients (n = 923), as well as in patients with non-small cell lung (n = 1779), colon (n = 893) and ovarian (n = 922) cancer. RESULTS Ten late- and 243 early-type genes were identified in adjuvantly untreated breast cancer. Adjustment to clinicopathological factors and an established proliferation-related signature markedly reduced the number of early-type genes to 16, whereas nine late-type genes still remained significant. These nine genes were associated with metastasis-free survival (MFS) also in a non-time restricted model, but not in the early period alone, stressing that their prognostic impact was primarily based on MFS more than three years after surgery. Four of the ten late-type genes, the ribosome-related factors EIF4B, RPL5, RPL3, and the tumor angiogenesis modifier EPN3 were significantly associated with MFS in the late period also in a meta-analysis of tamoxifen-treated breast cancer cohorts. In contrast, only one late-type gene (EPN3) showed consistent survival associations in more than one cohort in the other cancer types, being associated with worse outcome in two non-small cell lung cancer cohorts. No late-type gene was validated in ovarian and colon cancer. CONCLUSIONS Ribosome-related genes were associated with decreased risk of late metastasis in both adjuvantly untreated and tamoxifen-treated breast cancer patients. In contrast, high expression of epsin (EPN3) was associated with increased risk of late metastasis. This is of clinical relevance considering the well-understood role of epsins in tumor angiogenesis and the ongoing development of epsin antagonizing therapies.
Collapse
Affiliation(s)
- Birte Hellwig
- Department of Statistics, TU Dortmund University, Dortmund, Germany
| | - Katrin Madjar
- Department of Statistics, TU Dortmund University, Dortmund, Germany
| | - Karolina Edlund
- Leibniz Research Centre for Working Environment and Human Factors (IfADo) at TU Dortmund University, Dortmund, Germany
| | - Rosemarie Marchan
- Leibniz Research Centre for Working Environment and Human Factors (IfADo) at TU Dortmund University, Dortmund, Germany
| | - Cristina Cadenas
- Leibniz Research Centre for Working Environment and Human Factors (IfADo) at TU Dortmund University, Dortmund, Germany
| | - Anne-Sophie Heimes
- Department of Obstetrics and Gynaecology, University Hospital, Mainz, Germany
| | - Katrin Almstedt
- Department of Obstetrics and Gynaecology, University Hospital, Mainz, Germany
| | - Antje Lebrecht
- Department of Obstetrics and Gynaecology, University Hospital, Mainz, Germany
| | - Isabel Sicking
- Department of Obstetrics and Gynaecology, University Hospital, Mainz, Germany
| | - Marco J. Battista
- Department of Obstetrics and Gynaecology, University Hospital, Mainz, Germany
| | - Patrick Micke
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Marcus Schmidt
- Department of Obstetrics and Gynaecology, University Hospital, Mainz, Germany
| | - Jan G. Hengstler
- Leibniz Research Centre for Working Environment and Human Factors (IfADo) at TU Dortmund University, Dortmund, Germany
| | - Jörg Rahnenführer
- Department of Statistics, TU Dortmund University, Dortmund, Germany
- * E-mail:
| |
Collapse
|
79
|
Fahl SP, Wang M, Zhang Y, Duc ACE, Wiest DL. Regulatory Roles of Rpl22 in Hematopoiesis: An Old Dog with New Tricks. Crit Rev Immunol 2016; 35:379-400. [PMID: 26853850 DOI: 10.1615/critrevimmunol.v35.i5.30] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Ribosomal proteins have long been known to serve critical roles in facilitating the biogenesis of the ribosome and its ability to synthesize proteins. However, evidence is emerging that suggests ribosomal proteins are also capable of performing tissue-restricted, regulatory functions that impact normal development and pathological conditions, including cancer. The challenge in studying such regulatory functions is that elimination of many ribosomal proteins also disrupts ribosome biogenesis and/or function. Thus, it is difficult to determine whether developmental abnormalities resulting from ablation of a ribosomal protein result from loss of core ribosome functions or from loss of the regulatory function of the ribosomal protein. Rpl22, a ribosomal protein component of the large 60S subunit, provides insight into this conundrum; Rpl22 is dispensable for both ribosome biogenesis and protein synthesis yet its ablation causes tissue-restricted disruptions in development. Here we review evidence supporting the regulatory functions of Rpl22 and other ribosomal proteins.
