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Jang C, Lahens NF, Hogenesch JB, Sehgal A. Ribosome profiling reveals an important role for translational control in circadian gene expression. Genome Res 2015; 25:1836-47. [PMID: 26338483 PMCID: PMC4665005 DOI: 10.1101/gr.191296.115] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Accepted: 09/02/2015] [Indexed: 01/30/2023]
Abstract
Physiological and behavioral circadian rhythms are driven by a conserved transcriptional/translational negative feedback loop in mammals. Although most core clock factors are transcription factors, post-transcriptional control introduces delays that are critical for circadian oscillations. Little work has been done on circadian regulation of translation, so to address this deficit we conducted ribosome profiling experiments in a human cell model for an autonomous clock. We found that most rhythmic gene expression occurs with little delay between transcription and translation, suggesting that the lag in the accumulation of some clock proteins relative to their mRNAs does not arise from regulated translation. Nevertheless, we found that translation occurs in a circadian fashion for many genes, sometimes imposing an additional level of control on rhythmically expressed mRNAs and, in other cases, conferring rhythms on noncycling mRNAs. Most cyclically transcribed RNAs are translated at one of two major times in a 24-h day, while rhythmic translation of most noncyclic RNAs is phased to a single time of day. Unexpectedly, we found that the clock also regulates the formation of cytoplasmic processing (P) bodies, which control the fate of mRNAs, suggesting circadian coordination of mRNA metabolism and translation.
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Affiliation(s)
- Christopher Jang
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Nicholas F Lahens
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - John B Hogenesch
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Amita Sehgal
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA; Howard Hughes Medical Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
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52
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Protein synthesis as an integral quality control mechanism during ageing. Ageing Res Rev 2015; 23:75-89. [PMID: 25555680 DOI: 10.1016/j.arr.2014.12.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 12/18/2014] [Accepted: 12/22/2014] [Indexed: 01/17/2023]
Abstract
Ageing is manifested as functional and structural deterioration that affects cell and tissue physiology. mRNA translation is a central cellular process, supplying cells with newly synthesized proteins. Accumulating evidence suggests that alterations in protein synthesis are not merely a corollary but rather a critical factor for the progression of ageing. Here, we survey protein synthesis regulatory mechanisms and focus on the pre-translational regulation of the process exerted by non-coding RNA species, RNA binding proteins and alterations of intrinsic RNA properties. In addition, we discuss the tight relationship between mRNA translation and two central pathways that modulate ageing, namely the insulin/IGF-1 and TOR signalling cascades. A thorough understanding of the complex interplay between protein synthesis regulation and ageing will provide critical insights into the pathogenesis of age-related disorders, associated with impaired proteostasis and protein quality control.
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53
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Sobolewski C, Sanduja S, Blanco FF, Hu L, Dixon DA. Histone Deacetylase Inhibitors Activate Tristetraprolin Expression through Induction of Early Growth Response Protein 1 (EGR1) in Colorectal Cancer Cells. Biomolecules 2015; 5:2035-55. [PMID: 26343742 PMCID: PMC4598787 DOI: 10.3390/biom5032035] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 07/30/2015] [Accepted: 08/10/2015] [Indexed: 02/06/2023] Open
Abstract
The RNA-binding protein tristetraprolin (TTP) promotes rapid decay of mRNAs bearing 3' UTR AU-rich elements (ARE). In many cancer types, loss of TTP expression is observed allowing for stabilization of ARE-mRNAs and their pathologic overexpression. Here we demonstrate that histone deacetylase (HDAC) inhibitors (Trichostatin A, SAHA and sodium butyrate) promote TTP expression in colorectal cancer cells (HCA-7, HCT-116, Moser and SW480 cells) and cervix carcinoma cells (HeLa). We found that HDAC inhibitors-induced TTP expression, promote the decay of COX-2 mRNA, and inhibit cancer cell proliferation. HDAC inhibitors were found to promote TTP transcription through activation of the transcription factor Early Growth Response protein 1 (EGR1). Altogether, our findings indicate that loss of TTP in tumors occurs through silencing of EGR1 and suggests a therapeutic approach to rescue TTP expression in colorectal cancer.
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Affiliation(s)
- Cyril Sobolewski
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
| | - Sandhya Sanduja
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
| | - Fernando F Blanco
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
| | - Liangyan Hu
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
| | - Dan A Dixon
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
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54
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Lim CW, Lim S, Baek W, Lee SC. The pepper late embryogenesis abundant protein CaLEA1 acts in regulating abscisic acid signaling, drought and salt stress response. PHYSIOLOGIA PLANTARUM 2015; 154:526-42. [PMID: 25302464 DOI: 10.1111/ppl.12298] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 09/11/2014] [Accepted: 09/26/2014] [Indexed: 05/08/2023]
Abstract
As sessile organisms, plants are constantly challenged by environmental stresses, including drought and high salinity. Among the various abiotic stresses, osmotic stress is one of the most important factors for growth and significantly reduces crop productivity in agriculture. Here, we report a function of the CaLEA1 protein in the defense responses of plants to osmotic stress. Our analyses showed that the CaLEA1 gene was strongly induced in pepper leaves exposed to drought and increased salinity. Furthermore, we determined that the CaLEA1 protein has a late embryogenesis abundant (LEA)_3 homolog domain highly conserved among other known group 5 LEA proteins and is localized in the processing body. We generated CaLEA1-silenced peppers and CaLEA1-overexpressing (OX) transgenic Arabidopsis plants to evaluate their responses to dehydration and high salinity. Virus-induced gene silencing of CaLEA1 in pepper plants conferred enhanced sensitivity to drought and salt stresses, which was accompanied by high levels of lipid peroxidation in dehydrated and NaCl-treated leaves. CaLEA1-OX plants exhibited enhanced sensitivity to abscisic acid (ABA) during seed germination and in the seedling stage; furthermore, these plants were more tolerant to drought and salt stress than the wild-type plants because of enhanced stomatal closure and increased expression of stress-responsive genes. Collectively, our data suggest that CaLEA1 positively regulates drought and salinity tolerance through ABA-mediated cell signaling.
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Affiliation(s)
- Chae Woo Lim
- Department of Life Science (BK21 Program), Chung-Ang University, Seoul, 156-756, Republic of Korea
| | - Sohee Lim
- Department of Life Science (BK21 Program), Chung-Ang University, Seoul, 156-756, Republic of Korea
| | - Woonhee Baek
- Department of Life Science (BK21 Program), Chung-Ang University, Seoul, 156-756, Republic of Korea
| | - Sung Chul Lee
- Department of Life Science (BK21 Program), Chung-Ang University, Seoul, 156-756, Republic of Korea
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55
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Chistiakov DA, Sobenin IA, Orekhov AN, Bobryshev YV. Human miR-221/222 in Physiological and Atherosclerotic Vascular Remodeling. BIOMED RESEARCH INTERNATIONAL 2015; 2015:354517. [PMID: 26221589 PMCID: PMC4499635 DOI: 10.1155/2015/354517] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 10/29/2014] [Indexed: 12/11/2022]
Abstract
A cluster of miR-221/222 is a key player in vascular biology through exhibiting its effects on vascular smooth muscle cells (VSMCs) and endothelial cells (ECs). These miRNAs contribute to vascular remodeling, an adaptive process involving phenotypic and behavioral changes in vascular cells in response to vascular injury. In proliferative vascular diseases such as atherosclerosis, pathological vascular remodeling plays a prominent role. The miR-221/222 cluster controls development and differentiation of ECs but inhibits their proangiogenic activation, proliferation, and migration. miR-221/222 are primarily implicated in maintaining endothelial integrity and supporting quiescent EC phenotype. Vascular expression of miR-221/222 is upregulated in initial atherogenic stages causing inhibition of angiogenic recruitment of ECs and increasing endothelial dysfunction and EC apoptosis. In contrast, these miRNAs stimulate VSMCs and switching from the VSMC "contractile" phenotype to the "synthetic" phenotype associated with induction of proliferation and motility. In atherosclerotic vessels, miR-221/222 drive neointima formation. Both miRNAs contribute to atherogenic calcification of VSMCs. In advanced plaques, chronic inflammation downregulates miR-221/222 expression in ECs that in turn could activate intralesion neoangiogenesis. In addition, both miRNAs could contribute to cardiovascular pathology through their effects on fat and glucose metabolism in nonvascular tissues such as adipose tissue, liver, and skeletal muscles.
