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Kaur M, Mehta R, Muthuswami R, Mallick BN. Noradrenaline enhances Na-K ATPase subunit expression by HuR-induced mRNA stabilization and their transportation to the cell surface through PLC and PKC mediated pathway: Implications with REMS-loss associated disorders. J Neurochem 2024. [PMID: 38676340 DOI: 10.1111/jnc.16116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 03/08/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024]
Abstract
Rapid eye movement sleep (REMS) maintains brain excitability at least by regulating Na-K ATPase activity. Although REMS deprivation (REMSD)-associated elevated noradrenaline (NA) increases Na-K ATPase protein expression, its mRNA transcription did not increase. We hypothesized and confirmed both in vivo as well as in vitro that elevated mRNA stability explains the apparent puzzle. The mRNA stability was measured in control and REMSD rat brain with or without in vivo treatment with α1-adrenoceptor (AR) antagonist, prazosin (PRZ). Upon REMSD, Na-K ATPase α1-, and α2-mRNA stability increased significantly, which was prevented by PRZ. To decipher the molecular mechanism of action, we estimated NA-induced Na-K ATPase mRNA stability in Neuro-2a cells under controlled conditions and by transcription blockage using Actinomycin D (Act-D). NA increased Na-K ATPase mRNA stability, which was prevented by PRZ and propranolol (PRP, β-AR antagonist). The knockdown assay confirmed that the increased mRNA stabilization was induced by elevated cytoplasmic abundance of Human antigen R (HuR) and involving (Phospholipase C) PLC-mediated activation of Protein Kinase C (PKC). Additionally, using cell-impermeable Enz-link sulfo NHS-SS-Biotin, we observed that NA increased Na-K ATPase α1-subunits on the Neuro-2a cell surface. We conclude that REMSD-associated elevated NA, acting on α1- and β-AR, increases nucleocytoplasmic translocation of HuR and increases Na-K ATPase mRNA stability, resulting in increased Na-K ATPase protein expression. The latter then gets translocated to the neuronal membrane surface involving both PKC and (Protein Kinase A) PKA-mediated pathways. These findings may be exploited for the amelioration of REMSD-associated chronic disorders and symptoms.
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Affiliation(s)
- Manjeet Kaur
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rachna Mehta
- AMITY Institute of Neuropsychology and Neurosciences, AMITY University Uttar Pradesh, Noida, UP, India
| | - Rohini Muthuswami
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Birendra Nath Mallick
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
- AMITY Institute of Neuropsychology and Neurosciences, AMITY University Uttar Pradesh, Noida, UP, India
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2
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Sinitsky M, Repkin E, Sinitskaya A, Markova V, Shishkova D, Barbarash O. Proteomic Profiling of Endothelial Cells Exposed to Mitomycin C: Key Proteins and Pathways Underlying Genotoxic Stress-Induced Endothelial Dysfunction. Int J Mol Sci 2024; 25:4044. [PMID: 38612854 PMCID: PMC11011977 DOI: 10.3390/ijms25074044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/03/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
Mitomycin C (MMC)-induced genotoxic stress can be considered to be a novel trigger of endothelial dysfunction and atherosclerosis-a leading cause of cardiovascular morbidity and mortality worldwide. Given the increasing genotoxic load on the human organism, the decryption of the molecular pathways underlying genotoxic stress-induced endothelial dysfunction could improve our understanding of the role of genotoxic stress in atherogenesis. Here, we performed a proteomic profiling of human coronary artery endothelial cells (HCAECs) and human internal thoracic endothelial cells (HITAECs) in vitro that were exposed to MMC to identify the biochemical pathways and proteins underlying genotoxic stress-induced endothelial dysfunction. We denoted 198 and 71 unique, differentially expressed proteins (DEPs) in the MMC-treated HCAECs and HITAECs, respectively; only 4 DEPs were identified in both the HCAECs and HITAECs. In the MMC-treated HCAECs, 44.5% of the DEPs were upregulated and 55.5% of the DEPs were downregulated, while in HITAECs, these percentages were 72% and 28%, respectively. The denoted DEPs are involved in the processes of nucleotides and RNA metabolism, vesicle-mediated transport, post-translation protein modification, cell cycle control, the transport of small molecules, transcription and signal transduction. The obtained results could improve our understanding of the fundamental basis of atherogenesis and help in the justification of genotoxic stress as a risk factor for atherosclerosis.
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Affiliation(s)
- Maxim Sinitsky
- Laboratory of Genome Medicine, Research Institute for Complex Issues of Cardiovascular Diseases, 6 Academician Barbarash Boulevard, 650002 Kemerovo, Russia
| | - Egor Repkin
- Centre for Molecular and Cell Technologies, St. Petersburg State University, 7/9 Universitetskaya Embankment, 199034 St. Petersburg, Russia
| | - Anna Sinitskaya
- Laboratory of Genome Medicine, Research Institute for Complex Issues of Cardiovascular Diseases, 6 Academician Barbarash Boulevard, 650002 Kemerovo, Russia
| | - Victoria Markova
- Laboratory for Molecular, Translation and Digital Medicine, Research Institute for Complex Issues of Cardiovascular Diseases, 6 Academician Barbarash Boulevard, 650002 Kemerovo, Russia
| | - Daria Shishkova
- Laboratory for Molecular, Translation and Digital Medicine, Research Institute for Complex Issues of Cardiovascular Diseases, 6 Academician Barbarash Boulevard, 650002 Kemerovo, Russia
| | - Olga Barbarash
- Research Institute for Complex Issues of Cardiovascular Diseases, 6 Academician Barbarash Boulevard, 650002 Kemerovo, Russia
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3
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Joseph BP, Weber V, Knüpfer L, Giorgetti A, Alfonso-Prieto M, Krauß S, Carloni P, Rossetti G. Low Molecular Weight Inhibitors Targeting the RNA-Binding Protein HuR. Int J Mol Sci 2023; 24:13127. [PMID: 37685931 PMCID: PMC10488267 DOI: 10.3390/ijms241713127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/18/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
The RNA-binding protein human antigen R (HuR) regulates stability, translation, and nucleus-to-cytoplasm shuttling of its target mRNAs. This protein has been progressively recognized as a relevant therapeutic target for several pathologies, like cancer, neurodegeneration, as well as inflammation. Inhibitors of mRNA binding to HuR might thus be beneficial against a variety of diseases. Here, we present the rational identification of structurally novel HuR inhibitors. In particular, by combining chemoinformatic approaches, high-throughput virtual screening, and RNA-protein pulldown assays, we demonstrate that the 4-(2-(2,4,6-trioxotetrahydropyrimidin-5(2H)-ylidene)hydrazineyl)benzoate ligand exhibits a dose-dependent HuR inhibition effect in binding experiments. Importantly, the chemical scaffold is new with respect to the currently known HuR inhibitors, opening up a new avenue for the design of pharmaceutical agents targeting this important protein.
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Affiliation(s)
- Benjamin Philipp Joseph
- Institute for Neuroscience and Medicine and Institute for Advanced Simulations (INM-9/IAS-5), Computational Biomedicine, Forschungszentrum Jülich, 52425 Jülich, Germany; (B.P.J.); (V.W.); (A.G.); (M.A.-P.); (G.R.)
- Faculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen University, 52062 Aachen, Germany
| | - Verena Weber
- Institute for Neuroscience and Medicine and Institute for Advanced Simulations (INM-9/IAS-5), Computational Biomedicine, Forschungszentrum Jülich, 52425 Jülich, Germany; (B.P.J.); (V.W.); (A.G.); (M.A.-P.); (G.R.)
- Faculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen University, 52062 Aachen, Germany
| | - Lisa Knüpfer
- Institute of Biology, University of Siegen, 57076 Siegen, Germany;
| | - Alejandro Giorgetti
- Institute for Neuroscience and Medicine and Institute for Advanced Simulations (INM-9/IAS-5), Computational Biomedicine, Forschungszentrum Jülich, 52425 Jülich, Germany; (B.P.J.); (V.W.); (A.G.); (M.A.-P.); (G.R.)
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Mercedes Alfonso-Prieto
- Institute for Neuroscience and Medicine and Institute for Advanced Simulations (INM-9/IAS-5), Computational Biomedicine, Forschungszentrum Jülich, 52425 Jülich, Germany; (B.P.J.); (V.W.); (A.G.); (M.A.-P.); (G.R.)
| | - Sybille Krauß
- Institute of Biology, University of Siegen, 57076 Siegen, Germany;
| | - Paolo Carloni
- Institute for Neuroscience and Medicine and Institute for Advanced Simulations (INM-9/IAS-5), Computational Biomedicine, Forschungszentrum Jülich, 52425 Jülich, Germany; (B.P.J.); (V.W.); (A.G.); (M.A.-P.); (G.R.)
- Faculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen University, 52062 Aachen, Germany
| | - Giulia Rossetti
- Institute for Neuroscience and Medicine and Institute for Advanced Simulations (INM-9/IAS-5), Computational Biomedicine, Forschungszentrum Jülich, 52425 Jülich, Germany; (B.P.J.); (V.W.); (A.G.); (M.A.-P.); (G.R.)
- Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich, 52425 Jülich, Germany
- Department of Neurology, RWTH Aachen University, 44517 Aachen, Germany
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4
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Role of Heterogeneous Nuclear Ribonucleoproteins in the Cancer-Immune Landscape. Int J Mol Sci 2023; 24:ijms24065086. [PMID: 36982162 PMCID: PMC10049280 DOI: 10.3390/ijms24065086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 02/26/2023] [Accepted: 02/28/2023] [Indexed: 03/09/2023] Open
Abstract
Cancer remains the second leading cause of death, accounting for approximately 20% of all fatalities. Evolving cancer cells and a dysregulated immune system create complex tumor environments that fuel tumor growth, metastasis, and resistance. Over the past decades, significant progress in deciphering cancer cell behavior and recognizing the immune system as a hallmark of tumorigenesis has been achieved. However, the underlying mechanisms controlling the evolving cancer-immune landscape remain mostly unexplored. Heterogeneous nuclear ribonuclear proteins (hnRNP), a highly conserved family of RNA-binding proteins, have vital roles in critical cellular processes, including transcription, post-transcriptional modifications, and translation. Dysregulation of hnRNP is a critical contributor to cancer development and resistance. HnRNP contribute to the diversity of tumor and immune-associated aberrant proteomes by controlling alternative splicing and translation. They can also promote cancer-associated gene expression by regulating transcription factors, binding to DNA directly, or promoting chromatin remodeling. HnRNP are emerging as newly recognized mRNA readers. Here, we review the roles of hnRNP as regulators of the cancer-immune landscape. Dissecting the molecular functions of hnRNP will provide a better understanding of cancer-immune biology and will impact the development of new approaches to control and treat cancer.
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Hettinger ZR, Hu S, Mamiya H, Sahu A, Iijima H, Wang K, Gilmer G, Miller A, Nasello G, Dâ Amore A, Vorp DA, Rando TA, Xing J, Ambrosio F. Dynamical modeling reveals RNA decay mediates the effect of matrix stiffness on aged muscle stem cell fate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.24.529950. [PMID: 36865124 PMCID: PMC9980169 DOI: 10.1101/2023.02.24.529950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
Abstract
Loss of muscle stem cell (MuSC) self-renewal with aging reflects a combination of influences from the intracellular (e.g., post-transcriptional modifications) and extracellular (e.g., matrix stiffness) environment. Whereas conventional single cell analyses have revealed valuable insights into factors contributing to impaired self-renewal with age, most are limited by static measurements that fail to capture nonlinear dynamics. Using bioengineered matrices mimicking the stiffness of young and old muscle, we showed that while young MuSCs were unaffected by aged matrices, old MuSCs were phenotypically rejuvenated by young matrices. Dynamical modeling of RNA velocity vector fields in silico revealed that soft matrices promoted a self-renewing state in old MuSCs by attenuating RNA decay. Vector field perturbations demonstrated that the effects of matrix stiffness on MuSC self-renewal could be circumvented by fine-tuning the expression of the RNA decay machinery. These results demonstrate that post-transcriptional dynamics dictate the negative effect of aged matrices on MuSC self-renewal.