Collapse
Affiliation(s)
- Shawn P Fahl
- Blood Cell Development and Function Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111
| | - Minshi Wang
- Blood Cell Development and Function Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111
| | - Yong Zhang
- Blood Cell Development and Function Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111
| | - Anne-Cecile E Duc
- Blood Cell Development and Function Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111
| | - David L Wiest
- Blood Cell Development and Function Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111
| |
Collapse
|
80
|
Sugi Y, Takahashi K, Kurihara K, Nakata K, Narabayashi H, Hamamoto Y, Suzuki M, Tsuda M, Hanazawa S, Hosono A, Kaminogawa S. Post-Transcriptional Regulation of Toll-Interacting Protein in the Intestinal Epithelium. PLoS One 2016; 11:e0164858. [PMID: 27741296 PMCID: PMC5065231 DOI: 10.1371/journal.pone.0164858] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 10/03/2016] [Indexed: 02/06/2023] Open
Abstract
Immune responses against gut microbiota should be minimized to avoid unnecessary inflammation at mucosal surface. In this study, we analyzed the expression patterns of Toll-interacting protein (Tollip), an inhibitor of TLRs and IL-1 family cytokine-related intracellular signaling, in intestinal epithelial cells (IECs). Comparable mRNA expression was observed in murine small and large IECs (S-IECs and L-IECs). However, Tollip protein was only detected in L-IECs, but not in S-IECs. Similar results were obtained in germ-free mice, indicating that L-IEC-specific TOLLIP expression does not depend on bacterial colonization. Next, to understand the mechanisms underlying the post-transcriptional repression of Tollip, 3´-UTR-mediated translational regulation was evaluated. The region +1876/+2398 was responsible for the repression of Tollip expression. This region included the target sequence of miR-31. The inhibition of miR-31 restored the 3´-UTR-meditaed translational repression. In addition, miR-31 expression was significantly higher in S-IECs than in L-IECs, suggesting that miR-31 represses the translation of Tollip mRNA in S-IECs. Collectively, we conclude that the translation of Tollip is inhibited in S-IECs, at least in part, by miR-31 to yield L-IEC-specific high-level expression of the Tollip protein, which may contribute to the maintenance of intestinal homeostasis.
Collapse
Affiliation(s)
- Yutaka Sugi
- Department of Food Biochemistry and Biotechnology, College of Bioresource Sciences, Nihon University, Kanagawa, Japan
| | - Kyoko Takahashi
- Department of Food Biochemistry and Biotechnology, College of Bioresource Sciences, Nihon University, Kanagawa, Japan
- Department of Applied Biological Science, College of Bioresource Sciences, Nihon University, Kanagawa, Japan
- * E-mail:
| | - Kenta Kurihara
- Department of Food Biochemistry and Biotechnology, College of Bioresource Sciences, Nihon University, Kanagawa, Japan
| | - Kazuaki Nakata
- Department of Food Biochemistry and Biotechnology, College of Bioresource Sciences, Nihon University, Kanagawa, Japan
- Department of Applied Biological Science, College of Bioresource Sciences, Nihon University, Kanagawa, Japan
| | - Hikari Narabayashi
- Department of Applied Biological Science, College of Bioresource Sciences, Nihon University, Kanagawa, Japan
| | - Yuji Hamamoto
- Department of Food Biochemistry and Biotechnology, College of Bioresource Sciences, Nihon University, Kanagawa, Japan
| | - Makoto Suzuki
- Department of Food Biochemistry and Biotechnology, College of Bioresource Sciences, Nihon University, Kanagawa, Japan
| | - Masato Tsuda
- Department of Food Biochemistry and Biotechnology, College of Bioresource Sciences, Nihon University, Kanagawa, Japan
| | - Shigemasa Hanazawa
- Department of Applied Biological Science, College of Bioresource Sciences, Nihon University, Kanagawa, Japan
| | - Akira Hosono
- Department of Food Biochemistry and Biotechnology, College of Bioresource Sciences, Nihon University, Kanagawa, Japan
| | - Shuichi Kaminogawa
- Department of Food Biochemistry and Biotechnology, College of Bioresource Sciences, Nihon University, Kanagawa, Japan
| |
Collapse
|
81
|
Arif A, Jia J, Halawani D, Fox PL. Experimental approaches for investigation of aminoacyl tRNA synthetase phosphorylation. Methods 2016; 113:72-82. [PMID: 27729295 DOI: 10.1016/j.ymeth.2016.10.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 10/04/2016] [Accepted: 10/06/2016] [Indexed: 02/04/2023] Open
Abstract
Phosphorylation of many aminoacyl tRNA synthetases (AARSs) has been recognized for decades, but the contribution of post-translational modification to their primary role in tRNA charging and decryption of genetic code remains unclear. In contrast, phosphorylation is essential for performance of diverse noncanonical functions of AARSs unrelated to protein synthesis. Phosphorylation of glutamyl-prolyl tRNA synthetase (EPRS) has been investigated extensively in our laboratory for more than a decade, and has served as an archetype for studies of other AARSs. EPRS is a constituent of the IFN-γ-activated inhibitor of translation (GAIT) complex that directs transcript-selective translational control in myeloid cells. Stimulus-dependent phosphorylation of EPRS is essential for its release from the parental multi-aminoacyl tRNA synthetase complex (MSC), for binding to other GAIT complex proteins, and for regulating the binding to target mRNAs. Importantly, phosphorylation is the common driving force for the context- and stimulus-dependent release, and non-canonical activity, of other AARSs residing in the MSC, for example, lysyl tRNA synthetase (KARS). Here, we describe the concepts and experimental methodologies we have used to investigate the influence of phosphorylation on the structure and function of EPRS. We suggest that application of these approaches will help to identify new functional phosphorylation event(s) in other AARSs and elucidate their possible roles in noncanonical activities.
