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Rossi IV, de Souza DAS, Ramirez MI. The End Justifies the Means: Chagas Disease from a Perspective of the Host- Trypanosoma cruzi Interaction. Life (Basel) 2024; 14:488. [PMID: 38672758 PMCID: PMC11050810 DOI: 10.3390/life14040488] [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: 02/19/2024] [Revised: 04/03/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
The neglected Chagas disease (CD) is caused by the protozoan parasite Trypanosoma cruzi. Despite CD dispersion throughout the world, it prevails in tropical areas affecting mainly poor communities, causing devastating health, social and economic consequences. Clinically, CD is marked by a mildly symptomatic acute phase, and a chronic phase characterized by cardiac and/or digestive complications. Current treatment for CD relies on medications with strong side effects and reduced effectiveness. The complex interaction between the parasite and the host outlines the etiology and progression of CD. The unique characteristics and high adaptability of T. cruzi, its mechanisms of persistence, and evasion of the immune system seem to influence the course of the disease. Despite the efforts to uncover the pathology of CD, there are many gaps in understanding how it is established and reaches chronicity. Also, the lack of effective treatments and protective vaccines constitute challenges for public health. Here, we explain the background in which CD is established, from the peculiarities of T. cruzi molecular biology to the development of the host's immune response leading to the pathophysiology of CD. We also discuss the state of the art of treatments for CD and current challenges in basic and applied science.
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Affiliation(s)
- Izadora Volpato Rossi
- Graduate Program in Microbiology, Parasitology and Pathology, Federal University of Paraná, Curitiba 81531-980, PR, Brazil;
- Laboratory of Cell Biology, Carlos Chagas Institute/Oswaldo Cruz Foundation (FIOCRUZ-PR), Curitiba 81310-020, PR, Brazil;
| | - Denise Andréa Silva de Souza
- Laboratory of Cell Biology, Carlos Chagas Institute/Oswaldo Cruz Foundation (FIOCRUZ-PR), Curitiba 81310-020, PR, Brazil;
| | - Marcel Ivan Ramirez
- Graduate Program in Microbiology, Parasitology and Pathology, Federal University of Paraná, Curitiba 81531-980, PR, Brazil;
- Laboratory of Cell Biology, Carlos Chagas Institute/Oswaldo Cruz Foundation (FIOCRUZ-PR), Curitiba 81310-020, PR, Brazil;
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2
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Letelier P, Saldías R, Loren P, Riquelme I, Guzmán N. MicroRNAs as Potential Biomarkers of Environmental Exposure to Polycyclic Aromatic Hydrocarbons and Their Link with Inflammation and Lung Cancer. Int J Mol Sci 2023; 24:16984. [PMID: 38069307 PMCID: PMC10707120 DOI: 10.3390/ijms242316984] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/26/2023] [Accepted: 10/28/2023] [Indexed: 12/18/2023] Open
Abstract
Exposure to atmospheric air pollution containing volatile organic compounds such as polycyclic aromatic hydrocarbons (PAHs) has been shown to be a risk factor in the induction of lung inflammation and the initiation and progression of lung cancer. MicroRNAs (miRNAs) are small single-stranded non-coding RNA molecules of ~20-22 nucleotides that regulate different physiological processes, and their altered expression is implicated in various pathophysiological conditions. Recent studies have shown that the regulation of gene expression of miRNAs can be affected in diseases associated with outdoor air pollution, meaning they could also be useful as biomarkers of exposure to environmental pollution. In this article, we review the published evidence on miRNAs in relation to exposure to PAH pollution and discuss the possible mechanisms that may link these compounds with the expression of miRNAs.
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Affiliation(s)
- Pablo Letelier
- Laboratorio de Investigación en Salud de Precisión, Departamento de Procesos Diagnósticos y Evaluación, Facultad de Ciencias de la Salud, Universidad Católica de Temuco, Temuco 4813302, Chile; (R.S.); (N.G.)
| | - Rolando Saldías
- Laboratorio de Investigación en Salud de Precisión, Departamento de Procesos Diagnósticos y Evaluación, Facultad de Ciencias de la Salud, Universidad Católica de Temuco, Temuco 4813302, Chile; (R.S.); (N.G.)
| | - Pía Loren
- Center of Molecular Biology and Pharmacogenetics, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile;
| | - Ismael Riquelme
- Institute of Biomedical Sciences, Faculty of Health Sciences, Universidad Autónoma de Chile, Temuco 4810101, Chile;
| | - Neftalí Guzmán
- Laboratorio de Investigación en Salud de Precisión, Departamento de Procesos Diagnósticos y Evaluación, Facultad de Ciencias de la Salud, Universidad Católica de Temuco, Temuco 4813302, Chile; (R.S.); (N.G.)
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3
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Martinez De La Cruz B, Darsinou M, Riccio A. From form to function: m 6A methylation links mRNA structure to metabolism. Adv Biol Regul 2023; 87:100926. [PMID: 36513580 PMCID: PMC10585597 DOI: 10.1016/j.jbior.2022.100926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/17/2022] [Accepted: 11/03/2022] [Indexed: 11/19/2022]
Abstract
Reversible N6-methyladenosine (m6A) RNA modification is a posttranscriptional epigenetic modification of the RNA that regulates many key aspects of RNA metabolism and function. In this review, we highlight major recent advances in the field, with special emphasis on the potential link between m6A modifications and RNA structure. We will also discuss the role of RNA methylation of neuronal transcripts, and the emerging evidence of a potential role in RNA transport and local translation in dendrites and axons of transcripts involved in synaptic functions and axon growth.
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Affiliation(s)
| | - Marousa Darsinou
- UCL Laboratory for Molecular Cell Biology - University College London, Gower Street, WC1E 6BT, London, UK
| | - Antonella Riccio
- UCL Laboratory for Molecular Cell Biology - University College London, Gower Street, WC1E 6BT, London, UK.
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4
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Nst1, Densely Associated to P-Body in the Post-Exponential Phases of Saccharomyces cerevisiae, Shows an Intrinsic Potential of Producing Liquid-Like Condensates of P-Body Components in Cells. Int J Mol Sci 2022; 23:ijms23052501. [PMID: 35269643 PMCID: PMC8910029 DOI: 10.3390/ijms23052501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/17/2022] [Accepted: 02/22/2022] [Indexed: 12/19/2022] Open
Abstract
Membrane-less biomolecular compartmentalization is a core phenomenon involved in many physiological activities that occur ubiquitously in cells. Condensates, such as promyelocytic leukemia (PML) bodies, stress granules, and P-bodies (PBs), have been investigated to understand the process of membrane-less cellular compartmentalization. In budding yeast, PBs dispersed in the cytoplasm of exponentially growing cells rapidly accumulate in response to various stresses such as osmotic stress, glucose deficiency, and heat stress. In addition, cells start to accumulate PBs chronically in post-exponential phases. Specific protein-protein interactions are involved in accelerating PB accumulation in each circumstance, and discovering the regulatory mechanism for each is the key to understanding cellular condensation. Here, we demonstrate that Nst1 of budding yeast Saccharomyces cerevisiae is far more densely associated with PBs in post-exponentially growing phases from the diauxic shift to the stationary phase than during glucose deprivation of exponentially growing cells, while the PB marker Dcp2 exhibits a similar degree of condensation under these conditions. Similar to Edc3, ectopic Nst1 overexpression induces self-condensation and the condensation of other PB components, such as Dcp2 and Dhh1, which exhibit liquid-like properties. Altogether, these results suggest that Nst1 has the intrinsic potential for self-condensation and the condensation of other PB components, specifically in post-exponential phases.
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5
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Wu YFO, Bryant AT, Nelson NT, Madey AG, Fernandes GF, Goodson HV. Overexpression of the microtubule-binding protein CLIP-170 induces a +TIP network superstructure consistent with a biomolecular condensate. PLoS One 2021; 16:e0260401. [PMID: 34890409 PMCID: PMC8664194 DOI: 10.1371/journal.pone.0260401] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 11/09/2021] [Indexed: 12/02/2022] Open
Abstract
Proper regulation of microtubule (MT) dynamics is critical for cellular processes including cell division and intracellular transport. Plus-end tracking proteins (+TIPs) dynamically track growing MTs and play a key role in MT regulation. +TIPs participate in a complex web of intra- and inter- molecular interactions known as the +TIP network. Hypotheses addressing the purpose of +TIP:+TIP interactions include relieving +TIP autoinhibition and localizing MT regulators to growing MT ends. In addition, we have proposed that the web of +TIP:+TIP interactions has a physical purpose: creating a dynamic scaffold that constrains the structural fluctuations of the fragile MT tip and thus acts as a polymerization chaperone. Here we examine the possibility that this proposed scaffold is a biomolecular condensate (i.e., liquid droplet). Many animal +TIP network proteins are multivalent and have intrinsically disordered regions, features commonly found in biomolecular condensates. Moreover, previous studies have shown that overexpression of the +TIP CLIP-170 induces large “patch” structures containing CLIP-170 and other +TIPs; we hypothesized that these structures might be biomolecular condensates. To test this hypothesis, we used video microscopy, immunofluorescence staining, and Fluorescence Recovery After Photobleaching (FRAP). Our data show that the CLIP-170-induced patches have hallmarks indicative of a biomolecular condensate, one that contains +TIP proteins and excludes other known condensate markers. Moreover, bioinformatic studies demonstrate that the presence of intrinsically disordered regions is conserved in key +TIPs, implying that these regions are functionally significant. Together, these results indicate that the CLIP-170 induced patches in cells are phase-separated liquid condensates and raise the possibility that the endogenous +TIP network might form a liquid droplet at MT ends or other +TIP locations.
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Affiliation(s)
- Yueh-Fu O. Wu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States of America
- Integrated Biomedical Sciences Graduate Program, University of Notre Dame, Notre Dame, IN, United States of America
| | - Annamarie T. Bryant
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States of America
- Integrated Biomedical Sciences Graduate Program, University of Notre Dame, Notre Dame, IN, United States of America
| | - Nora T. Nelson
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States of America
| | - Alexander G. Madey
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States of America
| | - Gail F. Fernandes
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States of America
| | - Holly V. Goodson
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States of America
- Integrated Biomedical Sciences Graduate Program, University of Notre Dame, Notre Dame, IN, United States of America
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States of America
- * E-mail:
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6
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Pérez TD, Quintana A, De Lora JA, Shreve AP, López GP, Carroll NJ. DNA Binding by an Intrinsically Disordered Elastin-like Polypeptide for Assembly of Phase Separated Nucleoprotein Coacervates. Ind Eng Chem Res 2021. [DOI: 10.1021/acs.iecr.1c02823] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Telmo Díez Pérez
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, New Mexico 87131, United States,
- Center for Micro-Engineered Materials, University of New Mexico, Albuquerque, New Mexico 87131, United States,
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, New Mexico 87131, United States, and
| | - Adam Quintana
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, New Mexico 87131, United States, and
| | - Jacqueline A. De Lora
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, New Mexico 87131, United States,
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, New Mexico 87131, United States, and
- Max Planck Institute for Medical Research, Department of Cellular Biophysics, Heidelberg, 69120, Germany
| | - Andrew P. Shreve
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, New Mexico 87131, United States,
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, New Mexico 87131, United States, and
| | - Gabriel P. López
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, New Mexico 87131, United States,
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, New Mexico 87131, United States, and
| | - Nick J. Carroll
- Center for Micro-Engineered Materials, University of New Mexico, Albuquerque, New Mexico 87131, United States,
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, New Mexico 87131, United States, and
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7
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Liu XM, Ma L, Schekman R. Selective sorting of microRNAs into exosomes by phase-separated YBX1 condensates. eLife 2021; 10:71982. [PMID: 34766549 PMCID: PMC8612733 DOI: 10.7554/elife.71982] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 11/09/2021] [Indexed: 12/15/2022] Open
Abstract
Exosomes may mediate cell-to-cell communication by transporting various proteins and nucleic acids to neighboring cells. Some protein and RNA cargoes are significantly enriched in exosomes. How cells efficiently and selectively sort them into exosomes remains incompletely explored. Previously, we reported that YBX1 is required in sorting of miR-223 into exosomes. Here, we show that YBX1 undergoes liquid-liquid phase separation (LLPS) in vitro and in cells. YBX1 condensates selectively recruit miR-223 in vitro and into exosomes secreted by cultured cells. Point mutations that inhibit YBX1 phase separation impair the incorporation of YBX1 protein into biomolecular condensates formed in cells, and perturb miR-233 sorting into exosomes. We propose that phase separation-mediated local enrichment of cytosolic RNA-binding proteins and their cognate RNAs enables their targeting and packaging by vesicles that bud into multivesicular bodies. This provides a possible mechanism for efficient and selective engulfment of cytosolic proteins and RNAs into intraluminal vesicles which are then secreted as exosomes from cells.