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Tenza-Ferrer H, Collodetti M, Nicolau EDS, Birbrair A, Magno LAV, Romano-Silva MA. Transiently Nav1.8-expressing neurons are capable of sensing noxious stimuli in the brain. Front Cell Neurosci 2022; 16:933874. [PMID: 36106013 PMCID: PMC9464809 DOI: 10.3389/fncel.2022.933874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
While current research highlights the role of Nav1. 8 sensory neurons from the peripheral nervous system, the anatomical and physiological characterization of encephalic Nav1.8 neurons remains unknown. Here, we use a Cre/fluorescent reporter mouse driven by the Nav1.8 gene promoter to reveal unexpected subpopulations of transiently-expressing Nav1.8 neurons within the limbic circuitry, a key mediator of the emotional component of pain. We observed that Nav1.8 neurons from the bed nuclei of the stria terminalis (BST), amygdala, and the periaqueductal gray (vPAG) are sensitive to noxious stimuli from an experimental model of chronic inflammatory pain. These findings identify a novel role for central Nav1.8 neurons in sensing nociception, which could be researched as a new approach to treating pain disorders.
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Affiliation(s)
- Helia Tenza-Ferrer
- Centro de Tecnologia em Medicina Molecular, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Mélcar Collodetti
- Centro de Tecnologia em Medicina Molecular, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Eduardo de Souza Nicolau
- Centro de Tecnologia em Medicina Molecular, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Alexander Birbrair
- Departamento de Patologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
- Department of Dermatology, University of Wisconsin-Madison, Madison, WI, United States
- Department of Radiology, Columbia University Medical Center, New York, NY, United States
- Alexander Birbrair
| | - Luiz Alexandre Viana Magno
- Centro de Tecnologia em Medicina Molecular, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
- Curso de Medicina, Universidade José do Rosário Vellano (UNIFENAS), Belo Horizonte, Brazil
- Pós-graduação da Faculdade Ciências Médicas de Minas Gerais, Belo Horizonte, Brazil
- *Correspondence: Luiz Alexandre Viana Magno
| | - Marco Aurélio Romano-Silva
- Centro de Tecnologia em Medicina Molecular, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
- Departamento de Saúde Mental, Faculdade de Medicina, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
- Marco Aurélio Romano-Silva
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7
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Nataraj B, Maharajan K, Malafaia G, Hemalatha D, Ahmed MAI, Ramesh M. Gene expression profiling in liver of zebrafish exposed to ethylhexyl methoxycinnamate and its photoproducts. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 826:154046. [PMID: 35217044 DOI: 10.1016/j.scitotenv.2022.154046] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/16/2022] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
In recent decades, the ecotoxicological potential of organic ultraviolet filters (OU-VFs) has received growing attention. However, the toxicity of its photoproducts or transformation products on freshwater vertebrates has been little explored. Therefore, the aim of the present study is to evaluate the possible adverse effects of ethylhexyl methoxycinnamate (EHMC) and its photoproducts [2-ethylhexanol (2-EH) and 4-methoxybenzaldehyde (4-MBA)] on the expression of stress-responsive and antioxidant genes. For this, zebrafish (Danio rerio) adults were exposed to pollutants at an environmentally relevant concentration (3 μg/L) and evaluated after 7, 14, and 21 days of exposure. The results of the principal component analysis (PCA) and two-way repeated measures (RM) ANOVA revealed that EHMC, 2-EH, and 4-MBA exposure caused significant downregulation of the genes hsp70, nrf2, cyp1a, ahr, sod1, sod2, cat, gstp1, gpx1a, gss, and gsr (on all trial days) in the liver of the animals. On the other hand, taken together, our data did not show significant differences between the effects induced by EHMC and its photoproducts. The genes evaluated in the present study play a major role in regulating the defensive antioxidant response against EHMC and its photoproducts. Additionally, our study provides an insight into the mechanisms of those OU-VFs in freshwater fish.
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Affiliation(s)
- Bojan Nataraj
- Unit of Toxicology, Department of Zoology, School of Life Sciences, Bharathiar University, Coimbatore 641046, India
| | - Kannan Maharajan
- Unit of Toxicology, Department of Zoology, School of Life Sciences, Bharathiar University, Coimbatore 641046, India; Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), 28789 East Jingshi Road, Jinan 250103, Shandong Province, PR China
| | - Guilherme Malafaia
- Post-Graduation Program in Environmental Sciences, Federal University of Goiás, Goiânia, GO, Brazil; Post-Graduation Program in Ecology, Conservation and Biodiversity, Federal University of Uberlândia, Uberlândia, MG, Brazil; Post-Graduation Program in Biotechnology and Biodiversity, Federal University of Goiás, Goiânia, GO, Brazil
| | - Devan Hemalatha
- Department of Zoology, PSG College of Arts & Science, Coimbatore, Tamil Nadu - 641014, India
| | | | - Mathan Ramesh
- Unit of Toxicology, Department of Zoology, School of Life Sciences, Bharathiar University, Coimbatore 641046, India.
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Wang X, Yang D. The regulation of RNA metabolism in hormone signaling and breast cancer. Mol Cell Endocrinol 2021; 529:111221. [PMID: 33711334 PMCID: PMC8262629 DOI: 10.1016/j.mce.2021.111221] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 02/09/2021] [Accepted: 02/22/2021] [Indexed: 02/02/2023]
Abstract
As the most frequent women's cancer, breast cancer causes the second most cancer-related death in women worldwide. Majority of the breast cancers are hormone receptor-positive and commonly treated by hormone therapy. Thus, the expression levels of hormone receptors signaling pathways are pivotal in the development and therapy of breast cancer. The expression of hormone receptors signaling pathways is not only regulated at the transcription level but also at the post-transcription level by both proteins and RNAs. In addition to that, the function of hormone receptors can also be regulated by RNAs. In this review, we summarize the roles of RNAs in hormone receptor-positive breast cancer. We introduce how mRNA stability and protein function of genes in hormone receptors signaling pathways are regulated by RNA-binding proteins, miRNAs, and lncRNAs. We believe these proteins and RNAs can be potential therapeutic targets of breast cancer.
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Affiliation(s)
- Xiaofei Wang
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, PA, 15261, USA
| | - Da Yang
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, PA, 15261, USA; UPMC Hillman Cancer Institute, University of Pittsburgh, Pittsburgh, PA, 15261, USA; Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
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9
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Ouali R, Valentim de Brito KC, Salmon D, Bousbata S. High-Throughput Identification of the Rhodnius prolixus Midgut Proteome Unravels a Sophisticated Hematophagic Machinery. Proteomes 2020; 8:proteomes8030016. [PMID: 32722125 PMCID: PMC7564601 DOI: 10.3390/proteomes8030016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 12/15/2022] Open
Abstract
Chagas disease is one of the most common parasitic infections in Latin America, which is transmitted by hematophagous triatomine bugs, of which Rhodnius prolixus is the vector prototype for the study of this disease. The protozoan parasite Trypanosoma cruzi, the etiologic agent of this disease, is transmitted by the vector to humans through the bite wound or mucosa. The passage of the parasite through the digestive tract of its vector constitutes a key step in its developmental cycle. Herewith, by a using high-throughput proteomic tool in order to characterize the midgut proteome of R. prolixus, we describe a set of functional groups of proteins, as well as the biological processes in which they are involved. This is the first proteomic analysis showing an elaborated hematophagy machinery involved in the digestion of blood, among which, several families of proteases have been characterized. The evaluation of the activity of cathepsin D proteases in the anterior part of the digestive tract of the insect suggested the existence of a proteolytic activity within this compartment, suggesting that digestion occurs early in this compartment. Moreover, several heat shock proteins, blood clotting inhibitors, and a powerful antioxidant enzyme machinery against reactive oxygen species (ROS) and cell detoxification have been identified. Highlighting the complexity and importance of the digestive physiology of insects could be a starting point for the selection of new targets for innovative control strategies of Chagas disease.
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Affiliation(s)
- Radouane Ouali
- Proteomic Plateform, Laboratory of Microbiology, Department of Molecular Biology, Université Libre de Bruxelles, 6041 Gosselies, Belgium;
| | - Karen Caroline Valentim de Brito
- Institute of Medical Biochemistry Leopoldo de Meis, Centro de Ciências e da Saúde, Federal University of Rio de Janeiro, Rio de Janeiro RJ 21941-902, Brazil; (K.C.V.d.B.); (D.S.)
| | - Didier Salmon
- Institute of Medical Biochemistry Leopoldo de Meis, Centro de Ciências e da Saúde, Federal University of Rio de Janeiro, Rio de Janeiro RJ 21941-902, Brazil; (K.C.V.d.B.); (D.S.)
| | - Sabrina Bousbata
- Proteomic Plateform, Laboratory of Microbiology, Department of Molecular Biology, Université Libre de Bruxelles, 6041 Gosselies, Belgium;
- Correspondence:
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10
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Liu Y, Shi SL. The roles of hnRNP A2/B1 in RNA biology and disease. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1612. [PMID: 32588964 DOI: 10.1002/wrna.1612] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/25/2020] [Accepted: 05/26/2020] [Indexed: 12/12/2022]
Abstract
The RNA-binding protein hnRNPA2/B1 is a member of the hnRNPs family and is widely expressed in various tissues. hnRNPA2/B1 recognizes and binds specific RNA substrates and DNA motifs and is involved in the transcription, splicing processing, transport, stability, and translation regulation of a variety of RNA molecules and in regulating the expression of a large number of genes. hnRNPA2/B1 is also involved in telomere maintenance and DNA repair, while its expression changes and mutations are involved in the development of various tumors and neurodegenerative and autoimmune diseases. This paper reviews the role and mechanism of hnRNPA2/B1 in RNA metabolism, tumors, and neurodegenerative and autoimmune diseases. 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.
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Affiliation(s)
- Yu Liu
- Cancer Research Center, School of Medicine, Xiamen University, Xiamen, China.,School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Song-Lin Shi
- Cancer Research Center, School of Medicine, Xiamen University, Xiamen, China
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11
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Posttranscriptional control of the replication stress response via TTP-mediated Claspin mRNA stabilization. Oncogene 2020; 39:3245-3257. [PMID: 32086441 DOI: 10.1038/s41388-020-1220-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 02/09/2020] [Accepted: 02/11/2020] [Indexed: 11/08/2022]
Abstract
ATR and CHK1 play key roles in the protection and recovery of the stalled replication forks. Claspin, an adaptor for CHK1 activation, is essential for DNA damage signaling and efficient replication fork progression. Here, we show that tristetraprolin (TTP), an mRNA-binding protein, can modulate the replication stress response via stabilization of Claspin mRNA. TTP depletion compromised specifically in the phosphorylation of CHK1, but not p53 or H2AX among other ATR substrates, and produced CHK1-defective replication phenotypes including accumulation of stalled replication forks. Importantly, the expression of siRNA-resistant TTP in TTP-deficient cells restored CHK1 phosphorylation and reduced the number of stalled replication forks as close to the control cells. Besides, we found that TTP was required for efficient replication fork progression even in the absence of exogenous DNA damage in a Claspin-dependent manner. Mechanistically, TTP was able to bind to the 3'-untranslated region of Claspin mRNA to increase the stability of Claspin mRNA which eventually contributed to the subsequent ATR-CHK1 activation upon DNA damage. Taken together, our results revealed an intimate link between TTP-dependent Claspin mRNA stability and ATR-CHK1-dependent replication fork stability to maintain replication fork integrity and chromosomal stability.