Collapse
Affiliation(s)
- Abul Arif
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Jie Jia
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Dalia Halawani
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Paul L Fox
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
| |
Collapse
|
82
|
Walls J, Sinclair L, Finlay D. Nutrient sensing, signal transduction and immune responses. Semin Immunol 2016; 28:396-407. [DOI: 10.1016/j.smim.2016.09.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 09/13/2016] [Indexed: 12/11/2022]
|
83
|
Abstract
In multicellular organisms, the epithelia is a contact surface with the surrounding environment and is exposed to a variety of adverse biotic (pathogenic) and abiotic (chemical) factors. Multi-layered pathways that operate on different time scales have evolved to preserve cellular integrity and elicit stress-specific response. Several stress-response programs are activated until a complete elimination of the stress is achieved. The innate immune response, which is triggered by pathogenic invasion, is rather harmful when active over a prolonged time, thus the response follows characteristic oscillatory trajectories. Here, we review different translation programs that function to precisely fine-tune the time at which various components of the innate immune response dwell between active and inactive. We discuss how different pro-inflammatory pathways are co-ordinated to temporally offset single reactions and to achieve an optimal balance between fighting pathogens and being less harmful for healthy cells.
Collapse
|
84
|
Infection-specific phosphorylation of glutamyl-prolyl tRNA synthetase induces antiviral immunity. Nat Immunol 2016; 17:1252-1262. [PMID: 27595231 DOI: 10.1038/ni.3542] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 07/28/2016] [Indexed: 12/17/2022]
Abstract
The mammalian cytoplasmic multi-tRNA synthetase complex (MSC) is a depot system that regulates non-translational cellular functions. Here we found that the MSC component glutamyl-prolyl-tRNA synthetase (EPRS) switched its function following viral infection and exhibited potent antiviral activity. Infection-specific phosphorylation of EPRS at Ser990 induced its dissociation from the MSC, after which it was guided to the antiviral signaling pathway, where it interacted with PCBP2, a negative regulator of mitochondrial antiviral signaling protein (MAVS) that is critical for antiviral immunity. This interaction blocked PCBP2-mediated ubiquitination of MAVS and ultimately suppressed viral replication. EPRS-haploid (Eprs+/-) mice showed enhanced viremia and inflammation and delayed viral clearance. This stimulus-inducible activation of MAVS by EPRS suggests an unexpected role for the MSC as a regulator of immune responses to viral infection.
Collapse
|
85
|
Abstract
In recent years a substantial number of findings have been made in the area of immunometabolism, by which we mean the changes in intracellular metabolic pathways in immune cells that alter their function. Here, we provide a brief refresher course on six of the major metabolic pathways involved (specifically, glycolysis, the tricarboxylic acid (TCA) cycle, the pentose phosphate pathway, fatty acid oxidation, fatty acid synthesis and amino acid metabolism), giving specific examples of how precise changes in the metabolites of these pathways shape the immune cell response. What is emerging is a complex interplay between metabolic reprogramming and immunity, which is providing an extra dimension to our understanding of the immune system in health and disease.