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Affiliation(s)
- Xiao-Man Liu
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Liang Ma
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Randy Schekman
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
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8
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Zhang Y, Wang K, Yang K, Shi Y, Hong J. Insight into the interaction between the RNA helicase CGH-1 and EDC-3 and its implications. Sci Rep 2021; 11:20359. [PMID: 34645931 PMCID: PMC8514580 DOI: 10.1038/s41598-021-99919-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 09/30/2021] [Indexed: 12/03/2022] Open
Abstract
Previous studies indicated that the P-body components, CGH-1 and EDC-3 may play a crucial role in the regulation of lifespan in Caenorhabditis elegans. Homo sapiens DDX6 or Saccharomyces cerevisiae Dhh1p (CGH-1 in C. elegans) could form complexes with EDC3 (Edc3p in yeast), respectively, which is significant for translation inhibition and mRNA decay. However, it is currently unclear how CGH-1 can be recognized by EDC-3 in C. elegans. Here, we provided structural and biochemical insights into the interaction between CGH-1 and EDC-3. Combined with homology modeling, mutation, and ITC assays, we uncovered an interface between CGH-1 RecA2 domain and EDC-3 FDF-FEK. Additionally, GST-pulldown and co-localization experiments confirmed the interaction between CGH-1 and EDC-3 in vitro and in vivo. We also analyzed PATR-1-binding interface on CGH-1 RecA2 by ITC assays. Moreover, we unveiled the similarity and differences of the binding mode between EDC-3 and CAR-1 or PATR-1. Taken together, these findings provide insights into the recognition of DEAD-box protein CGH-1 by EDC-3 FDF-FEK motif, suggesting important functional implications.
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Affiliation(s)
- Yong Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, Hefei, People's Republic of China
| | - Ke Wang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, Hefei, People's Republic of China
| | - Kanglong Yang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, Hefei, People's Republic of China
| | - Yunyu Shi
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, Hefei, People's Republic of China
| | - Jingjun Hong
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China.
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China, Hefei, People's Republic of China.
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9
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Castelli LM, Cutillo L, Souza CDS, Sanchez-Martinez A, Granata I, Lin YH, Myszczynska MA, Heath PR, Livesey MR, Ning K, Azzouz M, Shaw PJ, Guarracino MR, Whitworth AJ, Ferraiuolo L, Milo M, Hautbergue GM. SRSF1-dependent inhibition of C9ORF72-repeat RNA nuclear export: genome-wide mechanisms for neuroprotection in amyotrophic lateral sclerosis. Mol Neurodegener 2021; 16:53. [PMID: 34376242 PMCID: PMC8353793 DOI: 10.1186/s13024-021-00475-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 07/16/2021] [Indexed: 12/13/2022] Open
Abstract
Background Loss of motor neurons in amyotrophic lateral sclerosis (ALS) leads to progressive paralysis and death. Dysregulation of thousands of RNA molecules with roles in multiple cellular pathways hinders the identification of ALS-causing alterations over downstream changes secondary to the neurodegenerative process. How many and which of these pathological gene expression changes require therapeutic normalisation remains a fundamental question. Methods Here, we investigated genome-wide RNA changes in C9ORF72-ALS patient-derived neurons and Drosophila, as well as upon neuroprotection taking advantage of our gene therapy approach which specifically inhibits the SRSF1-dependent nuclear export of pathological C9ORF72-repeat transcripts. This is a critical study to evaluate (i) the overall safety and efficacy of the partial depletion of SRSF1, a member of a protein family involved itself in gene expression, and (ii) a unique opportunity to identify neuroprotective RNA changes. Results Our study shows that manipulation of 362 transcripts out of 2257 pathological changes, in addition to inhibiting the nuclear export of repeat transcripts, is sufficient to confer neuroprotection in C9ORF72-ALS patient-derived neurons. In particular, expression of 90 disease-altered transcripts is fully reverted upon neuroprotection leading to the characterisation of a human C9ORF72-ALS disease-modifying gene expression signature. These findings were further investigated in vivo in diseased and neuroprotected Drosophila transcriptomes, highlighting a list of 21 neuroprotective changes conserved with 16 human orthologues in patient-derived neurons. We also functionally validated the high neuroprotective potential of one of these disease-modifying transcripts, demonstrating that inhibition of ALS-upregulated human KCNN1–3 (Drosophila SK) voltage-gated potassium channel orthologs mitigates degeneration of human motor neurons and Drosophila motor deficits. Conclusions Strikingly, the partial depletion of SRSF1 leads to expression changes in only a small proportion of disease-altered transcripts, indicating that not all RNA alterations need normalization and that the gene therapeutic approach is safe in the above preclinical models as it does not disrupt globally gene expression. The efficacy of this intervention is also validated at genome-wide level with transcripts modulated in the vast majority of biological processes affected in C9ORF72-ALS. Finally, the identification of a characteristic signature with key RNA changes modified in both the disease state and upon neuroprotection also provides potential new therapeutic targets and biomarkers. Supplementary Information The online version contains supplementary material available at 10.1186/s13024-021-00475-y.
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Affiliation(s)
- Lydia M Castelli
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Luisa Cutillo
- School of Mathematics, University of Leeds, Leeds, LS2 9JT, UK
| | - Cleide Dos Santos Souza
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Alvaro Sanchez-Martinez
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK
| | - Ilaria Granata
- National Research Council of Italy, High Performance Computing and Networking Institute (ICAR-CNR), 111 Via Pietro Castellino, 80131, Naples, Italy
| | - Ya-Hui Lin
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Monika A Myszczynska
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Paul R Heath
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Matthew R Livesey
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK.,Neuroscience Institute, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Ke Ning
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK.,Neuroscience Institute, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Mimoun Azzouz
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK.,Neuroscience Institute, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Pamela J Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK.,Neuroscience Institute, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Mario R Guarracino
- National Research Council of Italy, High Performance Computing and Networking Institute (ICAR-CNR), 111 Via Pietro Castellino, 80131, Naples, Italy
| | - Alexander J Whitworth
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK
| | - Laura Ferraiuolo
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK.,Neuroscience Institute, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Marta Milo
- Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK. .,Present Address: AstraZeneca, Academy House, 136 Hills Road, Cambridge, CB2 8PA, UK.
| | - Guillaume M Hautbergue
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK. .,Neuroscience Institute, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
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10
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Cellular 5'-3' mRNA Exoribonuclease XRN1 Inhibits Interferon Beta Activation and Facilitates Influenza A Virus Replication. mBio 2021; 12:e0094521. [PMID: 34311580 PMCID: PMC8406323 DOI: 10.1128/mbio.00945-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Cellular 5′-3′ exoribonuclease 1 (XRN1) is best known for its role as a decay factor, which by degrading 5′ monophosphate RNA after the decapping of DCP2 in P-bodies (PBs) in Drosophila, yeast, and mammals. XRN1 has been shown to degrade host antiviral mRNAs following the influenza A virus (IAV) PA-X-mediated exonucleolytic cleavage processes. However, the mechanistic details of how XRN1 facilitates influenza A virus replication remain unclear. In this study, we discovered that XRN1 and nonstructural protein 1 (NS1) of IAV are directly associated and colocalize in the PBs. Moreover, XRN1 downregulation impaired viral replication while the viral titers were significantly increased in cells overexpressing XRN1, which suggest that XRN1 is a positive regulator in IAV life cycle. We further demonstrated that the IAV growth curve could be suppressed by adenosine 3′,5′-bisphosphate (pAp) treatment, an inhibitor of XRN1. In virus-infected XRN1 knockout cells, the phosphorylated interferon regulatory factor 3 (p-IRF3) protein, interferon beta (IFN-β) mRNA, and interferon-stimulated genes (ISGs) were significantly increased, resulting in the enhancement of the host innate immune response and suppression of viral protein production. Our data suggest a novel mechanism by which the IAV hijacks the cellular XRN1 to suppress the host innate immune response and to facilitate viral replication.
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11
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Emenecker RJ, Holehouse AS, Strader LC. Biological Phase Separation and Biomolecular Condensates in Plants. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:17-46. [PMID: 33684296 PMCID: PMC8221409 DOI: 10.1146/annurev-arplant-081720-015238] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
A surge in research focused on understanding the physical principles governing the formation, properties, and function of membraneless compartments has occurred over the past decade. Compartments such as the nucleolus, stress granules, and nuclear speckles have been designated as biomolecular condensates to describe their shared property of spatially concentrating biomolecules. Although this research has historically been carried out in animal and fungal systems, recent work has begun to explore whether these same principles are relevant in plants. Effectively understanding and studying biomolecular condensates require interdisciplinary expertise that spans cell biology, biochemistry, and condensed matter physics and biophysics. As such, some involved concepts may be unfamiliar to any given individual. This review focuses on introducing concepts essential to the study of biomolecular condensates and phase separation for biologists seeking to carry out research in this area and further examines aspects of biomolecular condensates that are relevant to plant systems.
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Affiliation(s)
- Ryan J Emenecker
- Department of Biology, Washington University, St. Louis, Missouri 63130, USA
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA;
- Center for Science and Engineering of Living Systems, Washington University, St. Louis, Missouri 63130, USA
- Center for Engineering MechanoBiology, Washington University, St. Louis, Missouri 63130, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA;
- Center for Science and Engineering of Living Systems, Washington University, St. Louis, Missouri 63130, USA
| | - Lucia C Strader
- Center for Science and Engineering of Living Systems, Washington University, St. Louis, Missouri 63130, USA
- Center for Engineering MechanoBiology, Washington University, St. Louis, Missouri 63130, USA
- Department of Biology, Duke University, Durham, North Carolina 27708, USA;
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12
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Müller L, Tunger A, Wobus M, von Bonin M, Towers R, Bornhäuser M, Dazzi F, Wehner R, Schmitz M. Immunomodulatory Properties of Mesenchymal Stromal Cells: An Update. Front Cell Dev Biol 2021; 9:637725. [PMID: 33634139 PMCID: PMC7900158 DOI: 10.3389/fcell.2021.637725] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/19/2021] [Indexed: 12/29/2022] Open
Abstract
Mesenchymal stromal cells (MSCs) are characterized by an extraordinary capacity to modulate the phenotype and functional properties of various immune cells that play an essential role in the pathogenesis of inflammatory disorders. Thus, MSCs efficiently impair the phagocytic and antigen-presenting capacity of monocytes/macrophages and promote the expression of immunosuppressive molecules such as interleukin (IL)-10 and programmed cell death 1 ligand 1 by these cells. They also effectively inhibit the maturation of dendritic cells and their ability to produce proinflammatory cytokines and to stimulate potent T-cell responses. Furthermore, MSCs inhibit the generation and proinflammatory properties of CD4+ T helper (Th)1 and Th17 cells, while they promote the proliferation of regulatory T cells and their inhibitory capabilities. MSCs also impair the expansion, cytokine secretion, and cytotoxic activity of proinflammatory CD8+ T cells. Moreover, MSCs inhibit the differentiation, proliferation, and antibody secretion of B cells, and foster the generation of IL-10-producing regulatory B cells. Various cell membrane-associated and soluble molecules essentially contribute to these MSC-mediated effects on important cellular components of innate and adaptive immunity. Due to their immunosuppressive properties, MSCs have emerged as promising tools for the treatment of inflammatory disorders such as acute graft-versus-host disease, graft rejection in patients undergoing organ/cell transplantation, and autoimmune diseases.