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12
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Sahmi F, Sahmi M, Gévry N, Sahadevan P, Allen BG, Price CA. A putative protein-RNA complex regulates posttranscriptional processing of cytochrome P450 aromatase (CYP19A1) in bovine granulosa cells. Mol Reprod Dev 2019; 86:1901-1908. [PMID: 31713287 DOI: 10.1002/mrd.23289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 10/08/2019] [Indexed: 12/30/2022]
Abstract
Follicle growth and granulosa cell health are dependent on the secretion of estradiol from granulosa cells. Estradiol is synthesized from androgen precursor by cytochrome P450 aromatase (CYP19A1), and in cattle CYP19A1 messenger RNA has a short half-life but a long (3.5 kb) 3'-untranslated region (3'UTR), suggesting that posttranscriptional regulation may be important for control of enzyme activity. We tested this hypothesis by inserting the CYP19A1 3'UTR and fragments thereof into a reporter vector between the end of the luciferase coding region and the polyadenylation signal. The full-length aromatase 3'UTR suppressed luciferase activity to 10% of control levels, and smaller fragments showed that this inhibitory activity lies between +926 and +1134 of the 3'UTR. Protein-RNA cross-linking experiments revealed that these 3'UTR fragments formed an RNA-protein complex of approximately 70 kDa that was present in granulosa cells but not in corpus luteum, lung, liver, kidney, pancreas, or bladder extracts. The RNA-binding activity was specific to the 3'UTR, as shown by competition experiments with unlabeled RNA, and was present only in 3'UTR constructs that inhibited luciferase activity. These data suggest that posttranscriptional regulation is an important component of the control of CYP19A1 expression and involves protein binding to a specific sequence in the 3'UTR.
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Affiliation(s)
- Fatiha Sahmi
- Centre de Recherche en Reproduction et Fertilité, Faculté de Médecine Vétérinaire, Université de Montréal, St-Hyacinthe, Québec, Canada.,Département de médecine, Université de Montréal, Montréal, Québec, Canada
| | - Malha Sahmi
- Centre de Recherche en Reproduction et Fertilité, Faculté de Médecine Vétérinaire, Université de Montréal, St-Hyacinthe, Québec, Canada.,Institut de Recherche en Immunologie et en Cancérologie, Université de Montréal, Montréal, Québec, Canada
| | - Nicolas Gévry
- Centre de Recherche en Reproduction et Fertilité, Faculté de Médecine Vétérinaire, Université de Montréal, St-Hyacinthe, Québec, Canada.,Département de Biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Pramod Sahadevan
- Département de médecine, Université de Montréal, Montréal, Québec, Canada
| | - Bruce G Allen
- Département de médecine, Université de Montréal, Montréal, Québec, Canada
| | - Christopher A Price
- Centre de Recherche en Reproduction et Fertilité, Faculté de Médecine Vétérinaire, Université de Montréal, St-Hyacinthe, Québec, Canada
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13
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Cuzzoni E, Franca R, De Iudicibus S, Marcuzzi A, Lucafò M, Pelin M, Favretto D, Monti E, Morello W, Ghio L, La Scola C, Mencarelli F, Pasini A, Montini G, Decorti G, Stocco G. MIF plasma level as a possible tool to predict steroid responsiveness in children with idiopathic nephrotic syndrome. Eur J Clin Pharmacol 2019; 75:1675-1683. [PMID: 31463578 DOI: 10.1007/s00228-019-02749-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 08/13/2019] [Indexed: 12/17/2022]
Abstract
PURPOSE Idiopathic nephrotic syndrome (INS) is the most frequent form of childhood nephrotic syndrome. Steroids represent the best therapeutic option; however, inter-individual differences in their efficacy and side effects have been reported. To date, there is no way to predict patients' resistance and/or dependence. Alterations in the cytokine profile of INS patients might contribute to proteinuria and glomerular damage and affect drug sensitivity. METHODS The cytokine plasma levels were measured in 21 INS children at diagnosis to investigate the association among cytokines pattern and clinical response. Patients were selected on the basis of their clinical response: 7 steroid sensitive (SS), 7 dependent (SD), and 7 resistant (SR). Significant results were then analyzed in 41 additional pediatric INS patients. RESULTS Within the 48 cytokines analyzed, macrophage migration inhibitory factor (MIF) was a good predictor of steroid response. Indeed, SR patients showed significantly higher MIF plasma levels compared with all others (p = 0.022; OR = 4.3, 95%CI = 1.2-25.4): a cutoff concentration of MIF > 501 pg/ml significantly discriminated SR patients (sensitivity = 85.7%, specificity = 71.4%). On the contrary, SD patients showed lower MIF plasma levels compared with others (p = 0.010; OR = 0.12, 95%CI = 9.2 × 10-3-6.7 × 10-1). Significant results were confirmed in the entire cohort. CONCLUSIONS Our comprehensive cytokine analysis indicates that assessing MIF plasma levels at diagnosis could predict response to glucocorticoids in children with INS.
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Affiliation(s)
- Eva Cuzzoni
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Raffaella Franca
- Department of Medical Surgical and Health Sciences, University of Trieste, Trieste, 34127, Italy
| | - Sara De Iudicibus
- Institute for Maternal Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | - Annalisa Marcuzzi
- Institute for Maternal Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | - Marianna Lucafò
- Institute for Maternal Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | - Marco Pelin
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Diego Favretto
- Department of Medical Surgical and Health Sciences, University of Trieste, Trieste, 34127, Italy
| | - Elena Monti
- Nephrology and Dialysis Unit, Department of Pediatrics, Azienda Ospedaliera Universitaria Sant'Orsola, Bologna, Italy
| | - William Morello
- Pediatric Nephrology, Dialysis and Transplant Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Luciana Ghio
- Pediatric Nephrology, Dialysis and Transplant Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Claudio La Scola
- Nephrology and Dialysis Unit, Department of Pediatrics, Azienda Ospedaliera Universitaria Sant'Orsola, Bologna, Italy
| | - Francesca Mencarelli
- Nephrology and Dialysis Unit, Department of Pediatrics, Azienda Ospedaliera Universitaria Sant'Orsola, Bologna, Italy
| | - Andrea Pasini
- Nephrology and Dialysis Unit, Department of Pediatrics, Azienda Ospedaliera Universitaria Sant'Orsola, Bologna, Italy
| | - Giovanni Montini
- Pediatric Nephrology, Dialysis and Transplant Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Giuliana Decorti
- Department of Medical Surgical and Health Sciences, University of Trieste, Trieste, 34127, Italy.
- Institute for Maternal Health - IRCCS "Burlo Garofolo", Trieste, Italy.
| | - Gabriele Stocco
- Department of Life Sciences, University of Trieste, Trieste, Italy
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14
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Gyurján I, Rosskopf S, Coronell JAL, Muhr D, Singer C, Weinhäusel A. IgG based immunome analyses of breast cancer patients reveal underlying signaling pathways. Oncotarget 2019; 10:3491-3505. [PMID: 31191821 PMCID: PMC6544406 DOI: 10.18632/oncotarget.26834] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 03/23/2019] [Indexed: 12/21/2022] Open
Abstract
Background: Breast cancer is the most frequent and one of the most fatal malignancies among women. Within the concept of personalized medicine, molecular characterization of tumors is usually performed by analyzing somatic mutations, RNA gene expression signatures or the proteome by mass-spectrometry. Alternatively, the immunological fingerprint of the patients can be analyzed by protein microarrays, which is able to provide another layer of molecular pathological information without invasive intervention. Results: We have investigated the immune signature of breast cancer patients and compared them with healthy controls, using protein microarray-based IgG profiling. The identified differentially reactive antigens (n=517) were further evaluated by means of various pathway analysis tools. Our results indicate that the immune signature of breast cancer patients shows a clear distinction from healthy individuals characterized by differentially reactive antigens involved in known disease relevant signaling pathways, such as VEGF, AKT/PI3K/mTOR or c-KIT, which is in close agreement with the findings from RNA-based expression profiles. Conclusion: Differential antigenic properties between breast cancer patients and healthy individual classes can be defined by serum-IgG profiling on protein microarrays. These immunome profiles provide an additional layer of molecular pathological information, which has the potential to refine and complete the systems biological map of neoplastic disease.
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Affiliation(s)
- István Gyurján
- Austrian Institute of Technology AIT, Center for Health & Environment, Molecular Diagnostics Unit, Vienna, Austria
| | - Sandra Rosskopf
- Austrian Institute of Technology AIT, Center for Health & Environment, Molecular Diagnostics Unit, Vienna, Austria
| | - Johana A Luna Coronell
- Austrian Institute of Technology AIT, Center for Health & Environment, Molecular Diagnostics Unit, Vienna, Austria
| | - Daniela Muhr
- Department of Obstetrics and Gynecology, Medical University of Vienna, Vienna, Austria
| | - Christian Singer
- Department of Obstetrics and Gynecology, Medical University of Vienna, Vienna, Austria
| | - Andreas Weinhäusel
- Austrian Institute of Technology AIT, Center for Health & Environment, Molecular Diagnostics Unit, Vienna, Austria
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15
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Shahar N, Weiner I, Stotsky L, Tuller T, Yacoby I. Prediction and large-scale analysis of primary operons in plastids reveals unique genetic features in the evolution of chloroplasts. Nucleic Acids Res 2019; 47:3344-3352. [PMID: 30828719 PMCID: PMC6468310 DOI: 10.1093/nar/gkz151] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 01/30/2019] [Accepted: 02/21/2019] [Indexed: 11/14/2022] Open
Abstract
While bacterial operons have been thoroughly studied, few analyses of chloroplast operons exist, limiting the ability to study fundamental elements of these structures and utilize them for synthetic biology. Here, we describe the creation of a plastome-specific operon database (link provided below) achieved by combining experimental tools and predictive modeling. Using a Reverse-Transcription-PCR based method and published data, we determined the transcription-state of 213 gene pairs from four plastomes of evolutionary distinct organisms. By analyzing sequence-based features computed for our dataset, we were able to highlight fundamental characteristics differentiating between operon pairs and non-operon pairs. These include an interesting tendency toward maintaining similar messenger RNA-folding profiles in operon gene pairs, a feature that failed to yield any informative separation in cyanobacteria, suggesting that it catches unique traits of operon gene expression, which have evolved post-endosymbiosis. Subsequently, we used this feature set to train a random-forest classifier for operon prediction. As our results demonstrate the ability of our predictor to obtain accurate (84%) and robust predictions on unlabeled datasets, we proceeded to building operon maps for 2018 sequenced plastids. Our database may now present new opportunities for promoting metabolic engineering and synthetic biology in chloroplasts.