Collapse
Affiliation(s)
- Luke A J O'Neill
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Rigel J Kishton
- Vanderbilt Centre for Immunobiology, Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA
| | - Jeff Rathmell
- Vanderbilt Centre for Immunobiology, Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA
| |
Collapse
|
86
|
Vizzini A, Bonura A, Longo V, Sanfratello MA, Parrinello D, Cammarata M, Colombo P. LPS injection reprograms the expression and the 3' UTR of a CAP gene by alternative polyadenylation and the formation of a GAIT element in Ciona intestinalis. Mol Immunol 2016; 77:174-83. [PMID: 27514009 DOI: 10.1016/j.molimm.2016.08.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 08/03/2016] [Accepted: 08/04/2016] [Indexed: 12/27/2022]
Abstract
The diversification of cellular functions is one of the major characteristics of multicellular organisms which allow cells to modulate their gene expression, leading to the formation of transcripts and proteins with different functions and concentrations in response to different stimuli. CAP genes represent a widespread family of proteins belonging to the cysteine-rich secretory protein, antigen 5 and pathogenesis-related 1 superfamily which, it has been proposed, play key roles in the infection process and the modulation of immune responses in host animals. The ascidian Ciona intestinalis represents a group of proto-chordates with an exclusively innate immune system that has been widely studied in the field of comparative and developmental immunology. Using this biological system, we describe the identification of a novel APA mechanism by which an intronic polyadenylation signal is activated by LPS injection, leading to the formation of a shorter CAP mRNA capable of expressing the first CAP exon plus 19 amino acid residues whose sequence is contained within the first intron of the annotated gene. Furthermore, such an APA event causes the expression of a translational controlling cis-acting GAIT element which is not present in the previously isolated CAP isoform and identified in the 3'-UTR of other immune-related genes, suggesting an intriguing scenario in which both transcriptional and post-transcriptional control mechanisms are involved in the activation of the CAP gene during inflammatory response in C. intestinalis.
Collapse
Affiliation(s)
- Aiti Vizzini
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Via Archirafi 18, Palermo, Italy
| | - Angela Bonura
- Istituto di Biomedicina ed Immunologia Molecolare "Alberto Monroy" del Consiglio Nazionale delle Ricerche, Via Ugo La Malfa 153, Palermo, Italy
| | - Valeria Longo
- Istituto di Biomedicina ed Immunologia Molecolare "Alberto Monroy" del Consiglio Nazionale delle Ricerche, Via Ugo La Malfa 153, Palermo, Italy
| | | | - Daniela Parrinello
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Via Archirafi 18, Palermo, Italy
| | - Matteo Cammarata
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Via Archirafi 18, Palermo, Italy
| | - Paolo Colombo
- Istituto di Biomedicina ed Immunologia Molecolare "Alberto Monroy" del Consiglio Nazionale delle Ricerche, Via Ugo La Malfa 153, Palermo, Italy.
| |
Collapse
|
87
|
Storkebaum E. Peripheral neuropathy via mutant tRNA synthetases: Inhibition of protein translation provides a possible explanation. Bioessays 2016; 38:818-29. [PMID: 27352040 PMCID: PMC5094542 DOI: 10.1002/bies.201600052] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Recent evidence indicates that inhibition of protein translation may be a common pathogenic mechanism for peripheral neuropathy associated with mutant tRNA synthetases (aaRSs). aaRSs are enzymes that ligate amino acids to their cognate tRNA, thus catalyzing the first step of translation. Dominant mutations in five distinct aaRSs cause Charcot‐Marie‐Tooth (CMT) peripheral neuropathy, characterized by length‐dependent degeneration of peripheral motor and sensory axons. Surprisingly, loss of aminoacylation activity is not required for mutant aaRSs to cause CMT. Rather, at least for some mutations, a toxic‐gain‐of‐function mechanism underlies CMT‐aaRS. Interestingly, several mutations in two distinct aaRSs were recently shown to inhibit global protein translation in Drosophila models of CMT‐aaRS, by a mechanism independent of aminoacylation, suggesting inhibition of translation as a common pathogenic mechanism. Future research aimed at elucidating the molecular mechanisms underlying the translation defect induced by CMT‐mutant aaRSs should provide novel insight into the molecular pathogenesis of these incurable diseases.
Collapse
Affiliation(s)
- Erik Storkebaum
- Molecular Neurogenetics Laboratory, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Faculty of Medicine, University of Münster, Münster, Germany
| |
Collapse
|
88
|
Wong MKS, Pipil S, Kato A, Takei Y. Duplicated CFTR isoforms in eels diverged in regulatory structures and osmoregulatory functions. Comp Biochem Physiol A Mol Integr Physiol 2016; 199:130-141. [PMID: 27322796 DOI: 10.1016/j.cbpa.2016.06.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 06/15/2016] [Accepted: 06/15/2016] [Indexed: 12/20/2022]
Abstract
Two cystic fibrosis transmembrane conductance regulator (CFTR) isoforms, CFTRa and CFTRb, were cloned in Japanese eel and their structures and functions were studied in different osmoregulatory tissues in freshwater (FW) and seawater (SW) eels. Molecular phylogenetic results suggested that the CFTR duplication in eels occurred independently of the duplication event in salmonid. CFTRa was expressed in the intestine and kidney and downregulated in both tissues in SW eels, while CFTRb was specifically expressed in the gill and greatly upregulated in SW eels. Structurally, the CFTR isoforms are similar in most functional domains except the regulatory R domain, where the R domain of CFTRa is similar to that of human CFTR but the R domain of CFTRb is unique in having high intrinsic negative charges and fewer phosphorylation sites, suggesting divergence of isoforms in terms of gating properties and hormonal regulation. Immunohistochemical results showed that CFTR was localized on the apical regions of SW ionocytes, suggesting a Cl(-) secretory role as in other teleosts. In intestine and kidney, however, immunoreactive CFTR was mostly found in the cytosolic vesicles in FW eels, indicating that Cl(-) channel activity could be low at basal conditions, but could be rapidly increased by membrane insertion of the stored channels. Guanylin (GN), a known hormone that increases CFTR activity in mammalian intestine, failed to redistribute CFTR and to affect its expression in eel intestine. The results suggested that GN-independent CFTR regulation is present in eel intestine and kidney.