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Affiliation(s)
- Luise Müller
- Institute of Immunology, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Antje Tunger
- Institute of Immunology, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany.,National Center for Tumor Diseases (NCT), Partner Site Dresden, Dresden, Germany
| | - Manja Wobus
- Department of Medicine I, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Malte von Bonin
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Dresden, Germany.,Department of Medicine I, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany.,German Cancer Consortium (DKTK), Partner Site Dresden, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Russell Towers
- Department of Medicine I, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Martin Bornhäuser
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Dresden, Germany.,Department of Medicine I, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany.,German Cancer Consortium (DKTK), Partner Site Dresden, and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Center for Regenerative Therapies Dresden (CRTD), TU Dresden, Dresden, Germany
| | - Francesco Dazzi
- School of Cancer and Pharmacological Sciences and KHP Cancer Research UK Centre, King's College London, London, United Kingdom
| | - Rebekka Wehner
- Institute of Immunology, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany.,National Center for Tumor Diseases (NCT), Partner Site Dresden, Dresden, Germany.,German Cancer Consortium (DKTK), Partner Site Dresden, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marc Schmitz
- Institute of Immunology, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany.,National Center for Tumor Diseases (NCT), Partner Site Dresden, Dresden, Germany.,German Cancer Consortium (DKTK), Partner Site Dresden, and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Center for Regenerative Therapies Dresden (CRTD), TU Dresden, Dresden, Germany
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13
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Watt LG, Crawshaw S, Rhee SJ, Murphy AM, Canto T, Carr JP. The cucumber mosaic virus 1a protein regulates interactions between the 2b protein and ARGONAUTE 1 while maintaining the silencing suppressor activity of the 2b protein. PLoS Pathog 2020; 16:e1009125. [PMID: 33270799 PMCID: PMC7738167 DOI: 10.1371/journal.ppat.1009125] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 12/15/2020] [Accepted: 11/04/2020] [Indexed: 12/30/2022] Open
Abstract
The cucumber mosaic virus (CMV) 2b viral suppressor of RNA silencing (VSR) is a potent counter-defense and pathogenicity factor that inhibits antiviral silencing by titration of short double-stranded RNAs. It also disrupts microRNA-mediated regulation of host gene expression by binding ARGONAUTE 1 (AGO1). But in Arabidopsis thaliana complete inhibition of AGO1 is counterproductive to CMV since this triggers another layer of antiviral silencing mediated by AGO2, de-represses strong resistance against aphids (the insect vectors of CMV), and exacerbates symptoms. Using confocal laser scanning microscopy, bimolecular fluorescence complementation, and co-immunoprecipitation assays we found that the CMV 1a protein, a component of the viral replicase complex, regulates the 2b-AGO1 interaction. By binding 2b protein molecules and sequestering them in P-bodies, the 1a protein limits the proportion of 2b protein molecules available to bind AGO1, which ameliorates 2b-induced disease symptoms, and moderates induction of resistance to CMV and to its aphid vector. However, the 1a protein-2b protein interaction does not inhibit the ability of the 2b protein to inhibit silencing of reporter gene expression in agroinfiltration assays. The interaction between the CMV 1a and 2b proteins represents a novel regulatory system in which specific functions of a VSR are selectively modulated by another viral protein. The finding also provides a mechanism that explains how CMV, and possibly other viruses, modulates symptom induction and manipulates host-vector interactions.
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Affiliation(s)
- Lewis G. Watt
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Sam Crawshaw
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Sun-Ju Rhee
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Alex M. Murphy
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Tomás Canto
- Department of Microbial and Plant Biotechnology, Center for Biological Research, Madrid, Spain
| | - John P. Carr
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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14
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Madugalle SU, Meyer K, Wang DO, Bredy TW. RNA N 6-Methyladenosine and the Regulation of RNA Localization and Function in the Brain. Trends Neurosci 2020; 43:1011-1023. [PMID: 33041062 PMCID: PMC7688512 DOI: 10.1016/j.tins.2020.09.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/01/2020] [Accepted: 09/15/2020] [Indexed: 12/17/2022]
Abstract
A major challenge in neurobiology in the 21st century is to understand how the brain adapts with experience. Activity-dependent gene expression is integral to the synaptic plasticity underlying learning and memory; however, this process cannot be explained by a simple linear trajectory of transcription to translation within a specific neuronal population. Many other regulatory mechanisms can influence RNA metabolism and the capacity of neurons to adapt. In particular, the RNA modification N6-methyladenosine (m6A) has recently been shown to regulate RNA processing through alternative splicing, RNA stability, and translation. Here, we discuss the emerging idea that m6A could also coordinate the transport, localization, and local translation of key mRNAs in learning and memory and expand on the notion of dynamic functional RNA states in the brain.
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Affiliation(s)
- Sachithrani U Madugalle
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia.
| | - Kate Meyer
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA; Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA
| | - Dan Ohtan Wang
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan; Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, China
| | - Timothy W Bredy
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia.
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15
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Ferguson CM, Echeverria D, Hassler M, Ly S, Khvorova A. Cell Type Impacts Accessibility of mRNA to Silencing by RNA Interference. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 21:384-393. [PMID: 32650236 PMCID: PMC7340969 DOI: 10.1016/j.omtn.2020.06.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/04/2020] [Accepted: 06/08/2020] [Indexed: 12/28/2022]
Abstract
RNA interference (RNAi) is a potent mechanism that silences mRNA and protein expression in all cells and tissue types. RNAi is known to exert many of its functional effects in the cytoplasm, and thus, the cellular localization of target mRNA may impact observed potency. Here, we demonstrate that cell identity has a profound impact on accessibility of apolipoprotein E (ApoE) mRNA to RNAi. We show that, whereas both neuronal and glial cell lines express detectable ApoE mRNA, in neuronal cells, ApoE mRNA is not targetable by RNAi. Screening of a panel of thirty-five chemically modified small interfering RNAs (siRNAs) did not produce a single hit in a neuronal cell line, whereas up to fifteen compounds showed strong efficacy in glial cells. Further investigation of the cellular localization of ApoE mRNA demonstrates that ApoE mRNA is partially spliced and preferentially localized to the nucleus (∼80%) in neuronal cells, whereas more than 90% of ApoE mRNA is cytoplasmic in glial cells. Such an inconsistency in intracellular localization and splicing might provide an explanation for functional differences in RNAi compounds. Thus, cellular origin might have an impact on accessibility of mRNA to RNAi and should be taken into account during the screening process.
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Affiliation(s)
- Chantal M Ferguson
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Matthew Hassler
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Socheata Ly
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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16
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Cerro-Herreros E, González-Martínez I, Moreno-Cervera N, Overby S, Pérez-Alonso M, Llamusí B, Artero R. Therapeutic Potential of AntagomiR-23b for Treating Myotonic Dystrophy. MOLECULAR THERAPY-NUCLEIC ACIDS 2020; 21:837-849. [PMID: 32805487 PMCID: PMC7452101 DOI: 10.1016/j.omtn.2020.07.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/06/2020] [Accepted: 07/15/2020] [Indexed: 02/06/2023]
Abstract
Myotonic dystrophy type 1 (DM1) is a chronically debilitating, rare genetic disease that originates from an expansion of a noncoding CTG repeat in the dystrophia myotonica protein kinase (DMPK) gene. The expansion becomes pathogenic when DMPK transcripts contain 50 or more repetitions due to the sequestration of the muscleblind-like (MBNL) family of proteins. Depletion of MBNLs causes alterations in splicing patterns in transcripts that contribute to clinical symptoms such as myotonia and muscle weakness and wasting. We previously found that microRNA (miR)-23b directly regulates MBNL1 in DM1 myoblasts and mice and that antisense technology (“antagomiRs”) blocking this microRNA (miRNA) boosts MBNL1 protein levels. Here, we show the therapeutic effect over time in response to administration of antagomiR-23b as a treatment in human skeletal actin long repeat (HSALR) mice. Subcutaneous administration of antagomiR-23b upregulated the expression of MBNL1 protein and rescued splicing alterations, grip strength, and myotonia in a dose-dependent manner with long-lasting effects. Additionally, the effects of the treatment on grip strength and myotonia were still slightly notable after 45 days. The pharmacokinetic data obtained provide further evidence that miR-23b could be a valid therapeutic target for DM1.
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Affiliation(s)
- Estefanía Cerro-Herreros
- Interdisciplinary Research Structure for Biotechnology and Biomedicine (ERI BIOTECMED), Universidad de Valencia, 46100 Valencia, Spain; Translational Genomics Group, Incliva Health Research Institute, 46010 Valencia, Spain; Joint Unit Incliva-CIPF, Valencia, Spain
| | - Irene González-Martínez
- Interdisciplinary Research Structure for Biotechnology and Biomedicine (ERI BIOTECMED), Universidad de Valencia, 46100 Valencia, Spain; Translational Genomics Group, Incliva Health Research Institute, 46010 Valencia, Spain; Joint Unit Incliva-CIPF, Valencia, Spain
| | - Nerea Moreno-Cervera
- Interdisciplinary Research Structure for Biotechnology and Biomedicine (ERI BIOTECMED), Universidad de Valencia, 46100 Valencia, Spain; Translational Genomics Group, Incliva Health Research Institute, 46010 Valencia, Spain; Joint Unit Incliva-CIPF, Valencia, Spain
| | - Sarah Overby
- Interdisciplinary Research Structure for Biotechnology and Biomedicine (ERI BIOTECMED), Universidad de Valencia, 46100 Valencia, Spain; Translational Genomics Group, Incliva Health Research Institute, 46010 Valencia, Spain; Joint Unit Incliva-CIPF, Valencia, Spain
| | - Manuel Pérez-Alonso
- Interdisciplinary Research Structure for Biotechnology and Biomedicine (ERI BIOTECMED), Universidad de Valencia, 46100 Valencia, Spain; Translational Genomics Group, Incliva Health Research Institute, 46010 Valencia, Spain; Joint Unit Incliva-CIPF, Valencia, Spain
| | - Beatriz Llamusí
- Interdisciplinary Research Structure for Biotechnology and Biomedicine (ERI BIOTECMED), Universidad de Valencia, 46100 Valencia, Spain; Translational Genomics Group, Incliva Health Research Institute, 46010 Valencia, Spain; Joint Unit Incliva-CIPF, Valencia, Spain
| | - Rubén Artero
- Interdisciplinary Research Structure for Biotechnology and Biomedicine (ERI BIOTECMED), Universidad de Valencia, 46100 Valencia, Spain; Translational Genomics Group, Incliva Health Research Institute, 46010 Valencia, Spain; Joint Unit Incliva-CIPF, Valencia, Spain.
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17
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Torres-Fernández LA, Jux B, Bille M, Port Y, Schneider K, Geyer M, Mayer G, Kolanus W. The mRNA repressor TRIM71 cooperates with Nonsense-Mediated Decay factors to destabilize the mRNA of CDKN1A/p21. Nucleic Acids Res 2020; 47:11861-11879. [PMID: 31732746 PMCID: PMC7145526 DOI: 10.1093/nar/gkz1057] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 10/22/2019] [Accepted: 11/10/2019] [Indexed: 12/30/2022] Open
Abstract
Nonsense-mediated decay (NMD) plays a fundamental role in the degradation of premature termination codon (PTC)-containing transcripts, but also regulates the expression of functional transcripts lacking PTCs, although such 'non-canonical' functions remain ill-defined and require the identification of factors targeting specific mRNAs to the NMD machinery. Our work identifies the stem cell-specific mRNA repressor protein TRIM71 as one of these factors. TRIM71 plays an essential role in embryonic development and is linked to carcinogenesis. For instance, TRIM71 has been correlated with advanced stages and poor prognosis in hepatocellular carcinoma. Our data shows that TRIM71 represses the mRNA of the cell cycle inhibitor and tumor suppressor CDKN1A/p21 and promotes the proliferation of HepG2 tumor cells. CDKN1A specific recognition involves the direct interaction of TRIM71 NHL domain with a structural RNA stem-loop motif within the CDKN1A 3'UTR. Importantly, CDKN1A repression occurs independently of miRNA-mediated silencing. Instead, the NMD factors SMG1, UPF1 and SMG7 assist TRIM71-mediated degradation of CDKN1A mRNA, among other targets. Our data sheds light on TRIM71-mediated target recognition and repression mechanisms and uncovers a role for this stem cell-specific factor and oncogene in non-canonical NMD, revealing the existence of a novel mRNA surveillance mechanism which we have termed the TRIM71/NMD axis.