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Affiliation(s)
- Noam Shahar
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Iddo Weiner
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
- Department of Biomedical Engineering, The Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Lior Stotsky
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, The Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
- The Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Iftach Yacoby
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
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16
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Chromosome Conformation Capture Reveals Two Elements That Interact with the PTBP3 ( ROD1) Transcription Start Site. Int J Mol Sci 2019; 20:ijms20020242. [PMID: 30634466 PMCID: PMC6359592 DOI: 10.3390/ijms20020242] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 12/31/2018] [Accepted: 01/03/2019] [Indexed: 12/21/2022] Open
Abstract
The long-range control of gene expression is facilitated by chromatin looping and can be detected using chromosome conformation capture—3C. Here we focus on the chromatin architecture of the PTBP3 (Polypyrimidine tract binding protein 3) locus to evaluate its potential role in regulating expression of the gene. PTBP3 expression in prostate cancer cell lines is found significantly higher compared to skin fibroblasts using real-time PCR (p < 0.05) and digital droplet PCR (p < 0.01). Exploration of the chromatin spatial architecture of a nearly 200-kb fragment of chromosome 9 encompassing the PTBP3 gene identified two elements located 63 kb upstream and 48 kb downstream of PTBP3, which looped specifically to the PTBP3 promoter. These elements contain histone acetylation patterns characteristic of open chromatin regions with active enhancers. Our results reveal for the first time that long-range chromatin interactions between the −63 kb and +48 kb loci and the PTBP3 promoter regulate the expression of this gene in prostate cancer cells. These interactions support an open chromatin form for the PTBP3 locus in cancer cells and the three-dimensional structural model proposed in this paper.
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17
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Lixa C, Mujo A, de Magalhães MTQ, Almeida FCL, Lima LMTR, Pinheiro AS. Oligomeric transition and dynamics of RNA binding by the HuR RRM1 domain in solution. JOURNAL OF BIOMOLECULAR NMR 2018; 72:179-192. [PMID: 30535889 DOI: 10.1007/s10858-018-0217-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 12/04/2018] [Indexed: 06/09/2023]
Abstract
Human antigen R (HuR) functions as a major post-transcriptional regulator of gene expression through its RNA-binding activity. HuR is composed by three RNA recognition motifs, namely RRM1, RRM2, and RRM3. The two N-terminal RRM domains are disposed in tandem and contribute mostly to HuR interaction with adenine and uracil-rich elements (ARE) in mRNA. Here, we used a combination of NMR and electrospray ionization-ion mobility spectrometry-mass spectrometry (ESI-IMS-MS) to characterize the structure, dynamics, RNA recognition, and dimerization of HuR RRM1. Our solution structure reveals a canonical RRM fold containing a 19-residue, intrinsically disordered N-terminal extension, which is not involved in RNA binding. NMR titration results confirm the primary RNA-binding site to the two central β-strands, β1 and β3, for a cyclooxygenase 2 (Cox2) ARE I-derived, 7-nucleotide RNA ligand. We show by 15N relaxation that, in addition to the N- and C-termini, the β2-β3 loop undergoes fast backbone dynamics (ps-ns) both in the free and RNA-bound state, indicating that no structural ordering happens upon RNA interaction. ESI-IMS-MS reveals that HuR RRM1 dimerizes, however dimer population represents a minority. Dimerization occurs via the α-helical surface, which is oppositely orientated to the RNA-binding β-sheet. By using a DNA analog of the Cox2 ARE I, we show that DNA binding stabilizes HuR RRM1 monomer and shifts the monomer-dimer equilibrium toward the monomeric species. Altogether, our results deepen the current understanding of the mechanism of RNA recognition employed by HuR.
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Affiliation(s)
- Carolina Lixa
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-909, Brazil
| | - Amanda Mujo
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-909, Brazil
| | - Mariana T Q de Magalhães
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Fabio C L Almeida
- National Center for Nuclear Magnetic Resonance Jiri Jonas, Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Luis Mauricio T R Lima
- Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-590, Brazil
| | - Anderson S Pinheiro
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-909, Brazil.
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18
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Overexpression of neuronal RNA-binding protein HuD increases reward induced reinstatement of an instrumental response. Neurosci Lett 2018; 683:119-124. [PMID: 29940328 DOI: 10.1016/j.neulet.2018.06.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 06/20/2018] [Accepted: 06/21/2018] [Indexed: 11/21/2022]
Abstract
The neuronal RNA-binding protein HuD is involved in synaptic plasticity and the molecular mechanisms of learning and memory. Previously, we have shown that HuD is upregulated after both spatial and addiction-associated forms of learning, such as conditioned place preference. However, what role HuD plays in non-drug dependent learning and memory is not fully understood. In order to elucidate the role that HuD plays in non-drug appetitive behavior, we assessed mice over-expressing HuD (HuDOE) throughout the forebrain on the acquisition of an instrumental response for a non-sucrose food reward utilizing a touch-screen paradigm. Next, we examined whether HuD level would alter the extinction or reward-induced reinstatement of responding. We found that HuDOE acquired and extinguished the instrumental response at rates similar to control littermates with no significant alterations in secondary measures of motor behavior or motivation. However, HuDOE reinstated their responding for food reward at rates significantly higher than control animals after a brief presentation of reward. These results suggest that HuD positively regulates the reinstatement of natural reward seeking and supports the role of HuD in forms of learning and memory associated with seeking of appetitive rewards.
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19
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Oliver RJ, Brigman JL, Bolognani F, Allan AM, Neisewander JL, Perrone-Bizzozero NI. Neuronal RNA-binding protein HuD regulates addiction-related gene expression and behavior. GENES BRAIN AND BEHAVIOR 2018; 17:e12454. [PMID: 29283498 DOI: 10.1111/gbb.12454] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 12/12/2017] [Accepted: 12/21/2017] [Indexed: 12/12/2022]
Abstract
The neuronal RNA-binding protein HuD is involved in synaptic plasticity and learning and memory mechanisms. These effects are thought to be due to HuD-mediated stabilization and translation of target mRNAs associated with plasticity. To investigate the potential role of HuD in drug addiction, we first used bioinformatics prediction algorithms together with microarray analyses to search for specific genes and functional networks upregulated within the forebrain of HuD overexpressing mice (HuDOE ). When this set was further limited to genes in the knowledgebase of addiction-related genes database (KARG) that contains predicted HuD-binding sites in their 3' untranslated regions (3'UTRs), we found that HuD regulates networks that have been associated with addiction-like behavior. These genes included Bdnf and Camk2a, 2 previously validated HuD targets. Since addiction is hypothesized to be a disorder stemming from altered gene expression causing aberrant plasticity, we sought to test the role of HuD in cocaine conditioned placed preference (CPP), a model of addiction-related behaviors. HuD mRNA and protein were upregulated by CPP within the nucleus accumbens of wild-type C57BL/6J mice. These changes were associated with increased expression of Bdnf and Camk2a mRNA and protein. To test this further, we trained HuDOE and wild-type mice in CPP and found that HuDOE mice showed increased cocaine CPP compared with controls. This was also associated with elevated expression of HuD target mRNAs and proteins, CaMKIIα and BDNF. These findings suggest HuD involvement in addiction-related behaviors such as cocaine conditioning and seeking, through increased plasticity-related gene expression.
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Affiliation(s)
- R J Oliver
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, New Mexico
| | - J L Brigman
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, New Mexico
| | - F Bolognani
- Roche Pharma Research and Early Development; Neuroscience, Ophthalmology and Rare Diseases, Roche Innovation Center, Basel, Switzerland
| | - A M Allan
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, New Mexico
| | - J L Neisewander
- School of Life Sciences, Arizona State University, Tempe, Arizona
| | - N I Perrone-Bizzozero
- Department of Neurosciences, University of New Mexico School of Medicine, Albuquerque, New Mexico
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20
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Villalba M, Fredericksen F, Otth C, Olavarría VH. Molecular characterization of the bovine IER3 gene: Down-regulation of IL-8 by blocking NF-κB activity mediated by IER3 overexpression in MDBK cells infected with bovine viral diarrhea virus-1. Mol Immunol 2017; 92:169-179. [DOI: 10.1016/j.molimm.2017.10.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 07/19/2017] [Accepted: 10/15/2017] [Indexed: 10/18/2022]
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21
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Wang S, Sun C, Li J, Zhang E, Ma Z, Xu W, Li H, Qiu M, Xu Y, Xia W, Xu L, Yin R. Roles of RNA methylation by means of N6-methyladenosine (m6A) in human cancers. Cancer Lett 2017; 408:112-120. [DOI: 10.1016/j.canlet.2017.08.030] [Citation(s) in RCA: 172] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 08/17/2017] [Accepted: 08/23/2017] [Indexed: 10/18/2022]
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22
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Tumor protein D52 expression is post-transcriptionally regulated by T-cell intercellular antigen (TIA) 1 and TIA-related protein via mRNA stability. Biochem J 2017; 474:1669-1687. [PMID: 28298474 DOI: 10.1042/bcj20160942] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 03/09/2017] [Accepted: 03/15/2017] [Indexed: 12/13/2022]
Abstract
Although tumor protein D52 (TPD52) family proteins were first identified nearly 20 years ago, their molecular regulatory mechanisms remain unclear. Therefore, we investigated the post-transcriptional regulation of TPD52 family genes. An RNA immunoprecipitation (RIP) assay showed the potential binding ability of TPD52 family mRNAs to several RNA-binding proteins, and an RNA degradation assay revealed that TPD52 is subject to more prominent post-transcriptional regulation than are TPD53 and TPD54. We subsequently focused on the 3'-untranslated region (3'-UTR) of TPD52 as a cis-acting element in post-transcriptional gene regulation. Several deletion mutants of the 3'-UTR of TPD52 mRNA were constructed and ligated to the 3'-end of a reporter green fluorescence protein gene. An RNA degradation assay revealed that a minimal cis-acting region, located in the 78-280 region of the 5'-proximal region of the 3'-UTR, stabilized the reporter mRNA. Biotin pull-down and RIP assays revealed specific binding of the region to T-cell intracellular antigen 1 (TIA-1) and TIA-1-related protein (TIAR). Knockdown of TIA-1/TIAR decreased not only the expression, but also the stability of TPD52 mRNA; it also decreased the expression and stability of the reporter gene ligated to the 3'-end of the 78-280 fragment. Stimulation of transforming growth factor-β and epidermal growth factor decreased the binding ability of these factors, resulting in decreased mRNA stability. These results indicate that the 78-280 fragment and TIA-1/TIAR concordantly contribute to mRNA stability as a cis-acting element and trans-acting factor(s), respectively. Thus, we here report the specific interactions between these elements in the post-transcriptional regulation of the TPD52 gene.
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23
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Xie Q, Guo X, Gu J, Zhang L, Jin H, Huang H, Li J, Huang C. p85α promotes nucleolin transcription and subsequently enhances EGFR mRNA stability and EGF-induced malignant cellular transformation. Oncotarget 2016; 7:16636-49. [PMID: 26918608 PMCID: PMC4941340 DOI: 10.18632/oncotarget.7674] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 01/16/2016] [Indexed: 11/25/2022] Open
Abstract
p85α is a regulatory subunit of phosphatidylinositol 3-kinase (PI3K) that is a key lipid enzyme for generating phosphatidylinositol 3, 4, 5-trisphosphate, and subsequently activates signaling that ultimately regulates cell cycle progression, cell growth, cytoskeletal changes, and cell migration. In addition to form a complex with the p110 catalytic subunit, p85α also exists as a monomeric form due to that there is a greater abundance of p85α than p110 in many cell types. Our previous studies have demonstrated that monomeric p85α exerts a pro-apoptotic role in UV response through induction of TNF-α gene expression in PI3K-independent manner. In current studies, we identified a novel biological function of p85α as a positive regulator of epidermal growth factor receptor (EGFR) expression and cell malignant transformation via nucleolin-dependent mechanism. Our results showed that p85α was crucial for EGFR and nucleolin expression and subsequently resulted in an increase of malignant cellular transformation by using both specific knockdown and deletion of p85α in its normal expressed cells. Mechanistic studies revealed that p85α upregulated EGFR protein expression mainly through stabilizing its mRNA, whereas nucleolin (NCL) was able to bind to egfr mRNA and increase its mRNA stability. Consistently, overexpression of NCL in p85α-/- cells restored EGFR mRNA stabilization, protein expression and cell malignant transformation. Moreover, we discovered that p85α upregulated NCL gene transcription via enhancing C-Jun activation. Collectively, our studies demonstrate a novel function of p85α as a positive regulator of EGFR mRNA stability and cell malignant transformation, providing a significant insight into the understanding of biomedical nature of p85α protein in mammalian cells and further supporting that p85α might be a potential target for cancer prevention and therapy.