Collapse
Affiliation(s)
| | - Supriya Pipil
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan
| | - Akira Kato
- Department of Biological Sciences, Tokyo Institute of Technology, Yokohama, Japan
| | - Yoshio Takei
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan
| |
Collapse
|
89
|
The expanding universe of ribonucleoproteins: of novel RNA-binding proteins and unconventional interactions. Pflugers Arch 2016; 468:1029-40. [PMID: 27165283 PMCID: PMC4893068 DOI: 10.1007/s00424-016-1819-4] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 03/29/2016] [Accepted: 04/01/2016] [Indexed: 02/06/2023]
Abstract
Post-transcriptional regulation of gene expression plays a critical role in almost all cellular processes. Regulation occurs mostly by RNA-binding proteins (RBPs) that recognise RNA elements and form ribonucleoproteins (RNPs) to control RNA metabolism from synthesis to decay. Recently, the repertoire of RBPs was significantly expanded owing to methodological advances such as RNA interactome capture. The newly identified RNA binders are involved in diverse biological processes and belong to a broad spectrum of protein families, many of them exhibiting enzymatic activities. This suggests the existence of an extensive crosstalk between RNA biology and other, in principle unrelated, cell functions such as intermediary metabolism. Unexpectedly, hundreds of new RBPs do not contain identifiable RNA-binding domains (RBDs), raising the question of how they interact with RNA. Despite the many functions that have been attributed to RNA, our understanding of RNPs is still mostly governed by a rather protein-centric view, leading to the idea that proteins have evolved to bind to and regulate RNA and not vice versa. However, RNPs formed by an RNA-driven interaction mechanism (RNA-determined RNPs) are abundant and offer an alternative explanation for the surprising lack of classical RBDs in many RNA-interacting proteins. Moreover, RNAs can act as scaffolds to orchestrate and organise protein networks and directly control their activity, suggesting that nucleic acids might play an important regulatory role in many cellular processes, including metabolism.
Collapse
|
90
|
Ganguly K, Giddaluru J, August A, Khan N. Post-transcriptional Regulation of Immunological Responses through Riboclustering. Front Immunol 2016; 7:161. [PMID: 27199986 PMCID: PMC4850162 DOI: 10.3389/fimmu.2016.00161] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 04/15/2016] [Indexed: 12/22/2022] Open
Abstract
Immunological programing of immune cells varies in response to changing environmental signals. This process is facilitated by modifiers that regulate the translational fate of mRNAs encoding various immune mediators, including cytokines and chemokines, which in turn determine the rapid activation, tolerance, and plasticity of the immune system. RNA-binding proteins (RBPs) recruited by the specific sequence elements in mRNA transcripts are one such modifiers. These RBPs form RBP-RNA complexes known as "riboclusters." These riboclusters serve as RNA sorting machinery, where depending upon the composition of the ribocluster, translation, degradation, or storage of mRNA is controlled. Recent findings suggest that this regulation of mRNA homeostasis is critical for controlling the immune response. Here, we present the current knowledge of the ribocluster-mediated post-transcriptional regulation of immune mediators and highlight recent findings regarding their implications for the pathogenesis of acute or chronic inflammatory diseases.
Collapse
Affiliation(s)
- Koelina Ganguly
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad , Hyderabad , India
| | - Jeevan Giddaluru
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad , Hyderabad , India
| | - Avery August
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University , New York, NY , USA
| | - Nooruddin Khan
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad , Hyderabad , India
| |
Collapse
|
91
|
Abstract
The past several years have seen dramatic leaps in our understanding of how gene expression is rewired at the translation level during tumorigenesis to support the transformed phenotype. This work has been driven by an explosion in technological advances and is revealing previously unimagined regulatory mechanisms that dictate functional expression of the cancer genome. In this Review we discuss emerging trends and exciting new discoveries that reveal how this translational circuitry contributes to specific aspects of tumorigenesis and cancer cell function, with a particular focus on recent insights into the role of translational control in the adaptive response to oncogenic stress conditions.