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Affiliation(s)
- Lucia A Torres-Fernández
- Molecular Immunology and Cell Biology, Life & Medical Sciences Institute (LIMES), University of Bonn, 53115 Bonn, Germany
| | - Bettina Jux
- Molecular Immunology and Cell Biology, Life & Medical Sciences Institute (LIMES), University of Bonn, 53115 Bonn, Germany
| | - Maximilian Bille
- Molecular Immunology and Cell Biology, Life & Medical Sciences Institute (LIMES), University of Bonn, 53115 Bonn, Germany
| | - Yasmine Port
- Molecular Immunology and Cell Biology, Life & Medical Sciences Institute (LIMES), University of Bonn, 53115 Bonn, Germany
| | - Karin Schneider
- Molecular Immunology and Cell Biology, Life & Medical Sciences Institute (LIMES), University of Bonn, 53115 Bonn, Germany
| | - Matthias Geyer
- Institute of Structural Biology, University Clinics Bonn, University of Bonn, 53127 Bonn, Germany
| | - Günter Mayer
- Center of Aptamer Research & Development; Chemical Biology & Chemical Genetics, Life & Medical Sciences Institute (LIMES). University of Bonn, 53121 Bonn, Germany
| | - Waldemar Kolanus
- Molecular Immunology and Cell Biology, Life & Medical Sciences Institute (LIMES), University of Bonn, 53115 Bonn, Germany
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18
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Chowdhury MR, Basak J, Bahadur RP. Elucidating the Functional Role of Predicted miRNAs in Post- Transcriptional Gene Regulation Along with Symbiosis in Medicago truncatula. Curr Bioinform 2020. [DOI: 10.2174/1574893614666191003114202] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Background:
microRNAs are small non-coding RNAs which inhibit translational and
post-transcriptional processes whereas long non-coding RNAs are found to regulate both
transcriptional and post-transcriptional gene expression. Medicago truncatula is a well-known
model plant for studying legume biology and is also used as a forage crop. In spite of its
importance in nitrogen fixation and soil fertility improvement, little information is available about
Medicago non-coding RNAs that play important role in symbiosis.
Objective:
In this study we have tried to understand the role of Medicago ncRNAs in symbiosis
and regulation of transcription factors.
Methods:
We have identified novel miRNAs by computational methods considering various
parameters like length, MFEI, AU content, SSR signatures and tried to establish an interaction
model with their targets obtained through psRNATarget server.
Results:
149 novel miRNAs are predicted along with their 770 target proteins. We have also
shown that 51 of these novel miRNAs are targeting 282 lncRNAs.
Conclusion:
In this study role of Medicago miRNAs in the regulation of various transcription
factors are elucidated. Knowledge gained from this study will have a positive impact on the
nitrogen fixing ability of this important model plant, which in turn will improve the soil fertility.
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Affiliation(s)
- Moumita Roy Chowdhury
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur-721302, India
| | - Jolly Basak
- Laboratory of Plant Stress Biology, Department of Biotechnology, Visva-Bharati, Santiniketan-731235, India
| | - Ranjit Prasad Bahadur
- Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur-721302, India
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19
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Christou-Kent M, Dhellemmes M, Lambert E, Ray PF, Arnoult C. Diversity of RNA-Binding Proteins Modulating Post-Transcriptional Regulation of Protein Expression in the Maturing Mammalian Oocyte. Cells 2020; 9:cells9030662. [PMID: 32182827 PMCID: PMC7140715 DOI: 10.3390/cells9030662] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 03/02/2020] [Accepted: 03/03/2020] [Indexed: 12/18/2022] Open
Abstract
The oocyte faces a particular challenge in terms of gene regulation. When oocytes resume meiosis at the end of the growth phase and prior to ovulation, the condensed chromatin state prevents the transcription of genes as they are required. Transcription is effectively silenced from the late germinal vesicle (GV) stage until embryonic genome activation (EGA) following fertilisation. Therefore, during its growth, the oocyte must produce the mRNA transcripts needed to fulfil its protein requirements during the active period of meiotic completion, fertilisation, and the maternal-to zygote-transition (MZT). After meiotic resumption, gene expression control can be said to be transferred from the nucleus to the cytoplasm, from transcriptional regulation to translational regulation. Maternal RNA-binding proteins (RBPs) are the mediators of translational regulation and their role in oocyte maturation and early embryo development is vital. Understanding these mechanisms will provide invaluable insight into the oocyte's requirements for developmental competence, with important implications for the diagnosis and treatment of certain types of infertility. Here, we give an overview of post-transcriptional regulation in the oocyte, emphasising the current knowledge of mammalian RBP mechanisms, and develop the roles of these mechanisms in the timely activation and elimination of maternal transcripts.
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Affiliation(s)
- Marie Christou-Kent
- Université Grenoble Alpes, F-38000 Grenoble, France; (M.C.-K.); (M.D.); (E.L.); (P.F.R.)
- Institute for Advanced Biosciences INSERM U1209, CNRS UMR5309, F-38000 Grenoble, France
| | - Magali Dhellemmes
- Université Grenoble Alpes, F-38000 Grenoble, France; (M.C.-K.); (M.D.); (E.L.); (P.F.R.)
- Institute for Advanced Biosciences INSERM U1209, CNRS UMR5309, F-38000 Grenoble, France
| | - Emeline Lambert
- Université Grenoble Alpes, F-38000 Grenoble, France; (M.C.-K.); (M.D.); (E.L.); (P.F.R.)
- Institute for Advanced Biosciences INSERM U1209, CNRS UMR5309, F-38000 Grenoble, France
| | - Pierre F. Ray
- Université Grenoble Alpes, F-38000 Grenoble, France; (M.C.-K.); (M.D.); (E.L.); (P.F.R.)
- Institute for Advanced Biosciences INSERM U1209, CNRS UMR5309, F-38000 Grenoble, France
- CHU de Grenoble, UM GI-DPI, F-38000 Grenoble, France
| | - Christophe Arnoult
- Université Grenoble Alpes, F-38000 Grenoble, France; (M.C.-K.); (M.D.); (E.L.); (P.F.R.)
- Institute for Advanced Biosciences INSERM U1209, CNRS UMR5309, F-38000 Grenoble, France
- Correspondence: ; Tel.: +33-(0)4-76-63-74-08
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20
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Tabassum N, Eschen-Lippold L, Athmer B, Baruah M, Brode M, Maldonado-Bonilla LD, Hoehenwarter W, Hause G, Scheel D, Lee J. Phosphorylation-dependent control of an RNA granule-localized protein that fine-tunes defence gene expression at a post-transcriptional level. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:1023-1039. [PMID: 31628867 DOI: 10.1111/tpj.14573] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 09/18/2019] [Accepted: 10/03/2019] [Indexed: 05/12/2023]
Abstract
Mitogen-activated protein kinase (MAPK) cascades are key signalling modules of plant defence responses to pathogen-associated molecular patterns [PAMPs; e.g. the bacterial peptide flagellin (flg22)]. Tandem zinc finger protein 9 (TZF9) is a RNA-binding protein that is phosphorylated by two PAMP-responsive MAPKs, MPK3 and MPK6. We mapped the major phosphosites in TZF9 and showed their importance for controlling in vitro RNA-binding activity, in vivo flg22-induced rapid disappearance of TZF9-labelled processing body-like structures and TZF9 protein turnover. Microarray analysis showed a strong discordance between transcriptome (total mRNA) and translatome (polysome-associated mRNA) in the tzf9 mutant, with more mRNAs associated with ribosomes in the absence of TZF9. This suggests that TZF9 may sequester and inhibit the translation of subsets of mRNAs. Fittingly, TZF9 physically interacts with poly(A)-binding protein 2 (PAB2), a hallmark constituent of stress granules - sites for stress-induced translational stalling/arrest. TZF9 even promotes the assembly of stress granules in the absence of stress. Hence, MAPKs may control defence gene expression post-transcriptionally through release from translation arrest within TZF9-PAB2-containing RNA granules or by perturbing the function of PAB2 in translation control (e.g. in the mRNA closed-loop model of translation).
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Affiliation(s)
- Naheed Tabassum
- Leibniz Institute of Plant Biochemistry, Weinberg 3, Halle/Saale, D-06120, Germany
| | | | - Benedikt Athmer
- Leibniz Institute of Plant Biochemistry, Weinberg 3, Halle/Saale, D-06120, Germany
| | - Manaswita Baruah
- Leibniz Institute of Plant Biochemistry, Weinberg 3, Halle/Saale, D-06120, Germany
| | - Martina Brode
- Leibniz Institute of Plant Biochemistry, Weinberg 3, Halle/Saale, D-06120, Germany
| | | | | | - Gerd Hause
- Biocenter, Martin Luther University Halle-Wittenberg, Weinbergweg 22, D-06120, Halle/Saale, Germany
| | - Dierk Scheel
- Leibniz Institute of Plant Biochemistry, Weinberg 3, Halle/Saale, D-06120, Germany
| | - Justin Lee
- Leibniz Institute of Plant Biochemistry, Weinberg 3, Halle/Saale, D-06120, Germany
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21
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Xu M, Mazur MJ, Tao X, Kormelink R. Cellular RNA Hubs: Friends and Foes of Plant Viruses. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:40-54. [PMID: 31415225 DOI: 10.1094/mpmi-06-19-0161-fi] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
RNA granules are dynamic cellular foci that are widely spread in eukaryotic cells and play essential roles in cell growth and development, and immune and stress responses. Different types of granules can be distinguished, each with a specific function and playing a role in, for example, RNA transcription, modification, processing, decay, translation, and arrest. By means of communication and exchange of (shared) components, they form a large regulatory network in cells. Viruses have been reported to interact with one or more of these either cytoplasmic or nuclear granules, and act either proviral, to enable and support viral infection and facilitate viral movement, or antiviral, protecting or clearing hosts from viral infection. This review describes an overview and recent progress on cytoplasmic and nuclear RNA granules and their interplay with virus infection, first in animal systems and as a prelude to the status and current developments on plant viruses, which have been less well studied on this thus far.
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Affiliation(s)
- Min Xu
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- Laboratory of Virology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Magdalena J Mazur
- Laboratory of Virology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Xiaorong Tao
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Richard Kormelink
- Laboratory of Virology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
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22
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Stavast CJ, Erkeland SJ. The Non-Canonical Aspects of MicroRNAs: Many Roads to Gene Regulation. Cells 2019; 8:cells8111465. [PMID: 31752361 PMCID: PMC6912820 DOI: 10.3390/cells8111465] [Citation(s) in RCA: 191] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/14/2019] [Accepted: 11/16/2019] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) are critical regulators of gene expression. As miRNAs are frequently deregulated in many human diseases, including cancer and immunological disorders, it is important to understand their biological functions. Typically, miRNA-encoding genes are transcribed by RNA Polymerase II and generate primary transcripts that are processed by RNase III-endonucleases DROSHA and DICER into small RNAs of approximately 21 nucleotides. All miRNAs are loaded into Argonaute proteins in the RNA-induced silencing complex (RISC) and act as post-transcriptional regulators by binding to the 3'- untranslated region (UTR) of mRNAs. This seed-dependent miRNA binding inhibits the translation and/or promotes the degradation of mRNA targets. Surprisingly, recent data presents evidence for a target-mediated decay mechanism that controls the level of specific miRNAs. In addition, several non-canonical miRNA-containing genes have been recently described and unexpected functions of miRNAs have been identified. For instance, several miRNAs are located in the nucleus, where they are involved in the transcriptional activation or silencing of target genes. These epigenetic modifiers are recruited by RISC and guided by miRNAs to specific loci in the genome. Here, we will review non-canonical aspects of miRNA biology, including novel regulators of miRNA expression and functions of miRNAs in the nucleus.