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Affiliation(s)
- Dmitry A. Chistiakov
- Department of Medical Nanobiotechnology, Pirogov Russian State Medical University, Moscow 117997, Russia
- The Mount Sinai Community Clinical Oncology Program, Mount Sinai Comprehensive Cancer Center, Mount Sinai Medical Center, Miami Beach, FL 33140, USA
| | - Igor A. Sobenin
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, Russian Academy of Sciences, Moscow 125315, Russia
- Laboratory of Medical Genetics, Russian Cardiology Research and Production Complex, Moscow 121552, Russia
| | - Alexander N. Orekhov
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, Russian Academy of Sciences, Moscow 125315, Russia
- Institute for Atherosclerosis Research, Skolkovo Innovative Center, Moscow 121609, Russia
| | - Yuri V. Bobryshev
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, Russian Academy of Sciences, Moscow 125315, Russia
- Faculty of Medicine and St Vincent's Centre for Applied Medical Research, University of New South Wales, Sydney, NSW 2052, Australia
- School of Medicine, University of Western Sydney, Campbelltown, NSW 2560, Australia
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56
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Update on the Pathogenic Implications and Clinical Potential of microRNAs in Cardiac Disease. BIOMED RESEARCH INTERNATIONAL 2015. [PMID: 26221581 PMCID: PMC4499420 DOI: 10.1155/2015/105620] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
miRNAs, a unique class of endogenous noncoding RNAs, are highly conserved across species, repress gene translation upon binding to mRNA, and thereby influence many biological processes. As such, they have been recently recognized as regulators of virtually all aspects of cardiac biology, from the development and cell lineage specification of different cell populations within the heart to the survival of cardiomyocytes under stress conditions. Various miRNAs have been recently established as powerful mediators of distinctive aspects in many cardiac disorders. For instance, acute myocardial infarction induces cardiac tissue necrosis and apoptosis but also initiates a pathological remodelling response of the left ventricle that includes hypertrophic growth of cardiomyocytes and fibrotic deposition of extracellular matrix components. In this regard, recent findings place various miRNAs as unquestionable contributing factors in the pathogenesis of cardiac disorders, thus begging the question of whether miRNA modulation could become a novel strategy for clinical intervention. In the present review, we aim to expose the latest mechanistic concepts regarding miRNA function within the context of CVD and analyse the reported roles of specific miRNAs in the different stages of left ventricular remodelling as well as their potential use as a new class of disease-modifying clinical options.
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57
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Merret R, Nagarajan VK, Carpentier MC, Park S, Favory JJ, Descombin J, Picart C, Charng YY, Green PJ, Deragon JM, Bousquet-Antonelli C. Heat-induced ribosome pausing triggers mRNA co-translational decay in Arabidopsis thaliana. Nucleic Acids Res 2015; 43:4121-32. [PMID: 25845591 PMCID: PMC4417158 DOI: 10.1093/nar/gkv234] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 03/06/2015] [Indexed: 12/24/2022] Open
Abstract
The reprogramming of gene expression in heat stress is a key determinant to organism survival. Gene expression is downregulated through translation initiation inhibition and release of free mRNPs that are rapidly degraded or stored. In mammals, heat also triggers 5′-ribosome pausing preferentially on transcripts coding for HSC/HSP70 chaperone targets, but the impact of such phenomenon on mRNA fate remains unknown. Here, we provide evidence that, in Arabidopsis thaliana, heat provokes 5′-ribosome pausing leading to the XRN4-mediated 5′-directed decay of translating mRNAs. We also show that hindering HSC/HSP70 activity at 20°C recapitulates heat effects by inducing ribosome pausing and co-translational mRNA turnover. Strikingly, co-translational decay targets encode proteins with high HSC/HSP70 binding scores and hydrophobic N-termini, two characteristics that were previously observed for transcripts most prone to pausing in animals. This work suggests for the first time that stress-induced variation of translation elongation rate is an evolutionarily conserved process leading to the polysomal degradation of thousands of ‘non-aberrant’ mRNAs.
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Affiliation(s)
- Rémy Merret
- CNRS-LGDP UMR 5096, 58 av. Paul Alduy 66860 Perpignan, France Université de Perpignan Via Domitia, LGDP-UMR5096, 58 av. Paul Alduy, 66860 Perpignan, France
| | - Vinay K Nagarajan
- University of Delaware, Delaware Biotechnology Institute, 15 Innovation Way, Newark, DE 19711, USA
| | - Marie-Christine Carpentier
- CNRS-LGDP UMR 5096, 58 av. Paul Alduy 66860 Perpignan, France Université de Perpignan Via Domitia, LGDP-UMR5096, 58 av. Paul Alduy, 66860 Perpignan, France
| | - Sunhee Park
- University of Delaware, Delaware Biotechnology Institute, 15 Innovation Way, Newark, DE 19711, USA
| | - Jean-Jacques Favory
- CNRS-LGDP UMR 5096, 58 av. Paul Alduy 66860 Perpignan, France Université de Perpignan Via Domitia, LGDP-UMR5096, 58 av. Paul Alduy, 66860 Perpignan, France
| | - Julie Descombin
- CNRS-LGDP UMR 5096, 58 av. Paul Alduy 66860 Perpignan, France Université de Perpignan Via Domitia, LGDP-UMR5096, 58 av. Paul Alduy, 66860 Perpignan, France
| | - Claire Picart
- CNRS-LGDP UMR 5096, 58 av. Paul Alduy 66860 Perpignan, France Université de Perpignan Via Domitia, LGDP-UMR5096, 58 av. Paul Alduy, 66860 Perpignan, France
| | - Yee-Yung Charng
- Agricultural Biotechnology Research Center, Academia Sinica, 128 Academia Road Section 2, Taipei, Taiwan 11529, ROC
| | - Pamela J Green
- University of Delaware, Delaware Biotechnology Institute, 15 Innovation Way, Newark, DE 19711, USA
| | - Jean-Marc Deragon
- CNRS-LGDP UMR 5096, 58 av. Paul Alduy 66860 Perpignan, France Université de Perpignan Via Domitia, LGDP-UMR5096, 58 av. Paul Alduy, 66860 Perpignan, France
| | - Cécile Bousquet-Antonelli
- CNRS-LGDP UMR 5096, 58 av. Paul Alduy 66860 Perpignan, France Université de Perpignan Via Domitia, LGDP-UMR5096, 58 av. Paul Alduy, 66860 Perpignan, France
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58
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Vanevski F, Xu B. HuD interacts with Bdnf mRNA and is essential for activity-induced BDNF synthesis in dendrites. PLoS One 2015; 10:e0117264. [PMID: 25692578 PMCID: PMC4332865 DOI: 10.1371/journal.pone.0117264] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 12/23/2014] [Indexed: 12/19/2022] Open
Abstract
Highly specific activity-dependent neuronal responses are necessary for modulating synapses to facilitate learning and memory. We present evidence linking a number of important processes involved in regulating synaptic plasticity, suggesting a mechanistic pathway whereby activity-dependent signaling, likely through protein kinase C (PKC)-mediated phosphorylation of HuD, can relieve basal repression of Bdnf mRNA translation in dendrites, allowing for increased TrkB signaling and synaptic remodeling. We demonstrate that the neuronal ELAV family of RNA binding proteins associates in vivo with several Bdnf mRNA isoforms present in the adult brain in an activity-dependent manner, and that one member, HuD, interacts directly with sequences in the long Bdnf 3' untranslated region (3'UTR) and co-localizes with Bdnf mRNA in dendrites of hippocampal neurons. Activation of PKC leads to increased dendritic translation of mRNAs containing the long Bdnf 3'UTR, a process that is dependent on the presence of HuD and its phosphorylation at threonine residues 149 and/or 165. Thus, we found a direct effect of HuD on regulating translation of dendritic Bdnf mRNAs to mediate local and activity-dependent increases in dendritic BDNF synthesis.
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Affiliation(s)
- Filip Vanevski
- Department of Pharmacology and Physiology, Georgetown University Medical Center, Washington, D.C., United States of America
| | - Baoji Xu
- Department of Pharmacology and Physiology, Georgetown University Medical Center, Washington, D.C., United States of America
- * E-mail:
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59
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Antonicka H, Shoubridge EA. Mitochondrial RNA Granules Are Centers for Posttranscriptional RNA Processing and Ribosome Biogenesis. Cell Rep 2015; 10:920-932. [PMID: 25683715 DOI: 10.1016/j.celrep.2015.01.030] [Citation(s) in RCA: 201] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Revised: 12/10/2014] [Accepted: 01/09/2015] [Indexed: 02/07/2023] Open
Abstract
Cytoplasmic RNA granules play a central role in mRNA metabolism, but the importance of mitochondrial RNA granules remains relatively unexplored. We characterized their proteome and found that they contain a large toolbox of proteins dedicated to RNA metabolism. Investigation of four uncharacterized putative RNA-binding proteins-two RNA helicases, DHX30 and DDX28, and two proteins of the Fas-activated serine-threonine kinase (FASTKD) family, FASTKD2 and FASTKD5-demonstrated that both helicases and FASTKD2 are required for mitochondrial ribosome biogenesis. RNA-sequencing (RNA-seq) analysis showed that DDX28 and FASTKD2 bound the 16S rRNA. FASTKD5 is required for maturing precursor mRNAs that are not flanked by tRNAs and that therefore cannot be processed by the canonical mRNA maturation pathway. Silencing FASTKD5 rendered mature COX I mRNA almost undetectable, which severely reduced the synthesis of COX I, resulting in a complex IV assembly defect. These data demonstrate that mitochondrial RNA granules are centers for posttranscriptional RNA processing and the biogenesis of mitochondrial ribosomes.