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Affiliation(s)
- Qipeng Xie
- Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, School of Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Xirui Guo
- Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, School of Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Jiayan Gu
- Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, School of Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Liping Zhang
- Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, School of Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Honglei Jin
- Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, School of Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
- Nelson Institute of Environmental Medicine, New York University School of Medicine, Tuxedo, NY 10987, USA
| | - Haishan Huang
- Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, School of Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Jingxia Li
- Nelson Institute of Environmental Medicine, New York University School of Medicine, Tuxedo, NY 10987, USA
| | - Chuanshu Huang
- Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, School of Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
- Nelson Institute of Environmental Medicine, New York University School of Medicine, Tuxedo, NY 10987, USA
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24
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Recruitment, Duplex Unwinding and Protein-Mediated Inhibition of the Dead-Box RNA Helicase Dbp2 at Actively Transcribed Chromatin. J Mol Biol 2016; 428:1091-1106. [PMID: 26876600 DOI: 10.1016/j.jmb.2016.02.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 01/26/2016] [Accepted: 02/02/2016] [Indexed: 02/07/2023]
Abstract
RNA helicases play fundamental roles in modulating RNA structures and facilitating RNA-protein (RNP) complex assembly in vivo. Previously, our laboratory demonstrated that the DEAD-box RNA helicase Dbp2 in Saccharomyces cerevisiae is required to promote efficient assembly of the co-transcriptionally associated mRNA-binding proteins Yra1, Nab2, and Mex67 onto poly(A)(+)RNA. We also found that Yra1 associates directly with Dbp2 and functions as an inhibitor of Dbp2-dependent duplex unwinding, suggestive of a cycle of unwinding and inhibition by Dbp2. To test this, we undertook a series of experiments to shed light on the order of events for Dbp2 in co-transcriptional mRNP assembly. We now show that Dbp2 is recruited to chromatin via RNA and forms a large, RNA-dependent complex with Yra1 and Mex67. Moreover, single-molecule fluorescence resonance energy transfer and bulk biochemical assays show that Yra1 inhibits unwinding in a concentration-dependent manner by preventing the association of Dbp2 with single-stranded RNA. This inhibition prevents over-accumulation of Dbp2 on mRNA and stabilization of a subset of RNA polymerase II transcripts. We propose a model whereby Yra1 terminates a cycle of mRNP assembly by Dbp2.
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25
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Schwerk J, Savan R. Translating the Untranslated Region. THE JOURNAL OF IMMUNOLOGY 2016; 195:2963-71. [PMID: 26386038 DOI: 10.4049/jimmunol.1500756] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Gene expression programs undergo constant regulation to quickly adjust to environmental stimuli that alter the physiological status of the cell, like cellular stress or infection. Gene expression is tightly regulated by multilayered regulatory elements acting in both cis and trans. Posttranscriptional regulation of the 3' untranslated region (UTR) is a powerful regulatory process that determines the rate of protein translation from mRNA. Regulatory elements targeting the 3' UTR include microRNAs, RNA-binding proteins, and long noncoding RNAs, which dramatically alter the immune response. We provide an overview of our current understanding of posttranscriptional regulation of immune gene expression. The focus of this review is on regulatory elements that target the 3' UTR. We delineate how the synergistic or antagonistic interactions of posttranscriptional regulators determine gene expression levels and how dysregulation of 3' UTR-mediated posttranscriptional control associates with human diseases.
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Affiliation(s)
- Johannes Schwerk
- Department of Immunology, University of Washington, Seattle, WA 98109
| | - Ram Savan
- Department of Immunology, University of Washington, Seattle, WA 98109
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Fredericksen F, Villalba M, Olavarría VH. Characterization of bovine A20 gene: Expression mediated by NF-κB pathway in MDBK cells infected with bovine viral diarrhea virus-1. Gene 2016; 581:117-29. [PMID: 26809100 DOI: 10.1016/j.gene.2016.01.030] [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: 09/04/2015] [Revised: 12/03/2015] [Accepted: 01/17/2016] [Indexed: 02/06/2023]
Abstract
Cytokine production for immunological process is tightly regulated at the transcriptional and posttranscriptional levels. The NF-κB signaling pathway maintains immune homeostasis in the cell through the participation of molecules such as A20 (TNFAIP3), which is a key regulatory factor in the immune response, hematopoietic differentiation, and immunomodulation. Although A20 has been identified in mammals, and despite recent efforts to identify A20 members in other higher vertebrates, relatively little is known about the composition of this regulator in other classes of vertebrates, particularly for bovines. In this study, the genetic context of bovine A20 was explored and compared against homologous genes in the human, mouse, chicken, dog, and zebrafish chromosomes. Through in silico analysis, several regions of interest were found conserved between even phylogenetically distant species. Additionally, a protein-deduced sequence of bovine A20 evidenced many conserved domains in humans and mice. Furthermore, all potential amino acid residues implicated in the active site of A20 were conserved. Finally, bovine A20 mRNA expression as mediated by the bovine viral diarrhea virus and poly (I:C) was evaluated. These analyses evidenced a strong fold increase in A20 expression following virus exposure, a phenomenon blocked by a pharmacological NF-κB inhibitor (BAY 117085). Interestingly, A20 mRNA had a half-life of only 32min, likely due to adenylate- and uridylate-rich elements in the 3'-untranslated region. Collectively, these data identify bovine A20 as a regulator of immune marker expression. Finally, this is the first report to find the bovine viral diarrhea virus modulating bovine A20 activation through the NF-κB pathway.
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Affiliation(s)
- Fernanda Fredericksen
- Facultad de Ciencias, Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Campus Isla Teja S/N, Valdivia, Chile
| | - Melina Villalba
- Facultad de Ciencias, Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Campus Isla Teja S/N, Valdivia, Chile
| | - Víctor H Olavarría
- Facultad de Ciencias, Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Campus Isla Teja S/N, Valdivia, Chile.
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Inoue Y, Abe K, Onozaki K, Hayashi H. TGF-β decreases the stability of IL-18-induced IFN-γ mRNA through the expression of TGF-β-induced tristetraprolin in KG-1 cells. Biol Pharm Bull 2016; 38:536-44. [PMID: 25832634 DOI: 10.1248/bpb.b14-00673] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have previously reported that transforming growth factor-β (TGF-β) down-regulates interferon-γ (IFN-γ) production in an interleukin-18 (IL-18) treated mouse natural killer (NK) cell line, LNK5E6. In LNK5E6 cells, TGF-β exhibited no inhibition of the IL-18-induced transcription of IFN-γ, but did stimulate the degradation of IFN-γ mRNA induced by IL-18. In the present study, we investigated the mechanism of the down-regulatory effects of TGF-β on IFN-γ mRNA expression in a human myelomonocytic cell line, KG-1, which produces IFN-γ in response to IL-18 alone. Interestingly, IL-18 induced the production of the IFN-γ through the stabilization of IFN-γ mRNA, but not the enhanced transcription of IFN-γ gene. The stability of IFN-γ mRNA was regulated by mRNA destabilizing elements in the 3'untranslated region (UTR) of IFN-γ mRNA, especially adenylate-uridylate (AU)-rich elements (AREs) in the 5' half of 3'UTR. Tristetraprolin (TTP), one of the ARE-binding proteins, destabilizes IFN-γ mRNA, and IL-18 repressed the expression of TTP mRNA. Moreover, TGF-β repressed the IL-18-induced expression of IFN-γ mRNA through the induction of TTP mRNA to destabilize IFN-γ mRNA. Our data is the first to reveal that the crosstalk between IL-18 and TGF-β through the expression of TTP regulates the production of IFN-γ.
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Affiliation(s)
- Yasumichi Inoue
- Department of Drug Metabolism and Disposition, Graduate School of Pharmaceutical Sciences, Nagoya City University
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28
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Fan B, Dun SH, Gu JQ, Guo Y, Ikuyama S. Pycnogenol Attenuates the Release of Proinflammatory Cytokines and Expression of Perilipin 2 in Lipopolysaccharide-Stimulated Microglia in Part via Inhibition of NF-κB and AP-1 Activation. PLoS One 2015; 10:e0137837. [PMID: 26367267 PMCID: PMC4569068 DOI: 10.1371/journal.pone.0137837] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 08/22/2015] [Indexed: 01/29/2023] Open
Abstract
Over activation of microglia results in the production of proinflammatory agents that have been implicated in various brain diseases. Pycnogenol is a patented extract from French maritime pine bark (Pinus pinaster Aiton) with strong antioxidant and anti-inflammatory potency. The present study investigated whether pycnogenol may be associated with the production of proinflammatory mediators in lipopolysaccharide-stimulated BV2 (mouse-derived) microglia. It was found that pycnogenol treatment was dose-dependently associated with significantly less release of nitricoxide (NO), TNF-α, IL-6 and IL-1β, and lower levels of intercellular adhesion molecule1 (ICAM-1) and perilipin 2 (PLIN2). Furthermore, this effect was replicated in primary brain microglia. Levels of inducible NO synthase mRNA and protein were attenuated, whereas there was no change in the production of the anti-inflammatory cytokine IL-10. Further evidence indicated that pycnogenol treatment led to the suppression of NF-κB activation through inhibition of p65 translocation into the nucleus and inhibited DNA binding of AP-1, suggesting that these proinflammatory factors are associated with NF-κB and AP-1. We conclude that pycnogenol exerts anti-inflammatory effects through inhibition of the NF-κB and AP-1pathway, and may be useful as a therapeutic agent in the prevention of diseases caused by over activation of microglia.