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Di Stefano B, Luo EC, Haggerty C, Aigner S, Charlton J, Brumbaugh J, Ji F, Rabano Jiménez I, Clowers KJ, Huebner AJ, Clement K, Lipchina I, de Kort MAC, Anselmo A, Pulice J, Gerli MFM, Gu H, Gygi SP, Sadreyev RI, Meissner A, Yeo GW, Hochedlinger K. The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis. Cell Stem Cell 2019; 25:622-638.e13. [PMID: 31588046 DOI: 10.1016/j.stem.2019.08.018] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 07/19/2019] [Accepted: 08/29/2019] [Indexed: 01/02/2023]
Abstract
Post-transcriptional mechanisms have the potential to influence complex changes in gene expression, yet their role in cell fate transitions remains largely unexplored. Here, we show that suppression of the RNA helicase DDX6 endows human and mouse primed embryonic stem cells (ESCs) with a differentiation-resistant, "hyper-pluripotent" state, which readily reprograms to a naive state resembling the preimplantation embryo. We further demonstrate that DDX6 plays a key role in adult progenitors where it controls the balance between self-renewal and differentiation in a context-dependent manner. Mechanistically, DDX6 mediates the translational suppression of target mRNAs in P-bodies. Upon loss of DDX6 activity, P-bodies dissolve and release mRNAs encoding fate-instructive transcription and chromatin factors that re-enter the ribosome pool. Increased translation of these targets impacts cell fate by rewiring the enhancer, heterochromatin, and DNA methylation landscapes of undifferentiated cell types. Collectively, our data establish a link between P-body homeostasis, chromatin organization, and stem cell potency.
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Affiliation(s)
- Bruno Di Stefano
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA
| | - En-Ching Luo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Chuck Haggerty
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Stefan Aigner
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Jocelyn Charlton
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Justin Brumbaugh
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA
| | - Fei Ji
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
| | - Inés Rabano Jiménez
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Katie J Clowers
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Aaron J Huebner
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA
| | - Kendell Clement
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Inna Lipchina
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA
| | - Marit A C de Kort
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA
| | - Anthony Anselmo
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
| | - John Pulice
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA
| | - Mattia F M Gerli
- Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
| | - Hongcang Gu
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Ruslan I Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
| | - Alexander Meissner
- Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA; Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA 92093, USA.
| | - Konrad Hochedlinger
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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Prasad A, Kulkarni R, Shrivastava A, Jiang S, Lawson K, Groopman JE. Methamphetamine functions as a novel CD4 + T-cell activator via the sigma-1 receptor to enhance HIV-1 infection. Sci Rep 2019; 9:958. [PMID: 30700725 PMCID: PMC6353873 DOI: 10.1038/s41598-018-35757-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 11/05/2018] [Indexed: 11/09/2022] Open
Abstract
Methamphetamine (Meth) exacerbates HIV-1 pathobiology by increasing virus transmission and replication and accelerating clinical progression to AIDS. Meth has been shown to alter the expression of HIV-1 co-receptors and impair intrinsic resistance mechanisms of immune cells. However, the exact molecular mechanisms involved in augmenting HIV-1 replication in T-cells are still not yet clear. Here, we demonstrate that pretreatment with Meth of CD4+ T-cells enhanced HIV-1 replication. We observed upregulation of CD4+ T-cell activation markers and enhanced expression of miR-34c-5p and miR-155 in these cells. Further, we noted activation of the sigma-1 receptor and enhanced intracellular Ca2+ concentration and cAMP release in CD4+ T-cells upon Meth treatment, which resulted in increased phosphorylation and nuclear translocation of transcription factors NFκB, CREB, and NFAT1. Increased gene expression of IL-4 and IL-10 was also observed in Meth treated CD4+ T-cells. Moreover, proteasomal degradation of Ago1 occurred upon Meth treatment, further substantiating the drug as an activator of T-cells. Taken together, these findings show a previously unreported mechanism whereby Meth functions as a novel T-cell activator via the sigma-1 signaling pathway, enhancing replication of HIV-1 with expression of miR-34c-5p, and transcriptional activation of NFκB, CREB and NFAT1.
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Affiliation(s)
- Anil Prasad
- Division of Experimental Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Rutuja Kulkarni
- Division of Experimental Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Ashutosh Shrivastava
- Division of Experimental Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
- Molecular Biology Unit, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Shuxian Jiang
- Division of Experimental Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Kaycie Lawson
- Division of Experimental Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Jerome E Groopman
- Division of Experimental Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA.
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25
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Tang L, Zhao P, Kong D. Muscleblind‑like 1 destabilizes Snail mRNA and suppresses the metastasis of colorectal cancer cells via the Snail/E‑cadherin axis. Int J Oncol 2019; 54:955-965. [PMID: 30664186 PMCID: PMC6365040 DOI: 10.3892/ijo.2019.4691] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/13/2018] [Indexed: 12/11/2022] Open
Abstract
RNA-binding proteins (RBPs) play a fundamental role in the recurrence and metastasis of colorectal cancer (CRC). In this study, we identified muscleblind-like 1 (MBNL1), an RBP implicated in developmental control, as a robust suppressor of CRC cell metastasis in vitro. By using a scratch assay coupled with time-lapse live cell imaging, our findings revealed that the knockdown of MBNL1 induced epithelial-to-mesenchymal transition (EMT)-like morphological changes in the HCT-116 cells, accompanied by an enhanced cell motility, and by the downregulation of E-cadherin and the upregulation of Snail expression. By contrast, the ectopic overexpression of MBNL1 suppressed EMT, characterized by the upregulation of E-cadherin and the downregulation of Snail expression. Mechanistically, Snail rather than E-cadherin, was identified as a direct downstream target gene of MBNL1. The ectopic the overexpression of MBNL1 markedly enhanced the recruitment of Snail transcripts to processing bodies (P-bodies), leading to the increased degradation of Snail mRNA and consequent translational silencing. Furthermore, the effect of MBNL1 on CRC cell migration was confirmed in additional CRC cell lines. SW480 and HT-29 cells exhibited similar changes in migratory capacity and the expression of Snail/E-cadherin to those observed in HCT-116 cells. On the whole, this study demonstrates that MBNL1 destabilizes Snail transcripts and, in turn, suppresses the EMT of CRC cells through the Snail/E-cadherin axis in vitro. Therefore, this EMT-related MBNL1/Snail/E-cadherin axis may prove to be a novel therapeutic target for CRC metastasis.
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Affiliation(s)
- Liang Tang
- Department of Colorectal Cancer, Cancer Hospital of Tianjin Medical University, Key Laboratory of Cancer Prevention and Therapy, and National Clinical Research Center of Cancer, Tianjin 300060, P.R. China
| | - Peng Zhao
- Department of Colorectal Cancer, Cancer Hospital of Tianjin Medical University, Key Laboratory of Cancer Prevention and Therapy, and National Clinical Research Center of Cancer, Tianjin 300060, P.R. China
| | - Dalu Kong
- Department of Colorectal Cancer, Cancer Hospital of Tianjin Medical University, Key Laboratory of Cancer Prevention and Therapy, and National Clinical Research Center of Cancer, Tianjin 300060, P.R. China
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26
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Wang X, Jia Y, Wang X, Wang C, Lv C, Li X, Chu Z, Han Q, Xiao S, Zhang S, Yang Z. MiR-375 Has Contrasting Effects on Newcastle Disease Virus Growth Depending on the Target Gene. Int J Biol Sci 2019; 15:44-57. [PMID: 30662346 PMCID: PMC6329920 DOI: 10.7150/ijbs.25106] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 11/01/2018] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs regulate post-transcriptional gene expression via either translational repression or mRNA degradation. They have important roles in both viral infection and host anti-infection processes. We discovered that the miR-375 is significantly upregulated in Newcastle disease virus (NDV)-infected chicken embryonic visceral tissues using a small RNA sequencing approach. Further research revealed that the overexpression of miR-375 markedly decreases the replication of the velogenic NDV F48E9 and the lentogenic NDV La Sota by targeting the M gene of NDV in DF-1 cells. Interestingly, miR-375 has another target, ELAVL4, which regulates chicken fibrocyte cell cycle progression and decreases NDV proliferation. In addition, miR-375 can influence bystander cells by its secretion in culture medium. Our results indicated that miR-375 is an inhibitor of NDV, but can also enhance NDV growth by reducing the expression of its target ELAVL4. These results emphasize the complex roles of microRNAs in the regulation of viral infections.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Zengqi Yang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China
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27
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Abou Elela S, Ji X. Structure and function of Rnt1p: An alternative to RNAi for targeted RNA degradation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 10:e1521. [PMID: 30548404 DOI: 10.1002/wrna.1521] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 10/30/2018] [Accepted: 11/15/2018] [Indexed: 12/27/2022]
Abstract
The double-stranded RNA-binding protein (dsRBP) family controls RNA editing, stability, and function in all eukaryotes. The central feature of this family is the recognition of a generic RNA duplex using highly conserved double-stranded RNA-binding domain (dsRBD) that recognizes the characteristic distance between the minor grooves created by the RNA helix. Variations on this theme that confer species and functional specificities have been reported but most dsRBPs retain their capacity to bind generic dsRNA. The ribonuclease III (RNase III) family members fall into four classes, represented by bacterial RNase III, yeast Rnt1p, human Drosha, and human Dicer, respectively. Like all dsRBPs and most members of the RNase III family, Rnt1p has a dsRBD, but unlike most of its kin, it poorly binds to generic RNA helices. Instead, Rnt1p, the only known RNase III expressed in Saccharomyces cerevisiae that lacks the RNAi (RNA interference) machinery, recognizes a specific class of stem-loop structures. To recognize the specific substrates, the dsRBD of Rnt1p is specialized, featuring a αβββααα topology and a sequence-specific RNA-binding motif at the C-terminus. Since the discovery of Rnt1p in 1996, significant progress has been made in studies of its genetics, function, structure, and mechanism of action, explaining the reasons and mechanisms for the increased specificity of this enzyme and its impact on the mechanism of RNA degradation. This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Processing > Processing of Small RNAs RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
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Affiliation(s)
- Sherif Abou Elela
- Microbiology and Infectiology Department, University of Sherbrooke, Sherbrooke, Quebec, Canada
| | - Xinhua Ji
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, Maryland
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28
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Russell SJ, Stalker L, LaMarre J. PIWIs, piRNAs and Retrotransposons: Complex battles during reprogramming in gametes and early embryos. Reprod Domest Anim 2018; 52 Suppl 4:28-38. [PMID: 29052331 DOI: 10.1111/rda.13053] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Gamete and embryo development are indispensable processes for successful reproduction. Cells involved in these processes acquire pluripotency, the ability to differentiate into multiple different cell types, through a series of events known as reprogramming that lead to profound changes in histone and DNA methylation. While essential for pluripotency, this epigenetic remodelling removes constraints that normally limit the expression of genomic sequences known as transposable elements (TEs). Unconstrained TE expression can lead to many deleterious consequences including infertility, so organisms have evolved complex and potent mechanistic arsenals to target and suppress TE expression during reprogramming. This review will focus on the control of transposable elements in gametes and embryos, and one important TE suppressing system known as the PIWI pathway. This broadly conserved, small RNA-targeted silencing mechanism appears critical for fertility in many species and may participate in multiple aspects of gene regulation in reproduction and other contexts.