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Affiliation(s)
- Hana Antonicka
- Montreal Neurological Institute and Department of Human Genetics, McGill University, Montreal, QC H3A 2B4, Canada
| | - Eric A Shoubridge
- Montreal Neurological Institute and Department of Human Genetics, McGill University, Montreal, QC H3A 2B4, Canada.
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60
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Roux ME, Rasmussen MW, Palma K, Lolle S, Regué ÀM, Bethke G, Glazebrook J, Zhang W, Sieburth L, Larsen MR, Mundy J, Petersen M. The mRNA decay factor PAT1 functions in a pathway including MAP kinase 4 and immune receptor SUMM2. EMBO J 2015; 34:593-608. [PMID: 25603932 DOI: 10.15252/embj.201488645] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Multi-layered defense responses are activated in plants upon recognition of invading pathogens. Transmembrane receptors recognize conserved pathogen-associated molecular patterns (PAMPs) and activate MAP kinase cascades, which regulate changes in gene expression to produce appropriate immune responses. For example, Arabidopsis MAP kinase 4 (MPK4) regulates the expression of a subset of defense genes via at least one WRKY transcription factor. We report here that MPK4 is found in complexes in vivo with PAT1, a component of the mRNA decapping machinery. PAT1 is also phosphorylated by MPK4 and, upon flagellin PAMP treatment, PAT1 accumulates and localizes to cytoplasmic processing (P) bodies which are sites for mRNA decay. Pat1 mutants exhibit dwarfism and de-repressed immunity dependent on the immune receptor SUMM2. Since mRNA decapping is a critical step in mRNA turnover, linking MPK4 to mRNA decay via PAT1 provides another mechanism by which MPK4 may rapidly instigate immune responses.
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Affiliation(s)
- Milena Edna Roux
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Signe Lolle
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Àngels Mateu Regué
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Gerit Bethke
- Department of Plant Biology, University of Minnesota, St. Paul, MN, USA
| | - Jane Glazebrook
- Department of Plant Biology, University of Minnesota, St. Paul, MN, USA
| | - Weiping Zhang
- Department of Biology, University of Utah, Salt Lake City, UT, USA
| | - Leslie Sieburth
- Department of Biology, University of Utah, Salt Lake City, UT, USA
| | - Martin R Larsen
- University of Southern Denmark Institute for Biochemistry and Molecular Biology, Odense, Denmark
| | - John Mundy
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Morten Petersen
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
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61
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Corcoran JA, Johnston BP, McCormick C. Viral activation of MK2-hsp27-p115RhoGEF-RhoA signaling axis causes cytoskeletal rearrangements, p-body disruption and ARE-mRNA stabilization. PLoS Pathog 2015; 11:e1004597. [PMID: 25569678 PMCID: PMC4287613 DOI: 10.1371/journal.ppat.1004597] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 12/02/2014] [Indexed: 11/30/2022] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) is the infectious cause of several AIDS-related cancers, including the endothelial cell (EC) neoplasm Kaposi's sarcoma (KS). KSHV-infected ECs secrete abundant host-derived pro-inflammatory molecules and angiogenic factors that contribute to tumorigenesis. The precise contributions of viral gene products to this secretory phenotype remain to be elucidated, but there is emerging evidence for post-transcriptional regulation. The Kaposin B (KapB) protein is thought to contribute to the secretory phenotype in infected cells by binding and activating the stress-responsive kinase MK2, thereby selectively blocking decay of AU-rich mRNAs (ARE-mRNAs) encoding pro-inflammatory cytokines and angiogenic factors. Processing bodies (PBs) are cytoplasmic ribonucleoprotein foci in which ARE-mRNAs normally undergo rapid 5′ to 3′ decay. Here, we demonstrate that PB dispersion is a feature of latent KSHV infection, which is dependent on kaposin protein expression. KapB is sufficient to disperse PBs, and KapB-mediated ARE-mRNA stabilization could be partially reversed by treatments that restore PBs. Using a combination of genetic and chemical approaches we provide evidence that KapB-mediated PB dispersion is dependent on activation of a non-canonical Rho-GTPase signaling axis involving MK2, hsp27, p115RhoGEF and RhoA. PB dispersion in latently infected cells is likewise dependent on p115RhoGEF. In addition to PB dispersion, KapB-mediated RhoA activation in primary ECs caused actin stress fiber formation, increased cell motility and angiogenesis; these effects were dependent on the activity of the RhoA substrate kinases ROCK1/2. By contrast, KapB-mediated PB dispersion occurred in a ROCK1/2-independent manner. Taken together, these observations position KapB as a key contributor to viral reprogramming of ECs, capable of eliciting many of the phenotypes characteristic of KS tumor cells, and strongly contributing to the post-transcriptional control of EC gene expression and secretion. We have only scratched the surface in understanding how viruses control host gene expression. Several viruses disrupt important sites of post-transcriptional control of gene expression known as processing bodies (PBs), but underlying regulatory mechanisms and biological relevance remain poorly understood in most cases. Our study shows that the Kaposin B (KapB) protein of Kaposi's sarcoma (KS)-associated herpesvirus, known to block the degradation of a class of labile host mRNAs, does so by constitutively activating a signaling axis involving MK2, hsp27, p115RhoGEF and RhoA, thereby dispersing PBs. Thus, PB disruption may support the secretion of host pro-inflammatory cytokines and angiogenic factors that underlies KS tumor formation. Furthermore, by activating RhoA, KapB also causes cytoskeletal rearrangements, accelerated cell migration and angiogenesis in an endothelial cell model. Our findings position KapB as a key contributor to viral reprogramming of endothelial cells.
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Affiliation(s)
- Jennifer A. Corcoran
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, Nova Scotia, Canada
| | - Benjamin P. Johnston
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, Nova Scotia, Canada
| | - Craig McCormick
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, Nova Scotia, Canada
- * E-mail:
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62
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Abstract
For many animals, survival of severe environmental stress (e.g. to extremes of heat or cold, drought, oxygen limitation, food deprivation) is aided by entry into a hypometabolic state. Strong depression of metabolic rate, often to only 1–20% of normal resting rate, is a core survival strategy of multiple forms of hypometabolism across the animal kingdom, including hibernation, anaerobiosis, aestivation and freeze tolerance. Global biochemical controls are needed to suppress and reprioritize energy use; one such well-studied control is reversible protein phosphorylation. Recently, we turned our attention to the idea that mechanisms previously associated mainly with epigenetic regulation can also contribute to reversible suppression of gene expression in hypometabolic states. Indeed, situations as diverse as mammalian hibernation and turtle anoxia tolerance show coordinated changes in histone post-translational modifications (acetylation, phosphorylation) and activities of histone deacetylases, consistent with their use as mechanisms for suppressing gene expression during hypometabolism. Other potential mechanisms of gene silencing in hypometabolic states include altered expression of miRNAs that can provide post-transcriptional suppression of mRNA translation and the formation of ribonuclear protein bodies in the nucleus and cytoplasm to allow storage of mRNA transcripts until animals rouse themselves again. Furthermore, mechanisms first identified in epigenetic regulation (e.g. protein acetylation) are now proving to apply to many central metabolic enzymes (e.g. lactate dehydrogenase), suggesting a new layer of regulatory control that can contribute to coordinating the depression of metabolic rate.
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Affiliation(s)
- Kenneth B. Storey
- Institute of Biochemistry and Departments of Biology and Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada
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63
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Díaz NF, Cruz-Reséndiz MS, Flores-Herrera H, García-López G, Molina-Hernández A. MicroRNAs in central nervous system development. Rev Neurosci 2014; 25:675-86. [PMID: 24902008 DOI: 10.1515/revneuro-2014-0014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 05/13/2014] [Indexed: 12/23/2022]
Abstract
During early and late embryo neurodevelopment, a large number of molecules work together in a spatial and temporal manner to ensure the adequate formation of an organism. Diverse signals participate in embryo patterning and organization synchronized by time and space. Among the molecules that are expressed in a temporal and spatial manner, and that are considered essential in several developmental processes, are the microRNAs (miRNAs). In this review, we highlight some important aspects of the biogenesis and function of miRNAs as well as their participation in ectoderm commitment and their role in central nervous system (CNS) development. Instead of giving an extensive list of miRNAs involved in these processes, we only mention those miRNAs that are the most studied during the development of the CNS as well as the most likely mRNA targets for each miRNA and its protein functions.