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Affiliation(s)
- Bin Fan
- Department of Neurology, Shengjing Hospital, China Medical University, Shenyang, 110004, P. R. China
- * E-mail:
| | - Sai-Hong Dun
- Department of Neurology, Shengjing Hospital, China Medical University, Shenyang, 110004, P. R. China
| | - Jian-Qiu Gu
- Department of Endocrinology and Metabolism, First Affiliated Hospital, P. R. China Medical University, Shenyang, 110001, P. R. China
| | - Yang Guo
- Department of Neurology, Shengjing Hospital, China Medical University, Shenyang, 110004, P. R. China
| | - Shoichiro Ikuyama
- Department of Clinical Investigation & Department of Endocrine, Metabolic and Rheumatic Diseases, Oita San-ai Medical center, Oita, 870–1151, Japan
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29
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Kim YM, Choi WY, Oh CM, Han GH, Kim YJ. Secondary structure of the Irf7 5'-UTR, analyzed using SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension). BMB Rep 2015; 47:558-62. [PMID: 24393529 PMCID: PMC4261513 DOI: 10.5483/bmbrep.2014.47.10.281] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Indexed: 01/09/2023] Open
Abstract
OASL1 is a member of the 2’-5’-oligoadenylate synthetase (OAS) family and promotes viral clearance by activating RNase L. OASL1 interacts with the 5’-untranslated region (UTR) of interferon regulatory factor 7 (Irf7) and inhibits its translation. To identify the secondary structure required for OASL1 binding, we examined the 5’-UTR of the Irf7 transcript using “selective 2’-hydroxyl acylation analyzed by primer extension” (SHAPE). SHAPE takes advantage of the selective acylation of residues in single-stranded regions by 1-methyl-7-nitroisatoic anhydride (1M7). We found five major acylation sites located in, or next to, predicted single-stranded regions of the Irf7 5’-UTR. These results demonstrate the involvement of the stem structure of the Irf7 5’-UTR in the regulation of Irf7 translation, mediated by OASL1. [BMB Reports 2014; 47(10): 558-562]
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Affiliation(s)
- Yun-Mi Kim
- Departments of Integrated OMICs for Biomedical Science, Yonsei University, Seoul 120-749, Korea
| | - Won-Young Choi
- Department of Biochemistry, Yonsei University, Seoul 120-749, Korea
| | - Chang-Mok Oh
- Departments of Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Gyoon-Hee Han
- Departments of Integrated OMICs for Biomedical Science, Yonsei University, Seoul 120-749, Korea
| | - Young-Joon Kim
- Departments of Integrated OMICs for Biomedical Science, Yonsei University, Seoul 120-749, Korea
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Lever MA, Rogers KL, Lloyd KG, Overmann J, Schink B, Thauer RK, Hoehler TM, Jørgensen BB. Life under extreme energy limitation: a synthesis of laboratory- and field-based investigations. FEMS Microbiol Rev 2015; 39:688-728. [PMID: 25994609 DOI: 10.1093/femsre/fuv020] [Citation(s) in RCA: 181] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2015] [Indexed: 11/13/2022] Open
Abstract
The ability of microorganisms to withstand long periods with extremely low energy input has gained increasing scientific attention in recent years. Starvation experiments in the laboratory have shown that a phylogenetically wide range of microorganisms evolve fitness-enhancing genetic traits within weeks of incubation under low-energy stress. Studies on natural environments that are cut off from new energy supplies over geologic time scales, such as deeply buried sediments, suggest that similar adaptations might mediate survival under energy limitation in the environment. Yet, the extent to which laboratory-based evidence of starvation survival in pure or mixed cultures can be extrapolated to sustained microbial ecosystems in nature remains unclear. In this review, we discuss past investigations on microbial energy requirements and adaptations to energy limitation, identify gaps in our current knowledge, and outline possible future foci of research on life under extreme energy limitation.
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Affiliation(s)
- Mark A Lever
- Center for Geomicrobiology, Institute of Bioscience, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark
| | - Karyn L Rogers
- Rensselaer Polytechnic Institute, Earth and Environmental Sciences, Jonsson-Rowland Science Center, 1W19, 110 8th Street, Troy, NY 12180, USA
| | - Karen G Lloyd
- Department of Microbiology, University of Tennessee at Knoxville, M409 Walters Life Sciences, Knoxville, TN 37996-0845, USA
| | - Jörg Overmann
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B, D-38124 Braunschweig, Germany
| | - Bernhard Schink
- Microbial Ecology, Department of Biology, University of Konstanz, P.O. Box 55 60, D-78457 Konstanz, Germany
| | - Rudolf K Thauer
- Max Planck Institut für terrestrische Mikrobiologie, Karl-von-Frisch-Straße, D-35043 Marburg, Germany
| | - Tori M Hoehler
- NASA Ames Research Center, Mail Stop 239-4, Moffett Field, CA 94035-1000, USA
| | - Bo Barker Jørgensen
- Center for Geomicrobiology, Institute of Bioscience, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark
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Hess AK, Saffert P, Liebeton K, Ignatova Z. Optimization of translation profiles enhances protein expression and solubility. PLoS One 2015; 10:e0127039. [PMID: 25965266 PMCID: PMC4428881 DOI: 10.1371/journal.pone.0127039] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 04/11/2015] [Indexed: 12/12/2022] Open
Abstract
mRNA is translated with a non-uniform speed that actively coordinates co-translational folding of protein domains. Using structure-based homology we identified the structural domains in epoxide hydrolases (EHs) and introduced slow-translating codons to delineate the translation of single domains. These changes in translation speed dramatically improved the solubility of two EHs of metagenomic origin in Escherichia coli. Conversely, the importance of transient attenuation for the folding, and consequently solubility, of EH was evidenced with a member of the EH family from Agrobacterium radiobacter, which partitions in the soluble fraction when expressed in E. coli. Synonymous substitutions of codons shaping the slow-transiting regions to fast-translating codons render this protein insoluble. Furthermore, we show that low protein yield can be enhanced by decreasing the free folding energy of the initial 5’-coding region, which can disrupt mRNA secondary structure and enhance ribosomal loading. This study provides direct experimental evidence that mRNA is not a mere messenger for translation of codons into amino acids but bears an additional layer of information for folding, solubility and expression level of the encoded protein. Furthermore, it provides a general frame on how to modulate and fine-tune gene expression of a target protein.
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Affiliation(s)
- Anne-Katrin Hess
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Paul Saffert
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | | | - Zoya Ignatova
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Biochemistry, Department of Chemistry and Biochemistry, University of Hamburg, Hamburg, Germany
- * E-mail: (ZI); (KL)
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32
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King PH, Chen CY. Role of KSRP in control of type I interferon and cytokine expression. J Interferon Cytokine Res 2015; 34:267-74. [PMID: 24697204 DOI: 10.1089/jir.2013.0143] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Cytokines and chemokines are key participants in pathways that drive inflammatory, immune, and other cellular responses to exogenous insults such as infection, trauma, and physiological stress. Persistent and aberrant expression of these factors has been linked to autoimmune, degenerative, and neoplastic diseases. Consequently, cytokine and chemokine expression is tightly governed at each level of gene regulation. Recent studies have demonstrated a role for KH-type splicing regulatory protein (KSRP) in curtailing cytokine and chemokine expression through transcriptional and post-transcriptional mechanisms, including promotion of microRNA maturation. Understanding the role of KSRP in cytokine mRNA metabolism should identify promising targets for the modulation of immune and inflammatory responses.
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Affiliation(s)
- Peter H King
- 1 Department of Neurology, University of Alabama at Birmingham , Birmingham, Alabama
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33
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Tristetraprolin Recruits the Herpes Simplex Virion Host Shutoff RNase to AU-Rich Elements in Stress Response mRNAs To Enable Their Cleavage. J Virol 2015; 89:5643-50. [PMID: 25762736 DOI: 10.1128/jvi.00091-15] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 03/03/2015] [Indexed: 01/10/2023] Open
Abstract
UNLABELLED Herpes simplex viruses (HSV) package and bring into cells an RNase designated virion host shutoff (VHS) RNase. In infected cells, the VHS RNase targets primarily stress response mRNAs characterized by the presence of AU-rich elements in their 3' untranslated regions (UTRs). In uninfected cells, these RNAs are sequestered in exosomes or P bodies by host proteins that bind to the AU-rich elements. In infected cells, the AU-rich RNAs are deadenylated and cleaved close to the AU-rich elements, leading to long-term persistence of nontranslatable RNAs consisting of the 5' portions of the cleavage products. The host proteins that bind to the AU-rich elements are either resident in cells (e.g., TIA-1) or induced (e.g., tristetraprolin). Earlier, this laboratory reported that tristetraprolin binds VHS RNase. To test the hypothesis that tristetraprolin directs VHS RNase to the AU-rich elements, we mapped the domains of VHS and tristetraprolin required for their interactions. We report that VHS binds to the domain of tristetraprolin that enables its interaction with RNA. A single amino acid substitution in that domain abolished the interaction with RNA but did not block the binding to VHS RNase. In transfected cells, the mutant but not the wild-type tristetraprolin precluded the degradation of the AU-rich RNAs by VHS RNase. We conclude that TTP mediates the cleavage of the 3' UTRs of stress response mRNAs by recruiting the VHS RNase to the AU-rich elements. IMPORTANCE The primary host response to HSV infection is the synthesis of stress response mRNAs characterized by the presence of AU-rich elements in their 3' UTRs. These mRNAs are the targets of the virion host shutoff (VHS) RNase. The VHS RNase binds both to mRNA cap structure and to tristetraprolin, an inducible host protein that sequesters AU-rich mRNAs in exosomes or P bodies. Here we show that tristetraprolin recruits VHS RNase to the AU-rich elements and enables the degradation of the stress response mRNAs.
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34
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Kim SH, Lee KH, Kim DY, Kwak E, Kim S, Kim KT. Rhythmic control of mRNA stability modulates circadian amplitude of mouse Period3 mRNA. J Neurochem 2015; 132:642-56. [PMID: 25581122 DOI: 10.1111/jnc.13027] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 12/15/2014] [Accepted: 12/19/2014] [Indexed: 12/31/2022]
Abstract
The daily oscillations observed in most living organisms are endogenously generated with a period of 24 h, and the underlying structure of periodic oscillation is an autoregulatory transcription-translation feedback loop. The mechanisms of untranslated region (UTR)-mediated post-transcriptional regulation (e.g., mRNA degradation and internal ribosomal entry site (IRES)-mediated translation) have been suggested to fine-tune the expression of clock genes. Mouse Period3 (mPer3) is one of the paralogs of Period gene and its function is important in peripheral clocks and sleep physiology. mPer3 mRNA displays a circadian oscillation as well as a circadian phase-dependent stability, while the stability regulators still remain unknown. In this study, we identify three proteins - heterogeneous nuclear ribonucleoprotein (hnRNP) K, polypyrimidine tract-binding protein (PTB), and hnRNP D - that bind to mPer3 mRNA 3'-UTR. We show that hnRNP K is a stabilizer that increases the amplitude of circadian mPer3 mRNA oscillation and hnRNP D is a destabilizer that decreases it, while PTB exhibits no effect on mPer3 mRNA expression. Our experiments describe their cytoplasmic roles for the mRNA stability regulation and the circadian amplitude formation. Moreover, our mathematical model suggests a mechanism through which post-transcriptional mRNA stability modulation provides not only the flexibility of oscillation amplitude, but also the robustness of the period and the phase for circadian mPer3 expression. Mouse Period3 (mPer3) is one of well-known clock genes. We identified three 3'-UTR-binding proteins that modulate the mRNA stability, and they influenced to the amplitude of circadian mPer3 mRNA oscillation. Our mathematical model not only showed the relationship between mRNA stability and its oscillation profile but provided the molecular mechanism for the robustness of the period and the phase in circadian oscillation. hnK, heterogeneous nuclear ribonucleoprotein (hnRNP) K; hnD, hnRNP D; PTB, polypyrimidine tract-binding protein.