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Affiliation(s)
- S J Russell
- Department of Biomedical Sciences, University of Guelph, Guelph, ON, Canada
| | - L Stalker
- Department of Biomedical Sciences, University of Guelph, Guelph, ON, Canada
| | - J LaMarre
- Department of Biomedical Sciences, University of Guelph, Guelph, ON, Canada
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29
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Lee J, Kim M, Itoh TQ, Lim C. Ataxin-2: A versatile posttranscriptional regulator and its implication in neural function. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1488. [PMID: 29869836 DOI: 10.1002/wrna.1488] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 05/04/2018] [Accepted: 05/09/2018] [Indexed: 12/13/2022]
Abstract
Ataxin-2 (ATXN2) is a eukaryotic RNA-binding protein that is conserved from yeast to human. Genetic expansion of a poly-glutamine tract in human ATXN2 has been implicated in several neurodegenerative diseases, likely acting through gain-of-function effects. Emerging evidence, however, suggests that ATXN2 plays more direct roles in neural function via specific molecular and cellular pathways. ATXN2 and its associated protein complex control distinct steps in posttranscriptional gene expression, including poly-A tailing, RNA stabilization, microRNA-dependent gene silencing, and translational activation. Specific RNA substrates have been identified for the functions of ATXN2 in aspects of neural physiology, such as circadian rhythms and olfactory habituation. Genetic models of ATXN2 loss-of-function have further revealed its significance in stress-induced cytoplasmic granules, mechanistic target of rapamycin signaling, and cellular metabolism, all of which are crucial for neural homeostasis. Accordingly, we propose that molecular evolution has been selecting the ATXN2 protein complex as an important trans-acting module for the posttranscriptional control of diverse neural functions. This explains how ATXN2 intimately interacts with various neurodegenerative disease genes, and suggests that loss-of-function effects of ATXN2 could be therapeutic targets for ATXN2-related neurological disorders. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Jongbo Lee
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, South Korea
| | - Minjong Kim
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, South Korea
| | - Taichi Q Itoh
- Faculty of Arts and Science, Kyushu University, Fukuoka, Japan
| | - Chunghun Lim
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, South Korea
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30
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Delorme-Axford E, Abernathy E, Lennemann NJ, Bernard A, Ariosa A, Coyne CB, Kirkegaard K, Klionsky DJ. The exoribonuclease Xrn1 is a post-transcriptional negative regulator of autophagy. Autophagy 2018; 14:898-912. [PMID: 29465287 DOI: 10.1080/15548627.2018.1441648] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Macroautophagy/autophagy is a conserved catabolic process that promotes survival during stress. Autophagic dysfunction is associated with pathologies such as cancer and neurodegenerative diseases. Thus, autophagy must be strictly modulated at multiple levels (transcriptional, post-transcriptional, translational and post-translational) to prevent deregulation. Relatively little is known about the post-transcriptional control of autophagy. Here we report that the exoribonuclease Xrn1/XRN1 functions as a negative autophagy factor in the yeast Saccharomyces cerevisiae and in mammalian cells. In yeast, chromosomal deletion of XRN1 enhances autophagy and the frequency of autophagosome formation. Loss of Xrn1 results in the upregulation of autophagy-related (ATG) transcripts under nutrient-replete conditions, and this effect is dependent on the ribonuclease activity of Xrn1. Xrn1 expression is regulated by the yeast transcription factor Ash1 in rich conditions. In mammalian cells, siRNA depletion of XRN1 enhances autophagy and the replication of 2 picornaviruses. This work provides insight into the role of the RNA decay factor Xrn1/XRN1 as a post-transcriptional regulator of autophagy.
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Affiliation(s)
| | - Emma Abernathy
- b Department of Genetics , Stanford University School of Medicine , Stanford , CA , USA
| | | | - Amélie Bernard
- a Life Sciences Institute, University of Michigan , Ann Arbor , MI , USA
| | - Aileen Ariosa
- a Life Sciences Institute, University of Michigan , Ann Arbor , MI , USA
| | - Carolyn B Coyne
- c Department of Pediatrics , University of Pittsburgh , Pittsburgh , PA , USA
| | - Karla Kirkegaard
- b Department of Genetics , Stanford University School of Medicine , Stanford , CA , USA
| | - Daniel J Klionsky
- a Life Sciences Institute, University of Michigan , Ann Arbor , MI , USA
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31
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Wang C, Schmich F, Srivatsa S, Weidner J, Beerenwinkel N, Spang A. Context-dependent deposition and regulation of mRNAs in P-bodies. eLife 2018; 7:29815. [PMID: 29297464 PMCID: PMC5752201 DOI: 10.7554/elife.29815] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 12/13/2017] [Indexed: 12/21/2022] Open
Abstract
Cells respond to stress by remodeling their transcriptome through transcription and degradation. Xrn1p-dependent degradation in P-bodies is the most prevalent decay pathway, yet, P-bodies may facilitate not only decay, but also act as a storage compartment. However, which and how mRNAs are selected into different degradation pathways and what determines the fate of any given mRNA in P-bodies remain largely unknown. We devised a new method to identify both common and stress-specific mRNA subsets associated with P-bodies. mRNAs targeted for degradation to P-bodies, decayed with different kinetics. Moreover, the localization of a specific set of mRNAs to P-bodies under glucose deprivation was obligatory to prevent decay. Depending on its client mRNA, the RNA-binding protein Puf5p either promoted or inhibited decay. Furthermore, the Puf5p-dependent storage of a subset of mRNAs in P-bodies under glucose starvation may be beneficial with respect to chronological lifespan.
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Affiliation(s)
- Congwei Wang
- Growth and Development, Biozentrum, University of Basel, Basel, Switzerland
| | - Fabian Schmich
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.,Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Sumana Srivatsa
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.,Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Julie Weidner
- Growth and Development, Biozentrum, University of Basel, Basel, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.,Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Anne Spang
- Growth and Development, Biozentrum, University of Basel, Basel, Switzerland
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32
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Saraiva C, Esteves M, Bernardino L. MicroRNA: Basic concepts and implications for regeneration and repair of neurodegenerative diseases. Biochem Pharmacol 2017; 141:118-131. [DOI: 10.1016/j.bcp.2017.07.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 07/07/2017] [Indexed: 12/25/2022]
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33
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Lin J, Xu R, Wu X, Shen Y, Li QQ. Role of cleavage and polyadenylation specificity factor 100: anchoring poly(A) sites and modulating transcription termination. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:829-839. [PMID: 28621907 DOI: 10.1111/tpj.13611] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 05/17/2017] [Accepted: 05/22/2017] [Indexed: 05/28/2023]
Abstract
CPSF100 is a core component of the cleavage and polyadenylation specificity factor (CPSF) complex for 3'-end formation of mRNA, but it still has no clear functional assignment. CPSF100 was reported to play a role in RNA silencing and promote flowering in Arabidopsis. However, the molecular mechanisms underlying these phenomena are not fully understood. Our genetics analyses indicate that plants with a hypomorphic mutant of CPSF100 (esp5) show defects in embryogenesis, reduced seed production or altered root morphology. To unravel this puzzle, we employed a poly(A) tag sequencing protocol and uncovered a different poly(A) profile in esp5. This transcriptome-wide analysis revealed alternative polyadenylation of thousands of genes, most of which result in transcriptional read-through in protein-coding genes. AtCPSF100 also affects poly(A) signal recognition on the far-upstream elements; in particular it prefers less U-rich sequences. Importantly, AtCPSF100 was found to exert its functions through the change of poly(A) sites on genes encoding binding proteins, such as nucleotide-binding, RNA-binding and poly(U)-binding proteins. In addition, through its interaction with RNA Polymerase II C-terminal domain (CTD) and affecting the expression level of CTD phosphatase-like 3 (CPL3), AtCPSF100 is shown to potentially ensure transcriptional termination by dephosphorylation of Ser2 on the CTD. These data suggest a key role for CPSF100 in locating poly(A) sites and affecting transcription termination.
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Affiliation(s)
- Juncheng Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, 91766, USA
| | - Ruqiang Xu
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, China
| | - Xiaohui Wu
- Department of Automation, Xiamen University, Xiamen, Fujian, 361005, China
| | - Yingjia Shen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
| | - Qingshun Q Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, 91766, USA
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Wang X, Chang L, Wang H, Su A, Wu Z. Dcp1a and GW182 Induce Distinct Cellular Aggregates and Have Different Effects on microRNA Pathway. DNA Cell Biol 2017; 36:565-570. [DOI: 10.1089/dna.2017.3633] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Xiaohui Wang
- Department of Hematology, Affiliated Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, People's Republic of China
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, People's Republic of China
| | - Liang Chang
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, People's Republic of China
| | - Huanru Wang
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, People's Republic of China
| | - Airong Su
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, People's Republic of China
| | - Zhiwei Wu
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, People's Republic of China
- State Key Lab of Analytical Chemistry for Life Science, Nanjing University, Nanjing, People's Republic of China
- Jiangsu Laboratory for Molecular Medicines, Nanjing University, Nanjing, People's Republic of China
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Bruscella P, Bottini S, Baudesson C, Pawlotsky JM, Feray C, Trabucchi M. Viruses and miRNAs: More Friends than Foes. Front Microbiol 2017; 8:824. [PMID: 28555130 PMCID: PMC5430039 DOI: 10.3389/fmicb.2017.00824] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 04/21/2017] [Indexed: 02/06/2023] Open
Abstract
There is evidence that eukaryotic miRNAs (hereafter called host miRNAs) play a role in the replication and propagation of viruses. Expression or targeting of host miRNAs can be involved in cellular antiviral responses. Most times host miRNAs play a role in viral life-cycles and promote infection through complex regulatory pathways. miRNAs can also be encoded by a viral genome and be expressed in the host cell. Viral miRNAs can share common sequences with host miRNAs or have totally different sequences. They can regulate a variety of biological processes involved in viral infection, including apoptosis, evasion of the immune response, or modulation of viral life-cycle phases. Overall, virus/miRNA pathway interaction is defined by a plethora of complex mechanisms, though not yet fully understood. This article review summarizes recent advances and novel biological concepts related to the understanding of miRNA expression, control and function during viral infections. The article also discusses potential therapeutic applications of this particular host–pathogen interaction.
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Affiliation(s)
- Patrice Bruscella
- INSERM U955, Team "Pathophysiology and Therapy of Chronic Viral Hepatitis", Université Paris-EstCréteil, France
| | | | - Camille Baudesson
- INSERM U955, Team "Pathophysiology and Therapy of Chronic Viral Hepatitis", Université Paris-EstCréteil, France
| | - Jean-Michel Pawlotsky
- INSERM U955, Team "Pathophysiology and Therapy of Chronic Viral Hepatitis", Université Paris-EstCréteil, France
| | - Cyrille Feray
- INSERM U955, Team "Pathophysiology and Therapy of Chronic Viral Hepatitis", Université Paris-EstCréteil, France
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Galectin-3 is a non-classic RNA binding protein that stabilizes the mucin MUC4 mRNA in the cytoplasm of cancer cells. Sci Rep 2017; 7:43927. [PMID: 28262838 PMCID: PMC5338267 DOI: 10.1038/srep43927] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 02/01/2017] [Indexed: 12/22/2022] Open
Abstract
Pancreatic cancer cells express high levels of MUC1, MUC4 and MUC16 mRNAs that encode membrane-bound mucins. These mRNAs share unusual features such as a long half-life. However, it remains unknown how mucin mRNA stability is regulated. Galectin-3 (Gal-3) is an endogenous lectin playing important biological functions in epithelial cells. Gal-3 is encoded by LGALS3 which is up-regulated in pancreatic cancer. Despite the absence of a RNA-recognition motif, Gal-3 interacts indirectly with pre-mRNAs in the nucleus and promotes constitutive splicing. However a broader role of Gal-3 in mRNA fate is unexplored. We report herein that Gal-3 increases MUC4 mRNA stability through an intermediate, hnRNP-L which binds to a conserved CA repeat element in the 3′UTR in a Gal-3 dependent manner and also controls Muc4 mRNA levels in epithelial tissues of Gal3−/− mice. Gal-3 interacts with hnRNP-L in the cytoplasm, especially during cell mitosis, but only partly associates with protein markers of P-Bodies or Stress Granules. By RNA-IP plus RNA-seq analysis and imaging, we demonstrate that Gal-3 binds to mature spliced MUC4 mRNA in the perinuclear region, probably in hnRNP-L-containing RNA granules. Our findings highlight a new role for Gal-3 as a non-classic RNA-binding protein that regulates MUC4 mRNA post-transcriptionally.