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64
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Anderson P, Kedersha N, Ivanov P. Stress granules, P-bodies and cancer. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1849:861-70. [PMID: 25482014 DOI: 10.1016/j.bbagrm.2014.11.009] [Citation(s) in RCA: 272] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 11/21/2014] [Accepted: 11/26/2014] [Indexed: 12/27/2022]
Abstract
Cancer cells are exposed to adverse conditions in the tumor microenvironment, and utilize post-transcriptional control mechanisms to re-program gene expression in ways that enhance cell survival. Stress granules and processing bodies are RNA-containing granules that contribute to this process by modulating cellular signaling pathways, metabolic machinery, and stress response programs. This review examines evidence implicating RNA granules in the pathogenesis of cancer and discusses their potential as targets for anticancer therapies. This article is part of a Special Issue entitled: Translation and Cancer.
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Affiliation(s)
- Paul Anderson
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
| | - Nancy Kedersha
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Pavel Ivanov
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
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65
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Yang G, Smibert CA, Kaplan DR, Miller FD. An eIF4E1/4E-T complex determines the genesis of neurons from precursors by translationally repressing a proneurogenic transcription program. Neuron 2014; 84:723-39. [PMID: 25456498 DOI: 10.1016/j.neuron.2014.10.022] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2014] [Indexed: 02/06/2023]
Abstract
Here, we have addressed the mechanisms that determine genesis of the correct numbers of neurons during development, focusing on the embryonic cortex. We identify in neural precursors a repressive complex involving eIF4E1 and its binding partner 4E-T that coordinately represses translation of proteins that determine neurogenesis. This eIF4E1/4E-T complex is present in granules with the processing body proteins Lsm1 and Rck, and disruption of this complex causes premature and enhanced neurogenesis and neural precursor depletion. Analysis of the 4E-T complex shows that it is highly enriched in mRNAs encoding transcription factors and differentiation-related proteins. These include the proneurogenic bHLH mRNAs, which colocalize with 4E-T in granules and whose protein products are aberrantly upregulated following knockdown of eIF4E, 4E-T, or processing body proteins. Thus, neural precursors are transcriptionally primed to generate neurons, but an eIF4E/4E-T complex sequesters and represses translation of proneurogenic proteins to determine appropriate neurogenesis.
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Affiliation(s)
- Guang Yang
- Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
| | - Craig A Smibert
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - David R Kaplan
- Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Freda D Miller
- Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada.
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66
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Wollschlaeger C, Trevijano-Contador N, Wang X, Legrand M, Zaragoza O, Heitman J, Janbon G. Distinct and redundant roles of exonucleases in Cryptococcus neoformans: implications for virulence and mating. Fungal Genet Biol 2014; 73:20-8. [PMID: 25267175 DOI: 10.1016/j.fgb.2014.09.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 09/17/2014] [Accepted: 09/22/2014] [Indexed: 01/26/2023]
Abstract
Opportunistic pathogens like Cryptococcus neoformans are constantly exposed to changing environments, in their natural habitat as well as when encountering a human host. This requires a coordinated program to regulate gene expression that can act at the levels of mRNA synthesis and also mRNA degradation. Here, we find that deletion of the gene encoding the major cytoplasmic 5'→3' exonuclease Xrn1p in C. neoformans has important consequences for virulence associated phenotypes such as growth at 37 °C, capsule and melanin. In an invertebrate model of cryptococcosis the alteration of these virulence properties corresponds to avirulence of the xrn1Δ mutant strains. Additionally, deletion of XRN1 impairs uni- and bisexual mating. On a molecular level, the absence of XRN1 is associated with the upregulation of other major exonuclease encoding genes (i.e. XRN2 and RRP44). Using inducible alleles of RRP44 and XRN2, we show that artificial overexpression of these genes alters LAC1 gene expression and mating. Our data thus suggest the existence of a complex interdependent regulation of exonuclease encoding genes that impact upon virulence and mating in C. neoformans.
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Affiliation(s)
- Carolin Wollschlaeger
- Institut Pasteur, Unité Biologie et Pathogénicité Fongiques - INRA USC2019, 75015 Paris, France
| | - Nuria Trevijano-Contador
- Mycology Reference Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Xuying Wang
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Mélanie Legrand
- Institut Pasteur, Unité Biologie et Pathogénicité Fongiques - INRA USC2019, 75015 Paris, France
| | - Oscar Zaragoza
- Mycology Reference Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Guilhem Janbon
- Institut Pasteur, Unité Biologie et Pathogénicité Fongiques - INRA USC2019, 75015 Paris, France.
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67
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Fan M, Zhang Y, Huang Z, Liu J, Guo X, Zhang H, Luo H. Optimizations of siRNA design for the activation of gene transcription by targeting the TATA-box motif. PLoS One 2014; 9:e108253. [PMID: 25250958 PMCID: PMC4176967 DOI: 10.1371/journal.pone.0108253] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 08/20/2014] [Indexed: 12/24/2022] Open
Abstract
Small interfering RNAs (siRNAs) are widely used to repress gene expression by targeting mRNAs. Some reports reveal that siRNAs can also activate or inhibit gene expression through targeting the gene promoters. Our group has found that microRNAs (miRNAs) could activate gene transcription via interaction with the TATA-box motif in gene promoters. To investigate whether siRNA targeting the same region could upregulate the promoter activity, we test the activating efficiency of siRNAs targeting the TATA-box motif of 16 genes and perform a systematic analysis to identify the common features of the functional siRNAs for effective activation of gene promoters. Further, we try various modifications to improve the activating efficiency of siRNAs and find that it is quite useful to design the promoter-targeting activating siRNA by following several rules such as (a) complementary to the TATA-box-centered region; (b) UA usage at the first two bases of the antisense strand; (c) twenty-three nucleotides (nts) in length; (d) 2'-O-Methyl (2'-OMe) modification at the 3' terminus of the antisense strand; (e) avoiding mismatches at the 3' end of the antisense strand. The optimized activating siRNAs potently enhance the expression of interleukin-2 (IL-2) gene in human and mouse primary CD4+ T cells with a long-time effect. Taken together, our study provides a guideline for rational design the promoter-targeting siRNA to sequence-specifically enhance gene expression.
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Affiliation(s)
- Miaomiao Fan
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yijun Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zhuoqiong Huang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jun Liu
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xuemin Guo
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Hui Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- * E-mail: (HZ); (HL)
| | - Haihua Luo
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- * E-mail: (HZ); (HL)
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68
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Aizer A, Kalo A, Kafri P, Shraga A, Ben-Yishay R, Jacob A, Kinor N, Shav-Tal Y. Quantifying mRNA targeting to P-bodies in living human cells reveals their dual role in mRNA decay and storage. J Cell Sci 2014; 127:4443-56. [PMID: 25128566 DOI: 10.1242/jcs.152975] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The 5'-to-3' mRNA degradation machinery localizes to cytoplasmic processing bodies (P-bodies), which are non-membranous structures found in all eukaryotes. Although P-body function has been intensively studied in yeast, less is known about their role in mammalian cells, such as whether P-body enzymes are actively engaged in mRNA degradation or whether P-bodies serve as mRNA storage depots, particularly during cellular stress. We examined the fate of mammalian mRNAs in P-bodies during translational stress, and show that mRNAs accumulate within P-bodies during amino acid starvation. The 5' and 3' ends of the transcripts residing in P-bodies could be identified, but poly(A) tails were not detected. Using the MS2 mRNA-tagging system for mRNA visualization in living cells, we found that a stationary mRNA population formed in P-bodies during translational stress, which cleared gradually after the stress was relieved. Dcp2-knockdown experiments showed that there is constant degradation of part of the P-body-associated mRNA population. This analysis demonstrates the dual role of P-bodies as decay sites and storage areas under regular and stress conditions.