Collapse
Affiliation(s)
- Morgan L Truitt
- Department of Urology, University of California, San Francisco
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California 94158, USA
| | - Davide Ruggero
- Department of Urology, University of California, San Francisco
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California 94158, USA
| |
Collapse
|
92
|
Krzysiak TC, Chen BB, Lear T, Mallampalli RK, Gronenborn AM. Crystal structure and interaction studies of the human FBxo3 ApaG domain. FEBS J 2016; 283:2091-101. [PMID: 27010866 DOI: 10.1111/febs.13721] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 03/15/2016] [Accepted: 03/22/2016] [Indexed: 12/17/2022]
Abstract
UNLABELLED Transcriptional activation of proinflammatory cytokines, mediated by tumor necrosis factor receptor-associated factors (TRAFs), is in part triggered by the degradation of the F-box protein, FBxl2, via an E3 ligase that contains another F-box protein, FBxo3. The ApaG domain of FBxo3 is required for the interaction with and degradation of FBxl2 [Mallampalli RK et al., (2013) J Immunol 191, 5247-5255]. Here, we report the X-ray structure of the human FBxo3 ApaG domain, residues 278-407, at 2.0 Å resolution. Like bacterial ApaG proteins, this domain is characterized by a classic Immunoglobin/Fibronectin III-type fold, comprising a seven-stranded β-sheet core, surrounded by four extended loops. Although cation binding had been proposed for bacterial ApaG proteins, no interactions with Mg(2+) or Co(2+) were detected for the human ApaG domain. In addition, dinucleotide polyphosphates, which have been reported to be second messengers in the inflammation response and targets of the bacterial apaG-containing operon, are not bound by the human ApaG domain. In the context of the full-length protein, loop 1, comprising residues 294-303, is critical for the interaction with FBxl2. However, titration of the individual ApaG domain with a 15-mer FBxl2 peptide that was phosphorylated on the crucial T404, as well as the inability of the ApaG domain to interact with full-length FBxl2, assessed by coimmunoprecipitation, indicate that the ApaG domain alone is necessary, but not sufficient for binding and degradation of FBxl2. DATABASE PDB ID (5HDW).
Collapse
Affiliation(s)
- Troy C Krzysiak
- Department of Structural Biology, Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, PA, USA
| | - Bill B Chen
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, PA, USA.,Acute Lung Injury Center of Excellence, University of Pittsburgh School of Medicine, PA, USA
| | - Travis Lear
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, PA, USA.,Acute Lung Injury Center of Excellence, University of Pittsburgh School of Medicine, PA, USA.,Department of Environmental and Occupational Health, School of Public Health, University of Pittsburgh, PA, USA
| | - Rama K Mallampalli
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, PA, USA.,Acute Lung Injury Center of Excellence, University of Pittsburgh School of Medicine, PA, USA.,Department of Cell Biology and Physiology, University of Pittsburgh School of Medicine, PA, USA.,Medical Specialty Service Line, Veterans Affairs Pittsburgh Healthcare System, PA, USA
| | - Angela M Gronenborn
- Department of Structural Biology, Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, PA, USA
| |
Collapse
|
93
|
Fullerton JN, Gilroy DW. Resolution of inflammation: a new therapeutic frontier. Nat Rev Drug Discov 2016; 15:551-67. [PMID: 27020098 DOI: 10.1038/nrd.2016.39] [Citation(s) in RCA: 585] [Impact Index Per Article: 73.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Dysregulated inflammation is a central pathological process in diverse disease states. Traditionally, therapeutic approaches have sought to modulate the pro- or anti-inflammatory limbs of inflammation, with mixed success. However, insight into the pathways by which inflammation is resolved has highlighted novel opportunities to pharmacologically manipulate these processes - a strategy that might represent a complementary (and perhaps even superior) therapeutic approach. This Review discusses the state of the art in the biology of resolution of inflammation, highlighting the opportunities and challenges for translational research in this field.