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Montufar-Solis D, Williams A, Vigneswaran N, Klein JR. Involvement of Ly6C, 4-1BB, and KLRG1 in the activation of lamina propria lymphocytes in the small intestine of sanroque mice. Biochem Biophys Res Commun 2017; 483:590-595. [PMID: 28011265 DOI: 10.1016/j.bbrc.2016.12.099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 12/14/2016] [Indexed: 11/16/2022]
Abstract
Roquin is an E3 ligase that regulates mRNA stability. Mice with a mutation in the Rc3h1 gene and Roquin protein, referred to as Roquinsan/san or sanroque mice, develop broad-spectrum chronic inflammatory conditions and autoimmune pathologies. Our laboratory recently reported that sanroque mice also develop extensive inflammation that is localized in the small intestine but is rare in the colon. Here, we demonstrate that small intestinal intraepithelial lymphocytes (IELs) are present in the epithelium of sanroque mice but that cell recoverability is low using standard extraction techniques even though lamina propria lymphocytes (LPLs) can be recovered in normal numbers. In studies aimed at characterizing T cell costimulatory markers and activation molecules on LPLs in sanroque mice, we identified Ly6C and 4-1BB (CD137) as being expressed at elevated levels on sanroque small intestinal LPLs, and we show that both of those subsets, in conjunction with cells expressing the KLRG1 T cell activation molecule, are sources of IL-17A, IFN-γ, and TNFα. TNFα was primarily produced by 4-1BB+, KLRG1-cells, but was also made by some 4-1BB-, KLRG1-cells, and 4-1BB-, KLRG1+ cells. These findings collectively suggest that the small intestinal inflammatory response in sanroque mice is driven, at least in part, by LPL activation through Ly6C and 4-1BB signaling, and they provide further evidence in support of using the sanroque mouse as an animal model of chronic small intestinal inflammation.
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Affiliation(s)
- Dina Montufar-Solis
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, University of Texas Health Science Center at Houston, Houston TX, USA
| | - Alexander Williams
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, University of Texas Health Science Center at Houston, Houston TX, USA
| | - Nadarajah Vigneswaran
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, University of Texas Health Science Center at Houston, Houston TX, USA
| | - John R Klein
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, University of Texas Health Science Center at Houston, Houston TX, USA.
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Abstract
As obligate parasites, viruses strictly depend on host cell translation for the production of new progeny, yet infected cells also synthesize antiviral proteins to limit virus infection. Modulation of host cell translation therefore represents a frequent strategy by which viruses optimize their replication and spread. Here we sought to define how host cell translation is regulated during infection of human cells with dengue virus (DENV) and Zika virus (ZIKV), two positive-strand RNA flaviviruses. Polysome profiling and analysis of de novo protein synthesis revealed that flavivirus infection causes potent repression of host cell translation, while synthesis of viral proteins remains efficient. Selective repression of host cell translation was mediated by the DENV polyprotein at the level of translation initiation. In addition, DENV and ZIKV infection suppressed host cell stress responses such as the formation of stress granules and phosphorylation of the translation initiation factor eIF2α (α subunit of eukaryotic initiation factor 2). Mechanistic analyses revealed that translation repression was uncoupled from the disruption of stress granule formation and eIF2α signaling. Rather, DENV infection induced p38-Mnk1 signaling that resulted in the phosphorylation of the eukaryotic translation initiation factor eIF4E and was essential for the efficient production of virus particles. Together, these results identify the uncoupling of translation suppression from the cellular stress responses as a conserved strategy by which flaviviruses ensure efficient replication in human cells. For efficient production of new progeny, viruses need to balance their dependency on the host cell translation machinery with potentially adverse effects of antiviral proteins produced by the infected cell. To achieve this, many viruses evolved mechanisms to manipulate host cell translation. Here we find that infection of human cells with two major human pathogens, dengue virus (DENV) and Zika virus (ZIKV), leads to the potent repression of host cell translation initiation, while the synthesis of viral protein remains unaffected. Unlike other RNA viruses, these flaviviruses concomitantly suppress host cell stress responses, thereby uncoupling translation suppression from stress granule formation. We identified that the p38-Mnk1 cascade regulating phosphorylation of eIF4E is a target of DENV infection and plays an important role in virus production. Our results define several molecular interfaces by which flaviviruses hijack host cell translation and interfere with stress responses to optimize the production of new virus particles.
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Sharma N, Singh SK. Implications of non-coding RNAs in viral infections. Rev Med Virol 2016; 26:356-68. [PMID: 27401792 DOI: 10.1002/rmv.1893] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 05/30/2016] [Accepted: 05/31/2016] [Indexed: 02/06/2023]
Abstract
The advances in RNA sequencing have unveiled various non-coding RNAs (ncRNAs), which modulate the gene expression. ncRNAs do not get translated into proteins. These include transfer RNAs, ribosomal RNAs, microRNA (miRNA), short interfering RNA, long non-coding RNA, piwi-interacting RNA and small nuclear RNA. ncRNAs regulate gene expression at various levels and control cellular machinery. miRNAs have been reported in plants, animals, several invertebrates and viruses. The miRNAs regulate the gene expression post-transcriptionally. Viral infection strongly influences the abundance and the distribution of miRNAs and other ncRNAs within the host cells. Viruses may encode their own miRNA, which help in the viral life cycle and other aspects of pathogenesis. Viruses are known to successfully modulate the expression pattern of ncRNAs. The ncRNA-based strategies adopted by viruses for their survival present a complex picture of host-virus interactions. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Nikhil Sharma
- Laboratory of Neurovirology and Inflammation Biology, CSIR-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
| | - Sunit K Singh
- Laboratory of Human Molecular Virology and Immunology, Molecular Biology Unit, Faculty of Medicine, Institute of Medical Sciences (IMS), Banaras Hindu University (BHU), Varanasi, India.
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Post-transcriptional regulation of Wnt co-receptor LRP6 and RNA-binding protein HuR by miR-29b in intestinal epithelial cells. Biochem J 2016; 473:1641-9. [PMID: 27089893 PMCID: PMC4888462 DOI: 10.1042/bcj20160057] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 04/05/2016] [Indexed: 02/07/2023]
Abstract
MicroRNAs (miRNAs) control gene expression by binding to their target mRNAs for degradation and/or translation repression and are implicated in many aspects of cellular physiology. Our previous study shows that miR-29b acts as a biological repressor of intestinal mucosal growth, but its exact downstream targets remain largely unknown. In the present study, we found that mRNAs, encoding Wnt co-receptor LRP6 (low-density lipoprotein-receptor-related protein 6) and RNA-binding protein (RBP) HuR, are novel targets of miR-29b in intestinal epithelial cells (IECs) and that expression of LRP6 and HuR is tightly regulated by miR-29b at the post-transcriptional level. miR-29b interacted with both Lrp6 and HuR mRNAs via their 3′-UTRs and inhibited LRP6 and HuR expression by destabilizing Lrp6 and HuR mRNAs and repressing their translation. Studies using heterologous reporter constructs revealed a greater repressive effect of miR-29b through a single binding site in the Lrp6 or HuR 3′-UTR, whereas deletion mutation of this site prevented miR-29b-induced repression of LRP6 and HuR expression. Repression of HuR by miR-29b in turn also contributed to miR-29b-induced LRP6 inhibition, since ectopic overexpression of HuR in cells overexpressing miR-29b restored LRP6 expression to near normal levels. Taken together, our results suggest that miR-29b inhibits expression of LRP6 and HuR post-transcriptionally, thus playing a role in the regulation of IEC proliferation and intestinal epithelial homoeostasis.
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H19 Long Noncoding RNA Regulates Intestinal Epithelial Barrier Function via MicroRNA 675 by Interacting with RNA-Binding Protein HuR. Mol Cell Biol 2016; 36:1332-41. [PMID: 26884465 DOI: 10.1128/mcb.01030-15] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 02/12/2016] [Indexed: 01/13/2023] Open
Abstract
The disruption of the intestinal epithelial barrier function occurs commonly in various pathologies, but the exact mechanisms responsible are unclear. The H19 long noncoding RNA (lncRNA) regulates the expression of different genes and has been implicated in human genetic disorders and cancer. Here, we report that H19 plays an important role in controlling the intestinal epithelial barrier function by serving as a precursor for microRNA 675 (miR-675). H19 overexpression increased the cellular abundance of miR-675, which in turn destabilized and repressed the translation of mRNAs encoding tight junction protein ZO-1 and adherens junction E-cadherin, resulting in the dysfunction of the epithelial barrier. Increasing the level of the RNA-binding protein HuR in cells overexpressing H19 prevented the stimulation of miR-675 processing from H19, promoted ZO-1 and E-cadherin expression, and restored the epithelial barrier function to a nearly normal level. In contrast, the targeted deletion of HuR in intestinal epithelial cells enhanced miR-675 production in the mucosa and delayed the recovery of the gut barrier function after exposure to mesenteric ischemia/reperfusion. These results indicate that H19 interacts with HuR and regulates the intestinal epithelial barrier function via the H19-encoded miR-675 by altering ZO-1 and E-cadherin expression posttranscriptionally.
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Dong OX, Meteignier LV, Plourde MB, Ahmed B, Wang M, Jensen C, Jin H, Moffett P, Li X, Germain H. Arabidopsis TAF15b Localizes to RNA Processing Bodies and Contributes to snc1-Mediated Autoimmunity. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2016; 29:247-57. [PMID: 26713351 DOI: 10.1094/mpmi-11-15-0246-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
In both animals and plants, messenger (m)RNA export has been shown to contribute to immune response regulation. The Arabidopsis nuclear protein MOS11, along with the nucleoporins MOS3/Nup96/SAR3 and Nup160/SAR1 are components of the mRNA export machinery and contribute to immunity mediated by nucleotide binding leucine-rich repeat immune receptors (NLR). The human MOS11 ortholog CIP29 is part of a small protein complex with three additional members: the RNA helicase DDX39, ALY, and TAF15b. We systematically assessed the biological roles of the Arabidopsis homologs of these proteins in toll interleukin 1 receptor-type NLR (TNL)-mediated immunity using reverse genetics. Although mutations in ALY and DDX39 did not result in obvious defects, taf15b mutation partially suppressed the autoimmune phenotypes of a gain-of-function TNL mutant, snc1. An additive effect on snc1 suppression was observed in mos11-1 taf15b snc1 triple mutant plants, suggesting that MOS11 and TAF15b have independent functions. TAF15b-GFP fusion protein, which fully complemented taf15b mutant phenotypes, localized to nuclei similarly to MOS11. However, it was also targeted to cytosolic granules identified as processing bodies. In addition, we observed no change in SNC1 mRNA levels, whereas less SNC1 protein accumulated in taf15b mutant, suggesting that TAF15b contributes to SNC1 homeostasis through posttranscriptional mechanisms. In summary, this study highlights the importance of posttranscriptional RNA processing mediated by TAF15b in the regulation of TNL-mediated immunity.