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Affiliation(s)
- Adva Aizer
- The Mina & Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Alon Kalo
- The Mina & Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Pinhas Kafri
- The Mina & Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Amit Shraga
- The Mina & Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Rakefet Ben-Yishay
- The Mina & Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Avi Jacob
- The Mina & Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Noa Kinor
- The Mina & Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Yaron Shav-Tal
- The Mina & Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 52900, Israel
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69
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Abstract
In eukaryotic cells, non-translating mRNAs can accumulate into cytoplasmic mRNP (messenger ribonucleoprotein) granules such as P-bodies (processing bodies) and SGs (stress granules). P-bodies contain the mRNA decay and translational repression machineries and are ubiquitously expressed in mammalian cells and lower eukaryote species including Saccharomyces cerevisiae, Drosophila melanogaster and Caenorhabditis elegans. In contrast, SGs are only detected during cellular stress when translation is inhibited and form from aggregates of stalled pre-initiation complexes. SGs and P-bodies are related to NGs (neuronal granules), which are essential in the localization and control of mRNAs in neurons. Importantly, RNA granules are linked to the cytoskeleton, which plays an important role in mediating many of their dynamic properties. In the present review, we discuss how P-bodies, SGs and NGs are linked to cytoskeletal networks and the importance of these linkages in maintaining localization of their RNA cargoes.
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70
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Schaefer JS, Montufar-Solis D, Klein JR. A role for IL-10 in the transcriptional regulation of Roquin-1. Gene 2014; 549:134-40. [PMID: 25062971 DOI: 10.1016/j.gene.2014.07.056] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 07/03/2014] [Accepted: 07/21/2014] [Indexed: 01/25/2023]
Abstract
Roquin-1, a RING finger E3 ubiquitin ligase, functions as a modulator of inflammation; however, nothing is known about how Rc3h1 expression is regulated. Here, we describe an opposing relationship between Roquin-1 and the IL-17 proinflammatory cytokine by demonstrating that enforced expression of Rc3h1 restricts Il17a expression, and that exposure of T cells to IL-10, a cytokine with immunosuppressive activity, increases Rc3h1 expression. Luciferase reporter assays conducted using eight transcription factor plasmids (STAT1, STAT3, STAT5, GATA2, c-Rel, IKZF1, IKZF2, and IKZF3) demonstrated that STAT1, STAT3, GATA2, and c-Rel increased Rc3h1 promoter activity, whereas IKZF2 decreased activity. Gene expression of those five transcription factors increased in T cells exposed to IL-10. Transcription factor-specific siRNAs suppressed the IL-10 effect on Rc3h1 transcription. These findings identify a role for IL-10 in regulating Rc3h1 transcription, and they have implications for understanding how Roquin-1 controls the immune response.
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Affiliation(s)
- Jeremy S Schaefer
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
| | - Dina Montufar-Solis
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
| | - John R Klein
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA.
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71
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Schröder J, Ansaloni S, Schilling M, Liu T, Radke J, Jaedicke M, Schjeide BMM, Mashychev A, Tegeler C, Radbruch H, Papenberg G, Düzel S, Demuth I, Bucholtz N, Lindenberger U, Li SC, Steinhagen-Thiessen E, Lill CM, Bertram L. MicroRNA-138 is a potential regulator of memory performance in humans. Front Hum Neurosci 2014; 8:501. [PMID: 25071529 PMCID: PMC4093940 DOI: 10.3389/fnhum.2014.00501] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 06/20/2014] [Indexed: 01/01/2023] Open
Abstract
Genetic factors underlie a substantial proportion of individual differences in cognitive functions in humans, including processes related to episodic and working memory. While genetic association studies have proposed several candidate “memory genes,” these currently explain only a minor fraction of the phenotypic variance. Here, we performed genome-wide screening on 13 episodic and working memory phenotypes in 1318 participants of the Berlin Aging Study II aged 60 years or older. The analyses highlight a number of novel single nucleotide polymorphisms (SNPs) associated with memory performance, including one located in a putative regulatory region of microRNA (miRNA) hsa-mir-138-5p (rs9882688, P-value = 7.8 × 10−9). Expression quantitative trait locus analyses on next-generation RNA-sequencing data revealed that rs9882688 genotypes show a significant correlation with the expression levels of this miRNA in 309 human lymphoblastoid cell lines (P-value = 5 × 10−4). In silico modeling of other top-ranking GWAS signals identified an additional memory-associated SNP in the 3′ untranslated region (3′ UTR) of DCP1B, a gene encoding a core component of the mRNA decapping complex in humans, predicted to interfere with hsa-mir-138-5p binding. This prediction was confirmed in vitro by luciferase assays showing differential binding of hsa-mir-138-5p to 3′ UTR reporter constructs in two human cell lines (HEK293: P-value = 0.0470; SH-SY5Y: P-value = 0.0866). Finally, expression profiling of hsa-mir-138-5p and DCP1B mRNA in human post-mortem brain tissue revealed that both molecules are expressed simultaneously in frontal cortex and hippocampus, suggesting that the proposed interaction between hsa-mir-138-5p and DCP1B may also take place in vivo. In summary, by combining unbiased genome-wide screening with extensive in silico modeling, in vitro functional assays, and gene expression profiling, our study identified miRNA-138 as a potential molecular regulator of human memory function.
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Affiliation(s)
- Julia Schröder
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics Berlin, Germany ; Charité Research Group on Geriatrics, Charité - Universitätsmedizin Berlin Berlin, Germany
| | - Sara Ansaloni
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics Berlin, Germany
| | - Marcel Schilling
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics Berlin, Germany ; Max Delbrück Center for Molecular Medicine, Berlin Institute for Medical Systems Biology Berlin, Germany
| | - Tian Liu
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics Berlin, Germany ; Center for Lifespan Psychology, Max Planck Institute for Human Development Berlin, Germany
| | - Josefine Radke
- Department of Neuropathology, Charité - Universitätsmedizin Berlin Berlin, Germany
| | - Marian Jaedicke
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics Berlin, Germany
| | - Brit-Maren M Schjeide
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics Berlin, Germany
| | - Andriy Mashychev
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics Berlin, Germany
| | - Christina Tegeler
- Charité Research Group on Geriatrics, Charité - Universitätsmedizin Berlin Berlin, Germany
| | - Helena Radbruch
- Department of Neuropathology, Charité - Universitätsmedizin Berlin Berlin, Germany
| | - Goran Papenberg
- Center for Lifespan Psychology, Max Planck Institute for Human Development Berlin, Germany ; Aging Research Center, Karolinska Institute Stockholm, Sweden
| | - Sandra Düzel
- Center for Lifespan Psychology, Max Planck Institute for Human Development Berlin, Germany
| | - Ilja Demuth
- Charité Research Group on Geriatrics, Charité - Universitätsmedizin Berlin Berlin, Germany ; Institute of Medical and Human Genetics, Charité - Universitätsmedizin Berlin Berlin, Germany
| | - Nina Bucholtz
- Charité Research Group on Geriatrics, Charité - Universitätsmedizin Berlin Berlin, Germany
| | - Ulman Lindenberger
- Center for Lifespan Psychology, Max Planck Institute for Human Development Berlin, Germany
| | - Shu-Chen Li
- Center for Lifespan Psychology, Max Planck Institute for Human Development Berlin, Germany ; Department of Psychology, Lifespan Developmental Neuroscience, TU Dresden Dresden, Germany
| | | | - Christina M Lill
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics Berlin, Germany ; Focus Program Translational Neuroscience, Department of Neurology, University Medical Center of the Johannes Gutenberg University Mainz Mainz, Germany
| | - Lars Bertram
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics Berlin, Germany ; Faculty of Medicine, School of Public Health, Imperial College London London, UK
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72
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Fromm SA, Kamenz J, Nöldeke ER, Neu A, Zocher G, Sprangers R. In‐vitro‐Rekonstitution eines zellulären Phasenübergangs unter Beteiligung der mRNA‐Decapping‐Maschinerie. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402885] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Simon A. Fromm
- Max‐Planck‐Institut für Entwicklungsbiologie, Spemannstraße 35, 72076 Tübingen (Deutschland)
| | - Julia Kamenz
- Friedrich‐Miescher‐Laboratorium der Max‐Planck‐Gesellschaft, Tübingen (Deutschland)
| | - Erik R. Nöldeke
- Max‐Planck‐Institut für Entwicklungsbiologie, Spemannstraße 35, 72076 Tübingen (Deutschland)
| | - Ancilla Neu
- Max‐Planck‐Institut für Entwicklungsbiologie, Spemannstraße 35, 72076 Tübingen (Deutschland)
| | - Georg Zocher
- Interfakultäres Institut für Biochemie, Universität Tübingen (Deutschland)
| | - Remco Sprangers
- Max‐Planck‐Institut für Entwicklungsbiologie, Spemannstraße 35, 72076 Tübingen (Deutschland)
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73
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Fromm SA, Kamenz J, Nöldeke ER, Neu A, Zocher G, Sprangers R. In vitro reconstitution of a cellular phase-transition process that involves the mRNA decapping machinery. Angew Chem Int Ed Engl 2014; 53:7354-9. [PMID: 24862735 PMCID: PMC4320757 DOI: 10.1002/anie.201402885] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Indexed: 12/12/2022]
Abstract
In eukaryotic cells, components of the 5' to 3' mRNA degradation machinery can undergo a rapid phase transition. The resulting cytoplasmic foci are referred to as processing bodies (P-bodies). The molecular details of the self-aggregation process are, however, largely undetermined. Herein, we use a bottom-up approach that combines NMR spectroscopy, isothermal titration calorimetry, X-ray crystallography, and fluorescence microscopy to probe if mRNA degradation factors can undergo phase transitions in vitro. We show that the Schizosaccharomyces pombe Dcp2 mRNA decapping enzyme, its prime activator Dcp1, and the scaffolding proteins Edc3 and Pdc1 are sufficient to reconstitute a phase-separation process. Intermolecular interactions between the Edc3 LSm domain and at least 10 helical leucine-rich motifs in Dcp2 and Pdc1 build the core of the interaction network. We show that blocking of these interactions interferes with the clustering behavior, both in vitro and in vivo.