Collapse
Affiliation(s)
- James N Fullerton
- Centre for Clinical Pharmacology and Therapeutics, Division of Medicine, 5 University Street, University College London, London WC1E 6JJ, UK
| | - Derek W Gilroy
- Centre for Clinical Pharmacology and Therapeutics, Division of Medicine, 5 University Street, University College London, London WC1E 6JJ, UK
| |
Collapse
|
94
|
Young SK, Baird TD, Wek RC. Translation Regulation of the Glutamyl-prolyl-tRNA Synthetase Gene EPRS through Bypass of Upstream Open Reading Frames with Noncanonical Initiation Codons. J Biol Chem 2016; 291:10824-35. [PMID: 27002157 DOI: 10.1074/jbc.m116.722256] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Indexed: 11/06/2022] Open
Abstract
In the integrated stress response, phosphorylation of eIF2α (eIF2α-P) reduces protein synthesis while concomitantly promoting preferential translation of specific transcripts associated with stress adaptation. Translation of the glutamyl-prolyl-tRNA synthetase gene EPRS is enhanced in response to eIF2α-P. To identify the underlying mechanism of translation control, we employed biochemical approaches to determine the regulatory features by which upstream ORFs (uORFs) direct downstream translation control and expression of the EPRS coding region. Our findings reveal that translation of two inhibitory uORFs encoded by noncanonical CUG and UUG initiation codons in the EPRS mRNA 5'-leader serve to dampen levels of translation initiation at the EPRS coding region. By a mechanism suggested to involve increased translation initiation stringency during stress-induced eIF2α-P, we observed facilitated ribosome bypass of these uORFs, allowing for increased translation of the EPRS coding region. Importantly, EPRS protein expression is enhanced through this preferential translation mechanism in response to multiple known activators of eIF2α-P and likely serves to facilitate stress adaptation in response to a variety of cellular stresses. The rules presented here for the regulated ribosome bypass of noncanonical initiation codons in the EPRS 5'-leader add complexity into the nature of uORF-mediated translation control mechanisms during eIF2α-P and additionally illustrate the roles that previously unexamined uORFs with noncanonical initiation codons can play in modulating gene expression.
Collapse
Affiliation(s)
- Sara K Young
- From the Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202-5126
| | - Thomas D Baird
- From the Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202-5126
| | - Ronald C Wek
- From the Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202-5126
| |
Collapse
|
95
|
Montes M, Lund AH. Emerging roles of lncRNAs in senescence. FEBS J 2016; 283:2414-26. [PMID: 26866709 DOI: 10.1111/febs.13679] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Revised: 01/16/2016] [Accepted: 02/09/2016] [Indexed: 12/13/2022]
Abstract
Cellular senescence is a complex stress response that leads to an irreversible state of cell growth arrest. Senescence may be induced by various stimuli such as telomere shortening, DNA damage or oncogenic insult, among others. Senescent cells are metabolically highly active, producing a wealth of cytokines and chemokines that, depending on the context, may have a beneficial or deleterious effect on the organism. Senescence is considered a tightly regulated stress response that is largely governed by the p53/p21 and p16/Rb pathways. Many molecules have been identified as regulators of these two networks, such as transcription factors, chromatin modifiers and non-coding RNAs. The expression level of several long non-coding RNAs is affected during different types of senescence; however, which of these are important for the biological function remains poorly understood. Here we review our current knowledge of the mechanistic roles of lncRNAs affecting the main senescence pathways, and discuss the importance of identifying new regulators.
Collapse
Affiliation(s)
- Marta Montes
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Anders H Lund
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
96
|
Papavasiliou FN, Chung YC, Gagnidze K, Hajdarovic KH, Cole DC, Bulloch K. Epigenetic Modulators of Monocytic Function: Implication for Steady State and Disease in the CNS. Front Immunol 2016; 6:661. [PMID: 26834738 PMCID: PMC4713841 DOI: 10.3389/fimmu.2015.00661] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 12/24/2015] [Indexed: 01/03/2023] Open
Abstract
Epigenetic alterations are necessary for the establishment of functional and phenotypic diversity in the populations of immune cells of the monocytic lineage. The epigenetic status of individual genes at different time points defines their transcriptional responses throughout development and in response to environmental stimuli. Epigenetic states are defined at the level of DNA modifications, chromatin modifications, as well as at the level of RNA base changes through RNA editing. Drawing from lessons regarding the epigenome and epitranscriptome of cells of the monocytic lineage in the periphery, and from recently published RNAseq data deriving from brain-resident monocytes, we discuss the impact of modulation of these epigenetic states and how they affect processes important for the development of a healthy brain, as well as mechanisms of neurodegenerative disease and aging. An understanding of the varied brain responses and pathologies in light of these novel gene regulatory systems in monocytes will lead to important new insights in the understanding of the aging process and the treatment and diagnosis of neurodegenerative disease.