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Affiliation(s)
- Oliver X Dong
- 1 Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- 2 Michael Smith Laboratories, University of British Columbia
| | | | - Melodie B Plourde
- 4 Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, QC, G9A 5H7, Canada
- 5 Groupe de Recherche en Biologie Végétale (GRBV), Université du Québec à Trois-Rivières; and
| | - Bulbul Ahmed
- 4 Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, QC, G9A 5H7, Canada
- 5 Groupe de Recherche en Biologie Végétale (GRBV), Université du Québec à Trois-Rivières; and
| | - Ming Wang
- 6 Department of Plant Pathology and Microbiology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, U.S.A
| | | | - Hailing Jin
- 6 Department of Plant Pathology and Microbiology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, U.S.A
| | - Peter Moffett
- 3 Department of Biology, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
| | - Xin Li
- 1 Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- 2 Michael Smith Laboratories, University of British Columbia
| | - Hugo Germain
- 4 Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, QC, G9A 5H7, Canada
- 5 Groupe de Recherche en Biologie Végétale (GRBV), Université du Québec à Trois-Rivières; and
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Chaudhari A, Pathakota GB, Annam PK. Design and Construction of Shrimp Antiviral DNA Vaccines Expressing Long and Short Hairpins for Protection by RNA Interference. Methods Mol Biol 2016; 1404:225-240. [PMID: 27076302 DOI: 10.1007/978-1-4939-3389-1_16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
DNA vaccines present the aquaculture industry with an effective and economically viable method of controlling viral pathogens that drastically affect productivity. Since specific immune response is rudimentary in invertebrates, the presence of RNA interference (RNAi) pathway in shrimps provides a promising new approach to vaccination. Plasmid DNA vaccines that express short or long double stranded RNA in vivo have shown protection against viral diseases. The design, construction and considerations for preparing such vaccines are discussed.
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Affiliation(s)
- Aparna Chaudhari
- ICAR-Central Institute of Fisheries Education, Versova, Andheri West, Mumbai, 400061, India.
| | - Gireesh-Babu Pathakota
- ICAR-Central Institute of Fisheries Education, Versova, Andheri West, Mumbai, 400061, India
| | - Pavan-Kumar Annam
- ICAR-Central Institute of Fisheries Education, Versova, Andheri West, Mumbai, 400061, India
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Host cytoplasmic processing bodies assembled by Trypanosoma cruzi during infection exert anti-parasitic activity. Parasitol Int 2015; 64:540-6. [DOI: 10.1016/j.parint.2015.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 06/30/2015] [Accepted: 07/28/2015] [Indexed: 11/23/2022]
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Aulas A, Vande Velde C. Alterations in stress granule dynamics driven by TDP-43 and FUS: a link to pathological inclusions in ALS? Front Cell Neurosci 2015; 9:423. [PMID: 26557057 PMCID: PMC4615823 DOI: 10.3389/fncel.2015.00423] [Citation(s) in RCA: 160] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 10/06/2015] [Indexed: 12/12/2022] Open
Abstract
Stress granules (SGs) are RNA-containing cytoplasmic foci formed in response to stress exposure. Since their discovery in 1999, over 120 proteins have been described to be localized to these structures (in 154 publications). Most of these components are RNA binding proteins (RBPs) or are involved in RNA metabolism and translation. SGs have been linked to several pathologies including inflammatory diseases, cancer, viral infection, and neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). In ALS and FTD, the majority of cases have no known etiology and exposure to external stress is frequently proposed as a contributor to either disease initiation or the rate of disease progression. Of note, both ALS and FTD are characterized by pathological inclusions, where some well-known SG markers localize with the ALS related proteins TDP-43 and FUS. We propose that TDP-43 and FUS serve as an interface between genetic susceptibility and environmental stress exposure in disease pathogenesis. Here, we will discuss the role of TDP-43 and FUS in SG dynamics and how disease-linked mutations affect this process.
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Affiliation(s)
- Anaïs Aulas
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal Montréal, QC, Canada ; Department of Biochemistry, Université de Montréal Montréal, QC, Canada
| | - Christine Vande Velde
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal Montréal, QC, Canada ; Department of Neurosciences, Université de Montréal Montréal, QC, Canada
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Yu TX, Gu BL, Yan JK, Zhu J, Yan WH, Chen J, Qian LX, Cai W. CUGBP1 and HuR regulate E-cadherin translation by altering recruitment of E-cadherin mRNA to processing bodies and modulate epithelial barrier function. Am J Physiol Cell Physiol 2015; 310:C54-65. [PMID: 26491048 DOI: 10.1152/ajpcell.00112.2015] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 10/14/2015] [Indexed: 01/01/2023]
Abstract
The effectiveness and stability of epithelial barrier depend on apical junctional complexes, which consist of tight junctions (TJs) and adherens junctions (AJs). E-cadherin is the primary component of AJs, and it is essential for maintenance of cell-to-cell interactions and regulates the epithelial barrier. However, the exact mechanism underlying E-cadherin expression, particularly at the posttranscriptional level, remains largely unknown. RNA-binding proteins CUG-binding protein 1 (CUGBP1) and HU antigen R (HuR) are highly expressed in the intestinal epithelial tissues and modulate the stability and translation of target mRNAs. Here, we present evidence that CUGBP1 and HuR interact directly with the 3'-untranslated region of E-cadherin mRNA and regulate E-cadherin translation. CUGBP1 overexpression in Caco-2 cells inhibited E-cadherin translation by increasing the recruitment of E-cadherin mRNA to processing bodies (PBs), thus resulting in an increase in paracellular permeability. Overexpression of HuR exhibited an opposite effect on E-cadherin expression by preventing the translocation of E-cadherin mRNA to PBs and therefore prevented CUGBP1-induced repression of E-cadherin expression. Elevation of HuR also abolished the CUGBP1-induced epithelial barrier dysfunction. These findings indicate that CUGBP1 and HuR negate each other's effects in regulating E-cadherin translation by altering the recruitment of E-cadherin mRNA to PBs and play an important role in the regulation of intestinal barrier integrity under various pathophysiological conditions.
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Affiliation(s)
- Ting-Xi Yu
- Xin Hua Hospital Affiliated to School of Medicine, Shanghai JiaoTong University, Shanghai, China; and Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Bei-Lin Gu
- Xin Hua Hospital Affiliated to School of Medicine, Shanghai JiaoTong University, Shanghai, China; and Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Jun-Kai Yan
- Xin Hua Hospital Affiliated to School of Medicine, Shanghai JiaoTong University, Shanghai, China; and Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Jie Zhu
- Xin Hua Hospital Affiliated to School of Medicine, Shanghai JiaoTong University, Shanghai, China; and Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Wei-Hui Yan
- Xin Hua Hospital Affiliated to School of Medicine, Shanghai JiaoTong University, Shanghai, China; and Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Jie Chen
- Xin Hua Hospital Affiliated to School of Medicine, Shanghai JiaoTong University, Shanghai, China; and
| | - Lin-Xi Qian
- Xin Hua Hospital Affiliated to School of Medicine, Shanghai JiaoTong University, Shanghai, China; and Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Wei Cai
- Xin Hua Hospital Affiliated to School of Medicine, Shanghai JiaoTong University, Shanghai, China; and Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai Institute for Pediatric Research, Shanghai, China
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Corcoran JA, McCormick C. Viral activation of stress-regulated Rho-GTPase signaling pathway disrupts sites of mRNA degradation to influence cellular gene expression. Small GTPases 2015; 6:178-85. [PMID: 26480288 PMCID: PMC4905259 DOI: 10.1080/21541248.2015.1093068] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 09/07/2015] [Accepted: 09/08/2015] [Indexed: 01/09/2023] Open
Abstract
Viruses are useful tools that often reveal previously unrecognized levels of control within a cell. By studying the oncogenic Kaposi's sarcoma-associated herpesvirus (KSHV), we discovered a new signaling axis in endothelial cells (ECs) that links actin cytoskeleton dynamics to post-transcriptional control of gene expression. Translational repression and rapid decay of mRNAs containing AU-rich elements (AREs) occurs in cytoplasmic RNA granules known as processing bodies (PBs). Rho-GTPase activity influences PB dynamics but mechanistic details remain obscure. We have previously shown that the KSHV Kaposin B protein blocks the degradation of ARE-mRNAs that encode potent cytokines and angiogenic factors, at least in part by preventing PB formation. Moreover, Kaposin B is sufficient to cause marked alterations in endothelial cell physiology including the formation of long parallel actin stress fibers and accelerated migration and angiogenic phenotypes. All of these phenotypes depend on Kaposin B-mediated activation of a non-canonical signaling pathway comprising the stress-inducible kinase MK2, hsp27, p115RhoGEF and RhoA. Accelerated endothelial cell migration and angiogenesis depends on the subsequent activation of the RhoA-dependent kinase ROCK, but PB disruption is ROCK-independent. In this Commentary, we discuss implications of the activation of this signaling axis, and propose mechanistic links between RhoA activation and PB dynamics.
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Affiliation(s)
- Jennifer A Corcoran
- Department of Microbiology and Immunology; Dalhousie University; Halifax NS, Canada
| | - Craig McCormick
- Department of Microbiology and Immunology; Dalhousie University; Halifax NS, Canada
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49
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Cytoplasmic mRNA turnover and ageing. Mech Ageing Dev 2015; 152:32-42. [PMID: 26432921 PMCID: PMC4710634 DOI: 10.1016/j.mad.2015.09.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Revised: 09/17/2015] [Accepted: 09/27/2015] [Indexed: 12/12/2022]
Abstract
We address the cytoplasmic mRNA decay processes that determine the mRNAs half-life. We briefly describe the major, evolutionary conserved, ageing pathways and mechanisms. We summarize critical findings that link mRNA turnover and ageing modulators.
Messenger RNA (mRNA) turnover that determines the lifetime of cytoplasmic mRNAs is a means to control gene expression under both normal and stress conditions, whereas its impact on ageing and age-related disorders has just become evident. Gene expression control is achieved at the level of the mRNA clearance as well as mRNA stability and accessibility to other molecules. All these processes are regulated by cis-acting motifs and trans-acting factors that determine the rates of translation and degradation of transcripts. Specific messenger RNA granules that harbor the mRNA decay machinery or various factors, involved in translational repression and transient storage of mRNAs, are also part of the mRNA fate regulation. Their assembly and function can be modulated to promote stress resistance to adverse conditions and over time affect the ageing process and the lifespan of the organism. Here, we provide insights into the complex relationships of ageing modulators and mRNA turnover mechanisms.
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Bilanchone V, Clemens K, Kaake R, Dawson AR, Matheos D, Nagashima K, Sitlani P, Patterson K, Chang I, Huang L, Sandmeyer S. Ty3 Retrotransposon Hijacks Mating Yeast RNA Processing Bodies to Infect New Genomes. PLoS Genet 2015; 11:e1005528. [PMID: 26421679 PMCID: PMC4589538 DOI: 10.1371/journal.pgen.1005528] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 08/24/2015] [Indexed: 01/15/2023] Open
Abstract
Retrotransposition of the budding yeast long terminal repeat retrotransposon Ty3 is activated during mating. In this study, proteins that associate with Ty3 Gag3 capsid protein during virus-like particle (VLP) assembly were identified by mass spectrometry and screened for roles in mating-stimulated retrotransposition. Components of RNA processing bodies including DEAD box helicases Dhh1/DDX6 and Ded1/DDX3, Sm-like protein Lsm1, decapping protein Dcp2, and 5' to 3' exonuclease Xrn1 were among the proteins identified. These proteins associated with Ty3 proteins and RNA, and were required for formation of Ty3 VLP retrosome assembly factories and for retrotransposition. Specifically, Dhh1/DDX6 was required for normal levels of Ty3 genomic RNA, and Lsm1 and Xrn1 were required for association of Ty3 protein and RNA into retrosomes. This role for components of RNA processing bodies in promoting VLP assembly and retrotransposition during mating in a yeast that lacks RNA interference, contrasts with roles proposed for orthologous components in animal germ cell ribonucleoprotein granules in turnover and epigenetic suppression of retrotransposon RNAs.
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Affiliation(s)
- Virginia Bilanchone
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
| | - Kristina Clemens
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
| | - Robyn Kaake
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, California, United States of America
| | - Anthony R. Dawson
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
| | - Dina Matheos
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
| | - Kunio Nagashima
- Electron Microscope Laboratory, NCI-Frederick, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Parth Sitlani
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
| | - Kurt Patterson
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
| | - Ivan Chang
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
| | - Lan Huang
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, California, United States of America
| | - Suzanne Sandmeyer
- Department of Biological Chemistry, University of California, Irvine, Irvine, California, United States of America
- Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, California, United States of America
- * E-mail:
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