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Affiliation(s)
- Simon A Fromm
- Max Planck Institute for Developmental BiologySpemannstrasse 35, 72076 Tübingen (Germany)
| | - Julia Kamenz
- Friedrich Miescher Laboratory of the Max Planck SocietyTübingen (Germany)
| | - Erik R Nöldeke
- Max Planck Institute for Developmental BiologySpemannstrasse 35, 72076 Tübingen (Germany)
| | - Ancilla Neu
- Max Planck Institute for Developmental BiologySpemannstrasse 35, 72076 Tübingen (Germany)
| | - Georg Zocher
- Interfaculty Institute of Biochemistry, University of TübingenTübingen (Germany)
| | - Remco Sprangers
- Max Planck Institute for Developmental BiologySpemannstrasse 35, 72076 Tübingen (Germany)
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74
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López-Rosas I, Marchat LA, Olvera BG, Guillen N, Weber C, Hernández de la Cruz O, Ruíz-García E, Astudillo-de la Vega H, López-Camarillo C. Proteomic analysis identifies endoribouclease EhL-PSP and EhRRP41 exosome protein as novel interactors of EhCAF1 deadenylase. J Proteomics 2014; 111:59-73. [PMID: 24998979 DOI: 10.1016/j.jprot.2014.06.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 05/31/2014] [Accepted: 06/20/2014] [Indexed: 01/17/2023]
Abstract
UNLABELLED In higher eukaryotic cells mRNA degradation initiates by poly(A) tail shortening catalyzed by deadenylases CAF1 and CCR4. In spite of the key role of mRNA turnover in gene expression regulation, the underlying mechanisms remain poorly understood in parasites. Here, we aimed to study the function of EhCAF1 and identify associated proteins in Entamoeba histolytica. By biochemical assays, we evidenced that EhCAF1 has both RNA binding and deadenylase activities in vitro. EhCAF1 was located in cytoplasmic P-bodies that increased in number and size after cellular stress induced by DNA damage, heat shock, and nitric oxide. Using pull-down assays and ESI-MS/MS mass spectrometry, we identified 15 potential EhCAF1-interacting proteins, including the endoribonuclease EhL-PSP. Remarkably, EhCAF1 colocalized with EhL-PSP in cytoplasmic P-bodies in trophozoites. Bioinformatic analysis of EhL-PSP network proteins predicts a potential interaction with EhRRP41 exosome protein. Consistently, we evidenced that EhL-PSP colocalizes and physically interacts with EhRRP41. Strikingly, EhRRP41 did not coimmunoprecipitate EhCAF1, suggesting the existence of two EhL-PSP-containing complexes. In conclusion, our results showed novel interactions between mRNA degradation proteins and evidenced for the first time that EhCAF1 is a functional deadenylase that interacts with EhL-PSP endoribonuclease in P-bodies, while EhL-PSP interacts with EhRRP41 exosome protein in this early-branched eukaryote. BIOLOGICAL SIGNIFICANCE This study provides evidences for the functional deadenylase activity of EhCAF1 and shows a link between different mRNA degradation proteins in E. histolytica. By proteomic tools and pull down assays, we evidenced that EhCAF1 interacts with the putative endoribonuclease EhL-PSP, which in turn interacts with exosome EhRRP41 protein. Our data suggest for the first time the presence of two complexes, one containing the endoribonuclease EhL-PSP and the deadenylase EhCAF1 in P-bodies; and another containing the endoribonuclease EhL-PSP and the exosome EhRRP41 exoribonuclease. Overall, these results provide novel data that may help to understand mRNA decay mechanisms in this parasite.
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Affiliation(s)
- Itzel López-Rosas
- Autonomous University of Mexico City, Genomics Sciences Program, Mexico City, Mexico; Biotechnology Program, National School of Medicine and Homeopathy, National Polytechnic Institute, Mexico City, Mexico
| | - Laurence A Marchat
- Biotechnology Program, National School of Medicine and Homeopathy, National Polytechnic Institute, Mexico City, Mexico; Institutional Program of Molecular Biomedicine, National School of Medicine and Homeopathy, National Polytechnic Institute, Mexico City, Mexico
| | - Beatriz Gallo Olvera
- Biotechnology Program, National School of Medicine and Homeopathy, National Polytechnic Institute, Mexico City, Mexico; Institutional Program of Molecular Biomedicine, National School of Medicine and Homeopathy, National Polytechnic Institute, Mexico City, Mexico
| | - Nancy Guillen
- Unit of Cell Biology for Parasitism, Pasteur Institute, Paris, France; INSERM U786, Paris, France
| | - Christian Weber
- Unit of Cell Biology for Parasitism, Pasteur Institute, Paris, France; INSERM U786, Paris, France
| | | | - Erika Ruíz-García
- Translational Medicine Laboratory, National Institute of Cancerology, Mexico City, Mexico
| | - Horacio Astudillo-de la Vega
- Laboratory of Translational Cancer Research and Cellular Therapy, Oncology Hospital, Medical Center Siglo XXI, Mexico City, Mexico
| | - César López-Camarillo
- Autonomous University of Mexico City, Genomics Sciences Program, Mexico City, Mexico.
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75
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Ostareck DH, Naarmann-de Vries IS, Ostareck-Lederer A. DDX6 and its orthologs as modulators of cellular and viral RNA expression. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 5:659-78. [PMID: 24788243 DOI: 10.1002/wrna.1237] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 03/19/2014] [Accepted: 03/21/2014] [Indexed: 12/21/2022]
Abstract
DDX6 (Rck/p54), a member of the DEAD-box family of helicases, is highly conserved from unicellular eukaryotes to vertebrates. Functions of DDX6 and its orthologs in dynamic ribonucleoproteins contribute to global and transcript-specific messenger RNA (mRNA) storage, translational repression, and decay during development and differentiation in the germline and somatic cells. Its role in pathways that promote mRNA-specific alternative translation initiation has been shown to be linked to cellular homeostasis, deregulated tissue development, and the control of gene expression in RNA viruses. Recently, DDX6 was found to participate in mRNA regulation mediated by miRNA-mediated silencing. DDX6 and its orthologs have versatile functions in mRNA metabolism, which characterize them as important post-transcriptional regulators of gene expression.
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Affiliation(s)
- Dirk H Ostareck
- Experimental Research Unit, Department of Intensive Care and Intermediate Care, University Hospital, RWTH Aachen University, Aachen, Germany
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76
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Meikar O, Vagin VV, Chalmel F, Sõstar K, Lardenois A, Hammell M, Jin Y, Da Ros M, Wasik KA, Toppari J, Hannon GJ, Kotaja N. An atlas of chromatoid body components. RNA (NEW YORK, N.Y.) 2014; 20:483-95. [PMID: 24554440 PMCID: PMC3964910 DOI: 10.1261/rna.043729.113] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 01/10/2014] [Indexed: 05/10/2023]
Abstract
The genome of male germ cells is actively transcribed during spermatogenesis to produce phase-specific protein-coding mRNAs and a considerable amount of different noncoding RNAs. Ribonucleoprotein (RNP) granule-mediated RNA regulation provides a powerful means to secure the quality and correct expression of the requisite transcripts. Haploid spermatids are characterized by a unique, unusually large cytoplasmic granule, the chromatoid body (CB), which emerges during the switch between the meiotic and post-meiotic phases of spermatogenesis. To better understand the role of the CB in male germ cell differentiation, we isolated CBs from mouse testes and revealed its full RNA and protein composition. We showed that the CB is mainly composed of RNA-binding proteins and other proteins involved RNA regulation. The CB was loaded with RNA, including pachytene piRNAs, a diverse set of mRNAs, and a number of uncharacterized long noncoding transcripts. The CB was demonstrated to accumulate nascent RNA during all the steps of round spermatid differentiation. Our results revealed the CB as a large germ cell-specific RNP platform that is involved in the control of the highly complex transcriptome of haploid male germ cells.