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Affiliation(s)
- Sung-Hoon Kim
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea
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35
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Hulur I, Gamazon ER, Skol AD, Xicola RM, Llor X, Onel K, Ellis NA, Kupfer SS. Enrichment of inflammatory bowel disease and colorectal cancer risk variants in colon expression quantitative trait loci. BMC Genomics 2015; 16:138. [PMID: 25766683 PMCID: PMC4351699 DOI: 10.1186/s12864-015-1292-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 01/29/2015] [Indexed: 12/20/2022] Open
Abstract
Background Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) associated with diseases of the colon including inflammatory bowel diseases (IBD) and colorectal cancer (CRC). However, the functional role of many of these SNPs is largely unknown and tissue-specific resources are lacking. Expression quantitative trait loci (eQTL) mapping identifies target genes of disease-associated SNPs. This study provides a comprehensive eQTL map of distal colonic samples obtained from 40 healthy African Americans and demonstrates their relevance for GWAS of colonic diseases. Results 8.4 million imputed SNPs were tested for their associations with 16,252 expression probes representing 12,363 unique genes. 1,941 significant cis-eQTL, corresponding to 122 independent signals, were identified at a false discovery rate (FDR) of 0.01. Overall, among colon cis-eQTL, there was significant enrichment for GWAS variants for IBD (Crohn’s disease [CD] and ulcerative colitis [UC]) and CRC as well as type 2 diabetes and body mass index. ERAP2, ADCY3, INPP5E, UBA7, SFMBT1, NXPE1 and REXO2 were identified as target genes for IBD-associated variants. The CRC-associated eQTL rs3802842 was associated with the expression of C11orf93 (COLCA2). Enrichment of colon eQTL near transcription start sites and for active histone marks was demonstrated, and eQTL with high population differentiation were identified. Conclusions Through the comprehensive study of eQTL in the human colon, this study identified novel target genes for IBD- and CRC-associated genetic variants. Moreover, bioinformatic characterization of colon eQTL provides a tissue-specific tool to improve understanding of biological differences in diseases between different ethnic groups. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1292-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Imge Hulur
- Committee on Genetics, Genomics and Systems Biology, Chicago, IL, 60637, USA.
| | - Eric R Gamazon
- Department of Medicine, 900 East 57th Street, MB#9, Chicago, IL, 60637, USA. .,Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN, 37232, USA.
| | - Andrew D Skol
- Department of Medicine, 900 East 57th Street, MB#9, Chicago, IL, 60637, USA.
| | - Rosa M Xicola
- Department of Medicine, Yale University, New Haven, CT, 06510, USA.
| | - Xavier Llor
- Department of Medicine, Yale University, New Haven, CT, 06510, USA.
| | - Kenan Onel
- Department of Pediatrics, University of Chicago, Chicago, IL, 60637, USA.
| | - Nathan A Ellis
- University of Arizona Cancer Center, Tucson, AZ, 85724, USA.
| | - Sonia S Kupfer
- Department of Medicine, 900 East 57th Street, MB#9, Chicago, IL, 60637, USA.
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Chou CF, Zhu X, Lin YY, Gamble KL, Garvey WT, Chen CY. KSRP is critical in governing hepatic lipid metabolism through controlling Per2 expression. J Lipid Res 2014; 56:227-40. [PMID: 25514904 DOI: 10.1194/jlr.m050724] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Hepatic lipid metabolism is controlled by integrated metabolic pathways. Excess accumulation of hepatic TG is a hallmark of nonalcoholic fatty liver disease, which is associated with obesity and insulin resistance. Here, we show that KH-type splicing regulatory protein (KSRP) ablation reduces hepatic TG levels and diet-induced hepatosteatosis. Expression of period 2 (Per2) is increased during the dark period, and circadian oscillations of several core clock genes are altered with a delayed phase in Ksrp(-/-) livers. Diurnal expression of some lipid metabolism genes is also disturbed with reduced expression of genes involved in de novo lipogenesis. Using primary hepatocytes, we demonstrate that KSRP promotes decay of Per2 mRNA through an RNA-protein interaction and show that increased Per2 expression is responsible for the phase delay in cycling of several clock genes in the absence of KSRP. Similar to Ksrp(-/-) livers, both expression of lipogenic genes and intracellular TG levels are also reduced in Ksrp(-/-) hepatocytes due to increased Per2 expression. Using heterologous mRNA reporters, we show that the AU-rich element-containing 3' untranslated region of Per2 is responsible for KSRP-dependent mRNA decay. These findings implicate that KSRP is an important regulator of circadian expression of lipid metabolism genes in the liver likely through controlling Per2 mRNA stability.
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Affiliation(s)
- Chu-Fang Chou
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Xiaolin Zhu
- Department of Nutrition Sciences, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Yi-Yu Lin
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Karen L Gamble
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294
| | - W Timothy Garvey
- Department of Nutrition Sciences, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Ching-Yi Chen
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294
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Xiong H, Yang Y, Hu XP, He YM, Ma BG. Sequence determinants of prokaryotic gene expression level under heat stress. Gene 2014; 551:92-102. [PMID: 25168890 DOI: 10.1016/j.gene.2014.08.049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Accepted: 08/25/2014] [Indexed: 10/24/2022]
Abstract
Prokaryotic gene expression is environment-dependent and temperature plays an important role in shaping the gene expression profile. Revealing the regulation mechanisms of gene expression pertaining to temperature has attracted tremendous efforts in recent years particularly owning to the yielding of transcriptome and proteome data by high-throughput techniques. However, most of the previous works concentrated on the characterization of the gene expression profile of individual organism and little effort has been made to disclose the commonality among organisms, especially for the gene sequence features. In this report, we collected the transcriptome and proteome data measured under heat stress condition from recently published literature and studied the sequence determinants for the expression level of heat-responsive genes on multiple layers. Our results showed that there indeed exist commonness and consistent patterns of the sequence features among organisms for the differentially expressed genes under heat stress condition. Some features are attributed to the requirement of thermostability while some are dominated by gene function. The revealed sequence determinants of bacterial gene expression level under heat stress complement the knowledge about the regulation factors of prokaryotic gene expression responding to the change of environmental conditions. Furthermore, comparisons to thermophilic adaption have been performed to reveal the similarity and dissimilarity of the sequence determinants for the response to heat stress and for the adaption to high habitat temperature, which elucidates the complex landscape of gene expression related to the same physical factor of temperature.
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Affiliation(s)
- Heng Xiong
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yi Yang
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiao-Pan Hu
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yi-Ming He
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Bin-Guang Ma
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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Hu W, Wang H, Huang H. Analysis of gene expression and preliminary study of methylation about 11β-HSD2 gene in placentas of Chinese pre-eclampsia patients of Han ethnicity. J Obstet Gynaecol Res 2014; 41:343-9. [PMID: 25331012 DOI: 10.1111/jog.12555] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 07/25/2014] [Indexed: 02/02/2023]
Abstract
AIMS The aim of this study was to determine the promoter methylation status of type 2 isoform of 11β-hydroxysteroid dehydrogenase (11β-HSD2) and its regulatory correlation with 11β-HSD2 gene expression in placentas of pre-eclampsia (PE) patients of Chinese Han ethnicity. MATERIAL AND METHODS The pathological features of placental tissues were studied using hematoxylin-eosin staining and immunohistochemical staining. The 11β-HSD2 mRNA and protein expressions were detected by real-time polymerase chain reaction and Western blotting. The methylation of the 11β-HSD2 promoter sequence was examined by bisulfite sequencing polymerase chain reaction. RESULTS Trophoblast hyperplasia and discontinuous syncytial layer were observed in the PE group, and the 11β-HSD2 was distributed irregularly and its immunoreactivity was weakened distinctly. The expressions of 11β-HSD2 mRNA and protein decreased significantly in the PE group compared with the control group. Unexpectedly, almost no 11β-HSD2 methylation was detected in PE placental tissue (two fragments, 0.6% vs 0%) or normal placental tissue (1% vs 0.6%). No significant difference in 11β-HSD2 promoter methylation was found between the two groups. CONCLUSIONS The 11β-HSD2 expression decreased in PE women of Chinese Han ethnicity, but was not interrelated with the promoter methylation status.
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Affiliation(s)
- Wensheng Hu
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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Expression of gene, protein and immunohistochemical localization of the estrogen receptor isoform ERα1 in male rainbow trout lymphoid organs; indication of the role of estrogens in the regulation of immune mechanisms. Comp Biochem Physiol B Biochem Mol Biol 2014; 174:53-61. [DOI: 10.1016/j.cbpb.2014.06.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 04/19/2014] [Accepted: 06/08/2014] [Indexed: 11/22/2022]
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Abstract
Our laboratory has contributed to the areas of B cell receptor (BCR) and pre-BCR gene identification and transcription and has focused on the problem of the aged immune system in mice and humans for the last 15 years. We have found biomarkers for the decrease in B cell function in aged mice and humans. These include decreases in immunoglobulin (Ig) class switch (e.g., IgM to IgG), decreases in the enzyme AID (activation-induced cytidine deaminase) and decreases in the transcription factor E47. The E47 mRNA stability is decreased in old B cells due to decreased phospho-MAPKinase and phospho-TTP (tristetraprolin). Inflammation, e.g., TNF-α, which increases with age, impacts B cells directly by increasing their TNF-α and NF-κB and leads to the above decreased pathway. Both class switch and affinity maturation are decreased in elderly responses to the influenza vaccine and biomarkers we have found (numbers and percentages of switched memory B cells and AID in stimulated B cells in culture) can predict a beneficial or decreased immune response to the vaccine. Current and future avenues to improve the humoral immune response in the elderly are discussed.
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Affiliation(s)
- Bonnie B Blomberg
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, RMSB #3146A, P.O. Box 016960 (R-138), Miami, FL, 33101, USA,
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Sasaki T, Nakata R, Inoue H, Shimizu M, Inoue J, Sato R. Role of AMPK and PPARγ1 in exercise-induced lipoprotein lipase in skeletal muscle. Am J Physiol Endocrinol Metab 2014; 306:E1085-92. [PMID: 24644240 DOI: 10.1152/ajpendo.00691.2013] [Citation(s) in RCA: 32] [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: 02/06/2023]
Abstract
Exercise can effectively ameliorate type 2 diabetes and insulin resistance. Here we show that the mRNA levels of one of peroxisome proliferator-activated receptor (PPAR) family members, PPARγ1, and genes related to energy metabolism, including PPARγ coactivator-1 protein-1α (PGC-1α) and lipoprotein lipase (LPL), increased in the gastrocnemius muscle of habitual exercise-trained mice. When mice were intraperitoneally administered an AMP-activated protein kinase (AMPK) activator 5-aminoimidazole-4-carboxamide ribonucleoside (AICAR), the mRNA levels of the aforementioned three genes increased in gastrocnemius muscle. AICAR treatment to C2C12 differentiated myotubes also increased PPARγ1 mRNA levels, but not PPARα and -δ mRNA levels, concomitant with increased PGC-1α mRNA levels. An AMPK inhibitor, compound C, blocked these AICAR effects. AICAR treatment increased the half-life of PPARγ1 mRNA nearly threefold (4-12 h) by activating AMPK. When C2C12 myoblast cells infected with a PPARγ1 expression lentivirus were differentiated into myotubes, PPARγ1 overexpression dramatically increased LPL mRNA levels more than 40-fold. In contrast, when PPARγ1 expression was suppressed in C2C12 myotubes, LPL mRNA levels were significantly reduced, and the effect of AICAR on increased LPL gene expression was almost completely blocked. These results indicated that PPARγ1 was intimately involved in LPL gene expression in skeletal muscle and the AMPK-PPARγ1 pathway may play a role in exercise-induced LPL expression. Thus, we identified a novel critical role for PPARγ1 in response to AMPK activation for controlling the expression of a subset of genes associated with metabolic regulation in skeletal muscle.
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Affiliation(s)
- Takashi Sasaki
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan; and
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Mezan S, Ashwal-Fluss R, Shenhav R, Garber M, Kadener S. Genome-wide assessment of post-transcriptional control in the fly brain. Front Mol Neurosci 2013; 6:49. [PMID: 24367289 PMCID: PMC3856366 DOI: 10.3389/fnmol.2013.00049] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 11/20/2013] [Indexed: 11/13/2022] Open
Abstract
Post-transcriptional control of gene expression has central importance during development and adulthood and in physiology in general. However, little is known about the extent of post-transcriptional control of gene expression in the brain. Most post-transcriptional regulatory effectors (e.g., miRNAs) destabilize target mRNAs by shortening their polyA tails. Hence, the fraction of a given mRNA that it is fully polyadenylated should correlate with its stability and serves as a good measure of post-transcriptional control. Here, we compared RNA-seq datasets from fly brains that were generated either from total (rRNA-depleted) or polyA-selected RNA. By doing this comparison we were able to compute a coefficient that measures the extent of post-transcriptional control for each brain-expressed mRNA. In agreement with current knowledge, we found that mRNAs encoding ribosomal proteins, metabolic enzymes, and housekeeping genes are among the transcripts with least post-transcriptional control, whereas mRNAs that are known to be highly unstable, like circadian mRNAs and mRNAs expressing synaptic proteins and proteins with neuronal functions, are under strong post-transcriptional control. Surprisingly, the latter group included many specific groups of genes relevant to brain function and behavior. In order to determine the importance of miRNAs in this regulation, we profiled miRNAs from fly brains using oligonucleotide microarrays. Surprisingly, we did not find a strong correlation between the expression levels of miRNAs in the brain and the stability of their target mRNAs; however, genes identified as highly regulated post-transcriptionally were strongly enriched for miRNA targets. This demonstrates a central role of miRNAs for modulating the levels and turnover of brain-specific mRNAs in the fly.