Collapse
Affiliation(s)
- F Nina Papavasiliou
- Laboratory of Lymphocyte Biology, The Rockefeller University , New York, NY , USA
| | - Young Cheul Chung
- Neuroimmunology and Inflammation Program, The Rockefeller University, New York, NY, USA; Harold and Margaret Milliken Hatch Laboratory of Neuroendocrinology, The Rockefeller University, New York, NY, USA
| | - Khatuna Gagnidze
- Neuroimmunology and Inflammation Program, The Rockefeller University, New York, NY, USA; Harold and Margaret Milliken Hatch Laboratory of Neuroendocrinology, The Rockefeller University, New York, NY, USA
| | - Kaitlyn H Hajdarovic
- Neuroimmunology and Inflammation Program, The Rockefeller University, New York, NY, USA; Harold and Margaret Milliken Hatch Laboratory of Neuroendocrinology, The Rockefeller University, New York, NY, USA
| | - Dan C Cole
- Neuroimmunology and Inflammation Program, The Rockefeller University, New York, NY, USA; Harold and Margaret Milliken Hatch Laboratory of Neuroendocrinology, The Rockefeller University, New York, NY, USA
| | - Karen Bulloch
- Neuroimmunology and Inflammation Program, The Rockefeller University, New York, NY, USA; Harold and Margaret Milliken Hatch Laboratory of Neuroendocrinology, The Rockefeller University, New York, NY, USA
| |
Collapse
|
97
|
Fang P, Guo M. Evolutionary Limitation and Opportunities for Developing tRNA Synthetase Inhibitors with 5-Binding-Mode Classification. Life (Basel) 2015; 5:1703-25. [PMID: 26670257 PMCID: PMC4695845 DOI: 10.3390/life5041703] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 11/24/2015] [Accepted: 11/25/2015] [Indexed: 12/30/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are enzymes that catalyze the transfer of amino acids to their cognate tRNAs as building blocks for translation. Each of the aaRS families plays a pivotal role in protein biosynthesis and is indispensable for cell growth and survival. In addition, aaRSs in higher species have evolved important non-translational functions. These translational and non-translational functions of aaRS are attractive for developing antibacterial, antifungal, and antiparasitic agents and for treating other human diseases. The interplay between amino acids, tRNA, ATP, EF-Tu and non-canonical binding partners, had shaped each family with distinct pattern of key sites for regulation, with characters varying among species across the path of evolution. These sporadic variations in the aaRSs offer great opportunity to target these essential enzymes for therapy. Up to this day, growing numbers of aaRS inhibitors have been discovered and developed. Here, we summarize the latest developments and structural studies of aaRS inhibitors, and classify them with distinct binding modes into five categories.
Collapse
Affiliation(s)
- Pengfei Fang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
- Department of Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA.
| | - Min Guo
- Department of Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA.
| |
Collapse
|
98
|
Abstract
Among the multiple modes of regulation of gene expression, translational control is arguably the least investigated and understood, and its role in vascular biology and pathobiology is not an exception. Here, we review recent studies that have revealed exciting translational regulatory phenomena and mechanisms involving novel RNA binding proteins and microRNA machinery in vascular biology. From these studies, the importance of translational regulation in angiogenesis, atherosclerosis, and blood pressure maintenance is beginning to emerge. We believe that the recent development of powerful techniques such as ribosome profiling and translating ribosome affinity purification (TRAP) will motivate and facilitate additional research in these areas.
Collapse
|
99
|
Castello A, Hentze MW, Preiss T. Metabolic Enzymes Enjoying New Partnerships as RNA-Binding Proteins. Trends Endocrinol Metab 2015; 26:746-757. [PMID: 26520658 PMCID: PMC4671484 DOI: 10.1016/j.tem.2015.09.012] [Citation(s) in RCA: 183] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 09/26/2015] [Accepted: 09/28/2015] [Indexed: 12/21/2022]
Abstract
In the past century, few areas of biology advanced as much as our understanding of the pathways of intermediary metabolism. Initially considered unimportant in terms of gene regulation, crucial cellular fate changes, cell differentiation, or malignant transformation are now known to involve 'metabolic remodeling' with profound changes in the expression of many metabolic enzyme genes. This review focuses on the recent identification of RNA-binding activity of numerous metabolic enzymes. We discuss possible roles of this unexpected second activity in feedback gene regulation ('moonlighting') and/or in the control of enzymatic function. We also consider how metabolism-driven post-translational modifications could regulate enzyme-RNA interactions. Thus, RNA emerges as a new partner of metabolic enzymes with far-reaching possible consequences to be unraveled in the future.
Collapse
Affiliation(s)
- Alfredo Castello
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Matthias W Hentze
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| | - Thomas Preiss
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Acton (Canberra), ACT 2601, Australia; Victor Chang Cardiac Research Institute, Darlinghurst (Sydney), New South Wales 2010, Australia
| |
Collapse
|
100
|
Na YR, Jung D, Gu GJ, Jang AR, Suh YH, Seok SH. The early synthesis of p35 and activation of CDK5 in LPS-stimulated macrophages suppresses interleukin-10 production. Sci Signal 2015; 8:ra121. [DOI: 10.1126/scisignal.aab3156] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|