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Affiliation(s)
- Oliver Meikar
- Institute of Biomedicine, Department of Physiology, University of Turku, Turku FI-20520, Finland
| | - Vasily V. Vagin
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Frédéric Chalmel
- Inserm Unité 1085-Irset, Université de Rennes 1, IFR140, Rennes F-35042, France
| | - Karin Sõstar
- Institute of Biomedicine, Department of Physiology, University of Turku, Turku FI-20520, Finland
| | - Aurélie Lardenois
- INRA, UMR703 PAnTher, F-44307 Nantes, France
- LUNAM Université, Oniris, École national vétérinaire, agro-alimentaire et de l'alimentation Nantes-Atlantique, F-44307 Nantes, France
| | - Molly Hammell
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Ying Jin
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Matteo Da Ros
- Institute of Biomedicine, Department of Physiology, University of Turku, Turku FI-20520, Finland
| | - Kaja A. Wasik
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Jorma Toppari
- Institute of Biomedicine, Department of Physiology, University of Turku, Turku FI-20520, Finland
- Department of Pediatrics, University of Turku, Turku FI-20520, Finland
| | - Gregory J. Hannon
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Noora Kotaja
- Institute of Biomedicine, Department of Physiology, University of Turku, Turku FI-20520, Finland
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77
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Cheng CJ, Saltzman WM, Slack FJ. Canonical and non-canonical barriers facing antimiR cancer therapeutics. Curr Med Chem 2014; 20:3582-93. [PMID: 23745563 DOI: 10.2174/0929867311320290004] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 03/27/2013] [Accepted: 03/27/2013] [Indexed: 12/14/2022]
Abstract
Once considered genetic "oddities", microRNAs (miRNAs) are now recognized as key epigenetic regulators of numerous biological processes, including some with a causal link to the pathogenesis, maintenance, and treatment of cancer. The crux of small RNA-based therapeutics lies in the antagonism of potent cellular targets; the main shortcoming of the field in general, lies in ineffective delivery. Inhibition of oncogenic miRNAs is a relatively nascent therapeutic concept, but as with predecessor RNA-based therapies, success hinges on delivery efficacy. This review will describes the canonical (e.g. pharmacokinetics and clearance, cellular uptake, endosome escape, etc.) and non-canonical (e.g. spatial localization and accessibility of miRNA, technical limitations of miRNA inhibition, off-target impacts, etc.) challenges to the delivery of antisense-based anti-miRNA therapeutics (i.e. antimiRs) for the treatment of cancer. Emphasis will be placed on how the current leading antimiR platforms-ranging from naked chemically modified oligonucleotides to nanoscale delivery vehicles-are affected by and overcome these barriers. The perplexity of antimiR delivery presents both engineering and biological hurdles that must be overcome in order to capitalize on the extensive pharmacological benefits of antagonizing tumor-associated miRNAs.
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Affiliation(s)
- Christopher J Cheng
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
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78
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Yang H, Rao JN, Wang JY. Posttranscriptional Regulation of Intestinal Epithelial Tight Junction Barrier by RNA-binding Proteins and microRNAs. Tissue Barriers 2014; 2:e28320. [PMID: 24843843 PMCID: PMC4022605 DOI: 10.4161/tisb.28320] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 02/16/2014] [Accepted: 02/21/2014] [Indexed: 12/19/2022] Open
Abstract
Intestinal epithelial tight junctions (TJs) are a specialized structure that determines the cell polarity and prevents the diffusion of toxins, allergens, and pathogens from the lumen into the tissue. TJs are highly dynamic and its constituent protein complexes undergo continuously remodeling and turnover under tight regulation by numerous extracellular and intracellular factors. RNA-binding proteins (RBPs) and microRNAs (miRNAs) regulate gene expression at the posttranscriptional level and are involved in many aspects of cellular physiology. An increasing body of evidence indicates that RBPs including HuR and CUG-binding protein 1 and miRNAs such as miR-192 modulate the stability and translation of mRNAs encoding TJ proteins and play an important role in the control of intestinal epithelial TJ barrier function. In this mini-review article, we highlight the changes in TJ expression and intestinal epithelial TJ barrier function after activation or inactivation of RBPs and miRNAs and further analyze in some detail the mechanisms through which the stability and translation of TJ mRNAs are regulated by RBPs and miRNAs.
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Affiliation(s)
- Hong Yang
- Cell Biology Group; Department of Surgery; University of Maryland School of Medicine; Baltimore, MD USA ; Baltimore Veterans Affairs Medical Center; Baltimore, MD USA
| | - Jaladanki N Rao
- Cell Biology Group; Department of Surgery; University of Maryland School of Medicine; Baltimore, MD USA ; Baltimore Veterans Affairs Medical Center; Baltimore, MD USA
| | - Jian-Ying Wang
- Cell Biology Group; Department of Surgery; University of Maryland School of Medicine; Baltimore, MD USA ; Department of Pathology; University of Maryland School of Medicine; Baltimore, MD USA ; Baltimore Veterans Affairs Medical Center; Baltimore, MD USA
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79
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Droppelmann CA, Campos-Melo D, Ishtiaq M, Volkening K, Strong MJ. RNA metabolism in ALS: When normal processes become pathological. Amyotroph Lateral Scler Frontotemporal Degener 2014; 15:321-36. [DOI: 10.3109/21678421.2014.881377] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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80
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Cao S, Xiao L, Rao JN, Zou T, Liu L, Zhang D, Turner DJ, Gorospe M, Wang JY. Inhibition of Smurf2 translation by miR-322/503 modulates TGF-β/Smad2 signaling and intestinal epithelial homeostasis. Mol Biol Cell 2014; 25:1234-43. [PMID: 24554769 PMCID: PMC3982989 DOI: 10.1091/mbc.e13-09-0560] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Smurf2 is an E3 ubiquitin ligase that regulates TGF-β/Smad signaling and is implicated in a wide variety of cellular responses. miR-322 and miR-503 repress Smurf2 translation and thus modulate TGF-β/Smad2 signaling and intestinal epithelial homeostasis. Smad ubiquitin regulatory factor 2 (Smurf2) is an E3 ubiquitin ligase that regulates transforming growth factor β (TGF-β)/Smad signaling and is implicated in a wide variety of cellular responses, but the exact mechanisms that control Smurf2 abundance are largely unknown. Here we identify microRNA-322 (miR-322) and miR-503 as novel factors that regulate Smurf2 expression posttranscriptionally. Both miR-322 and miR-503 interact with Smurf2 mRNA via its 3′-untranslated region (UTR) and repress Smurf2 translation but do not affect total Smurf2 mRNA levels. Studies using heterologous reporter constructs reveal a greater repressive effect of miR-322/503 through a single binding site in the Smurf2 3′-UTR, whereas point mutation of this site prevents miR-322/503–induced repression of Smurf2 translation. Increased levels of endogenous Smurf2 via antagonism of miR-322/503 inhibits TGF-β–induced Smad2 activation by increasing degradation of phosphorylated Smad2. Furthermore, the increase in Smurf2 in intestinal epithelial cells (IECs) expressing lower levels of miR-322/503 is associated with increased resistance to apoptosis, which is abolished by Smurf2 silencing. These findings indicate that miR-322/503 represses Smurf2 translation, in turn affecting intestinal epithelial homeostasis by altering TGF-β/Smad2 signaling and IEC apoptosis.
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Affiliation(s)
- Shan Cao
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, MD 21201 Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201 Baltimore Veterans Affairs Medical Center, Baltimore, MD 21201 Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224
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81
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Abstract
Spermatogenesis is characterized by meiotic divisions and major morphological changes to produce spermatozoa that are capable of independent movement and fertilization of an egg. Male germ cell differentiation is governed by orchestrated, phase-specific gene expression patterns that are tightly controlled at transcriptional and post-transcriptional level. Post-transcriptional regulation of protein-coding mRNAs becomes prominent during the late steps of spermatogenesis when the compacting sperm nucleus becomes transcriptionally inhibited. Small non-coding RNAs are important regulators of gene expression that mainly function post-transcriptionally to control the properties of their target mRNAs. Male germ cells express several classes of small RNAs, including Dicer-dependent microRNAs (miRNAs) and endogenous small interfering RNAs (endo-siRNAs), as well as Dicer-independent piwi-interacting RNAs (piRNAs). Increasing evidence supports the essential role of small RNA-mediated RNA regulation in normal spermatogenesis and male fertility.