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Affiliation(s)
- Shaul Mezan
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem Jerusalem, Israel
| | - Reut Ashwal-Fluss
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem Jerusalem, Israel
| | - Rom Shenhav
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem Jerusalem, Israel
| | - Manuel Garber
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School Worcester, MA, USA
| | - Sebastian Kadener
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem Jerusalem, Israel
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Chou CF, Lin WJ, Lin CC, Luber CA, Godbout R, Mann M, Chen CY. DEAD box protein DDX1 regulates cytoplasmic localization of KSRP. PLoS One 2013; 8:e73752. [PMID: 24023901 PMCID: PMC3762726 DOI: 10.1371/journal.pone.0073752] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 07/22/2013] [Indexed: 11/19/2022] Open
Abstract
mRNA decay mediated by the AU-rich elements (AREs) is one of the most studied post-transcriptional mechanisms and is modulated by ARE-binding proteins (ARE-BPs). To understand the regulation of K homology splicing regulatory protein (KSRP), a decay-promoting ARE-BP, we purified KSRP protein complexes and identified an RNA helicase, DDX1. We showed that down-regulation of DDX1 expression elevated cytoplasmic levels of KSRP and facilitated ARE-mediated mRNA decay. Association of KSRP with 14-3-3 proteins, that are predominately located in the cytoplasm, increased upon reduction of DDX1. We also demonstrated that KSRP associated with DDX1 or 14-3-3, but not both. These observations indicate that subcellular localization of KSRP is regulated by competing interactions with DDX1 or 14-3-3.
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Affiliation(s)
- Chu-Fang Chou
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Wei-Jye Lin
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Chen-Chung Lin
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Christian A. Luber
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Roseline Godbout
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Alberta, Canada
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Ching-Yi Chen
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- * E-mail:
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Chang YT, Lin CY, Tsai CY, Siva VS, Chu CY, Tsai HJ, Song YL. The new face of the old molecules: crustin Pm4 and transglutaminase type I serving as rnps down-regulate astakine-mediated hematopoiesis. PLoS One 2013; 8:e72793. [PMID: 24013515 PMCID: PMC3754954 DOI: 10.1371/journal.pone.0072793] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 07/12/2013] [Indexed: 12/31/2022] Open
Abstract
Astakine is an important cytokine that is involved in crustacean hematopoiesis. Interestingly, the protein levels of astakine increased dramatically in plasma of LPS-injected shrimp while mRNA levels remained unchanged. Here, we investigated the involvement of astakine 3'-untranslated region (UTR) in its protein expression. The 3'-UTR of astakine down-regulated the expression of reporter protein but the mRNA stability of reporter gene was unaffected. We identified the functional regulatory elements of astakine 3'-UTR, where 3'-UTR242-483 acted as repressor. The electrophoresis mobility shift assay (EMSA), RNA pull-down assay and LC/MS/MS were performed to identify the protein association. We noted that crustin Pm4 and shrimp transglutaminase I (STG I) were associated to astakine 3'-UTR242-483, while two other proteins have yet to be revealed. Depletion of hemocytic crustin Pm4 and STG I significantly increased the protein level of astakine while astakine mRNA level remained unaffected. Lipopolysaccharide (LPS) stimulated the secretion of crustin Pm4 and STG I from hemocytes to plasma and increased the astakine level to stimulate the hemocytes proliferation. Altogether, we identified the shrimp crustin Pm4 and STG I as novel RNA binding proteins that play an important role in down-regulating astakine expression at post-transcriptional level and are crucial for the maintenance of hematopoiesis.
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Affiliation(s)
- Yun-Tsan Chang
- Institute of Zoology, National Taiwan University, Taipei, Taiwan, ROC
| | - Cheng-Yung Lin
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan, ROC
| | - Che-Yiang Tsai
- Institute of Zoology, National Taiwan University, Taipei, Taiwan, ROC
| | - Vinu S. Siva
- Institute of Zoology, National Taiwan University, Taipei, Taiwan, ROC
| | - Chia-Ying Chu
- Institute of Zoology, National Taiwan University, Taipei, Taiwan, ROC
- Department of Life Science, National Taiwan University, Taipei, Taiwan, ROC
| | - Huai-Jen Tsai
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan, ROC
- Department of Life Science, National Taiwan University, Taipei, Taiwan, ROC
| | - Yen-Ling Song
- Institute of Zoology, National Taiwan University, Taipei, Taiwan, ROC
- Department of Life Science, National Taiwan University, Taipei, Taiwan, ROC
- * E-mail:
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Krol K, Morozov IY, Jones MG, Wyszomirski T, Weglenski P, Dzikowska A, Caddick MX. RrmA regulates the stability of specific transcripts in response to both nitrogen source and oxidative stress. Mol Microbiol 2013; 89:975-88. [PMID: 23841692 PMCID: PMC4282371 DOI: 10.1111/mmi.12324] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2013] [Indexed: 01/10/2023]
Abstract
Differential regulation of transcript stability is an effective means by which an organism can modulate gene expression. A well-characterized example is glutamine signalled degradation of specific transcripts in Aspergillus nidulans. In the case of areA, which encodes a wide-domain transcription factor mediating nitrogen metabolite repression, the signal is mediated through a highly conserved region of the 3′ UTR. Utilizing this RNA sequence we isolated RrmA, an RNA recognition motif protein. Disruption of the respective gene led to loss of both glutamine signalled transcript degradation as well as nitrate signalled stabilization of niaD mRNA. However, nitrogen starvation was shown to act independently of RrmA in stabilizing certain transcripts. RrmA was also implicated in the regulation of arginine catabolism gene expression and the oxidative stress responses at the level of mRNA stability. ΔrrmA mutants are hypersensitive to oxidative stress. This phenotype correlates with destabilization of eifE and dhsA mRNA. eifE encodes eIF5A, a translation factor within which a conserved lysine is post-translationally modified to hypusine, a process requiring DhsA. Intriguingly, for specific transcripts RrmA mediates both stabilization and destabilization and the specificity of the signals transduced is transcript dependent, suggesting it acts in consort with other factors which differ between transcripts.
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Affiliation(s)
- Kinga Krol
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, ul. Pawińskiego 5A, 02-106, Warsaw, Poland
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Downregulation of Nipah virus N mRNA occurs through interaction between its 3' untranslated region and hnRNP D. J Virol 2013; 87:6582-8. [PMID: 23514888 DOI: 10.1128/jvi.02495-12] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nipah virus (NiV) is a nonsegmented, single-stranded, negative-sense RNA virus belonging to the genus Henipavirus, family Paramyxoviridae. NiV causes acute encephalitis and respiratory disease in humans, is associated with high mortality, and poses a threat in southern Asia. The genomes of henipaviruses are about 18,246 nucleotides (nt) long, which is longer than those of other paramyxoviruses (around 15,384 nt). This difference is caused by the noncoding RNA region, particularly the 3' untranslated region (UTR), which occupies more than half of the noncoding RNA region. To determine the function(s) of the NiV noncoding RNA region, we investigated the effects of NiV 3' UTRs on reporter gene expression. The NiV N 3' UTR (nt 1 to 100) demonstrated strong repressor activity associated with hnRNP D protein binding to that region. Mutation of the hnRNP D binding site or knockdown of hnRNP D resulted in increased expression of the NiV N 3' UTR reporter. Our findings suggest that NiV N expression is repressed by hnRNP D through the NiV N 3' UTR and demonstrate the involvement of posttranscriptional regulation in the NiV life cycle. To the best of our knowledge, this provides the first report of the functions of the NiV noncoding RNA region.
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Wang H, Zeng F, Liu Q, Liu H, Liu Z, Niu L, Teng M, Li X. The structure of the ARE-binding domains of Hu antigen R (HuR) undergoes conformational changes during RNA binding. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:373-80. [PMID: 23519412 DOI: 10.1107/s0907444912047828] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 11/21/2012] [Indexed: 11/11/2022]
Abstract
Human RNA-binding protein (HuR), a ubiquitously expressed member of the Hu protein family, plays an important role in mRNA degradation and has been implicated as a key post-transcriptional regulator. HuR contains three RNA-recognition motif (RRM) domains. The two N-terminal tandem RRM domains can selectively bind AU-rich elements (AREs), while the third RRM domain (RRM3) contributes to interactions with the poly-A tail of target mRNA and other ligands. Here, the X-ray structure of two methylated tandem RRM domains (RRM1/2) of HuR in their RNA-free form was solved at 2.9 Å resolution. The crystal structure of RRM1/2 complexed with target mRNA was also solved at 2.0 Å resolution; comparisons of the two structures show that HuR RRM1/2 undergoes conformational changes upon RNA binding. Fluorescence polarization assays (FPA) were used to study the protein-RNA interactions. Both the structure and the FPA analysis indicated that RRM1 is the primary ARE-binding domain in HuR and that the conformational changes induce subsequent contacts of the RNA substrate with the inter-domain linker and RRM2 which greatly improve the RNA-binding affinity of HuR.
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Affiliation(s)
- Hong Wang
- School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China
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Interaction of Human Genes WT1 and CML28 in Leukemic Cells. ACTA ACUST UNITED AC 2013; 33:37-42. [DOI: 10.1007/s11596-013-1068-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Indexed: 10/27/2022]
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Yashiro T, Nanmoku M, Shimizu M, Inoue J, Sato R. 5-Aminoimidazole-4-carboxamide ribonucleoside stabilizes low density lipoprotein receptor mRNA in hepatocytes via ERK-dependent HuR binding to an AU-rich element. Atherosclerosis 2013; 226:95-101. [DOI: 10.1016/j.atherosclerosis.2012.09.033] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2012] [Revised: 08/23/2012] [Accepted: 09/24/2012] [Indexed: 10/27/2022]
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Damgaard CK, Lykke-Andersen J. Regulation of ARE-mRNA Stability by Cellular Signaling: Implications for Human Cancer. Cancer Treat Res 2013; 158:153-80. [PMID: 24222358 DOI: 10.1007/978-3-642-31659-3_7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
During recent years, it has become clear that regulation of mRNA stability is an important event in the control of gene expression. The stability of a large class of mammalian mRNAs is regulated by AU-rich elements (AREs) located in the mRNA 3' UTRs. mRNAs with AREs are inherently labile but as a response to different cellular cues they can become either stabilized, allowing expression of a given gene, or further destabilized to silence their expression. These tightly regulated mRNAs include many that encode growth factors, proto-oncogenes, cytokines, and cell cycle regulators. Failure to properly regulate their stability can therefore lead to uncontrolled expression of factors associated with cell proliferation and has been implicated in several human cancers. A number of transfactors that recognize AREs and regulate the translation and degradation of ARE-mRNAs have been identified. These transfactors are regulated by signal transduction pathways, which are often misregulated in cancers. This chapter focuses on the function of ARE-binding proteins with an emphasis on their regulation by signaling pathways and the implications for human cancer.
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