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Affiliation(s)
- Ram Prakash Yadav
- Department of Physiology, Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, FIN-20520 Turku, Finland.
| | - Noora Kotaja
- Department of Physiology, Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, FIN-20520 Turku, Finland.
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82
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Güth R, Pinch M, Unguez GA. Mechanisms of muscle gene regulation in the electric organ of Sternopygus macrurus. ACTA ACUST UNITED AC 2014; 216:2469-77. [PMID: 23761472 DOI: 10.1242/jeb.082404] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Animals perform a remarkable diversity of movements through the coordinated mechanical contraction of skeletal muscle. This capacity for a wide range of movements is due to the presence of muscle cells with a very plastic phenotype that display many different biochemical, physiological and morphological properties. What factors influence the maintenance and plasticity of differentiated muscle fibers is a fundamental question in muscle biology. We have exploited the remarkable potential of skeletal muscle cells of the gymnotiform electric fish Sternopygus macrurus to trans-differentiate into electrocytes, the non-contractile electrogenic cells of the electric organ (EO), to investigate the mechanisms that regulate the skeletal muscle phenotype. In S. macrurus, mature electrocytes possess a phenotype that is intermediate between muscle and non-muscle cells. How some genes coding for muscle-specific proteins are downregulated while others are maintained, and novel genes are upregulated, is an intriguing problem in the control of skeletal muscle and EO phenotype. To date, the intracellular and extracellular factors that generate and maintain distinct patterns of gene expression in muscle and EO have not been defined. Expression studies in S. macrurus have started to shed light on the role that transcriptional and post-transcriptional events play in regulating specific muscle protein systems and the muscle phenotype of the EO. In addition, these findings also represent an important step toward identifying mechanisms that affect the maintenance and plasticity of the muscle cell phenotype for the evolution of highly specialized non-contractile tissues.
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Affiliation(s)
- Robert Güth
- Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA
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83
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Maldonado-Bonilla LD. Composition and function of P bodies in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2014; 5:201. [PMID: 24860588 PMCID: PMC4030149 DOI: 10.3389/fpls.2014.00201] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Accepted: 04/24/2014] [Indexed: 05/20/2023]
Abstract
mRNA accumulation is tightly regulated by diverse molecular pathways. The identification and characterization of enzymes and regulatory proteins involved in controlling the fate of mRNA offers the possibility to broaden our understanding of posttranscriptional gene regulation. Processing bodies (P bodies, PB) are cytoplasmic protein complexes involved in degradation and translational arrest of mRNA. Composition and dynamics of these subcellular structures have been studied in animal systems, yeasts and in the model plant Arabidopsis. Their assembly implies the aggregation of specific factors related to decapping, deadenylation, and exoribonucleases that operate synchronously to regulate certain mRNA targets during development and adaptation to stress. Although the general function of PB along with the flow of genetic information is understood, several questions still remain open. This review summarizes data on the composition, potential molecular roles, and biological significance of PB and potentially related proteins in Arabidopsis.
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Affiliation(s)
- Luis D. Maldonado-Bonilla
- *Correspondence: Luis D. Maldonado-Bonilla, Laboratory of Plant Molecular Biology, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José 2055, San Luis Potosí 78216, Mexico e-mail:
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84
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Contreras X, Benkirane M, Kiernan R. Premature termination of transcription by RNAP II: the beginning of the end. Transcription 2013; 4:72-6. [PMID: 23714697 DOI: 10.4161/trns.24148] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Transcription elongation is now recognized as an important mechanism of gene regulation in eukaryotes. A large number of genes undergo an early step in transcription that is rate limiting for expression. Genome-wide studies showing that RNA polymerase II accumulates to high densities near the promoters of many genes has led to the idea that promoter-proximal pausing of transcription is a widespread, rate-limiting step in early elongation. Recent evidence suggests that much of this paused RNA polymerase II is competent for transcription elongation. Here, we discuss recent studies suggesting that RNA polymerase II that accumulates nearby the promoter of a subset of genes is undergoing premature termination of transcription.
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Affiliation(s)
- Xavier Contreras
- Institut de Génétique Humaine; CNRS UPR1142, Laboratoire de Régulation des Gènes, Montpellier, France
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85
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Kamenska A, Lu WT, Kubacka D, Broomhead H, Minshall N, Bushell M, Standart N. Human 4E-T represses translation of bound mRNAs and enhances microRNA-mediated silencing. Nucleic Acids Res 2013; 42:3298-313. [PMID: 24335285 PMCID: PMC3950672 DOI: 10.1093/nar/gkt1265] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
A key player in translation initiation is eIF4E, the mRNA 5' cap-binding protein. 4E-Transporter (4E-T) is a recently characterized eIF4E-binding protein, which regulates specific mRNAs in several developmental model systems. Here, we first investigated the role of its enrichment in P-bodies and eIF4E-binding in translational regulation in mammalian cells. Identification of the conserved C-terminal sequences that target 4E-T to P-bodies was enabled by comparison of vertebrate proteins with homologues in Drosophila (Cup and CG32016) and Caenorhabditis elegans by sequence and cellular distribution. In tether function assays, 4E-T represses bound mRNA translation, in a manner independent of these localization sequences, or of endogenous P-bodies. Quantitative polymerase chain reaction and northern blot analysis verified that bound mRNA remained intact and polyadenylated. Ectopic 4E-T reduces translation globally in a manner dependent on eIF4E binding its consensus Y30X4L site. In contrast, tethered 4E-T continued to repress translation when eIF4E-binding was prevented by mutagenesis of YX4L, and modestly enhanced the decay of bound mRNA, compared with wild-type 4E-T, mediated by increased binding of CNOT1/7 deadenylase subunits. As depleting 4E-T from HeLa cells increased steady-state translation, in part due to relief of microRNA-mediated silencing, this work demonstrates the conserved yet unconventional mechanism of 4E-T silencing of particular subsets of mRNAs.
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Affiliation(s)
- Anastasiia Kamenska
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB21QW, UK and MRC Toxicology Unit, University of Leicester, Lancaster Road, Leicester LE19HN, UK
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86
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Merret R, Descombin J, Juan YT, Favory JJ, Carpentier MC, Chaparro C, Charng YY, Deragon JM, Bousquet-Antonelli C. XRN4 and LARP1 Are Required for a Heat-Triggered mRNA Decay Pathway Involved in Plant Acclimation and Survival during Thermal Stress. Cell Rep 2013; 5:1279-93. [DOI: 10.1016/j.celrep.2013.11.019] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 10/08/2013] [Accepted: 11/09/2013] [Indexed: 01/22/2023] Open
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87
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Transforming growth factor β regulates P-body formation through induction of the mRNA decay factor tristetraprolin. Mol Cell Biol 2013; 34:180-95. [PMID: 24190969 DOI: 10.1128/mcb.01020-13] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Transforming growth factor β (TGF-β) is a potent growth regulator and tumor suppressor in normal intestinal epithelium. Likewise, epithelial cell growth is controlled by rapid decay of growth-related mRNAs mediated through 3' untranslated region (UTR) AU-rich element (ARE) motifs. We demonstrate that treatment of nontransformed intestinal epithelial cells with TGF-β inhibited ARE-mRNA expression. This effect of TGF-β was promoted through increased assembly of cytoplasmic RNA processing (P) bodies where ARE-mRNA localization was observed. P-body formation was dependent on TGF-β/Smad signaling, as Smad3 deletion abrogated P-body formation. In concert with increased P-body formation, TGF-β induced expression of the ARE-binding protein tristetraprolin (TTP), which colocalized to P bodies. TTP expression was necessary for TGF-β-dependent P-body formation and promoted growth inhibition by TGF-β. The significance of this was observed in vivo, where colonic epithelium deficient in TGF-β/Smad signaling or TTP expression showed attenuated P-body levels. These results provide new insight into TGF-β's antiproliferative properties and identify TGF-β as a novel mRNA stability regulator in intestinal epithelium through its ability to promote TTP expression and subsequent P-body formation.
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88
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Hutson TH, Foster E, Moon LDF, Yáñez-Muñoz RJ. Lentiviral vector-mediated RNA silencing in the central nervous system. Hum Gene Ther Methods 2013; 25:14-32. [PMID: 24090197 DOI: 10.1089/hgtb.2013.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
RNA silencing is an established method for investigating gene function and has attracted particular interest because of the potential for generating RNA-based therapeutics. Using lentiviral vectors as an efficient delivery system that offers stable, long-term expression in postmitotic cells further enhances the applicability of an RNA-based gene therapy for the CNS. In this review we provide an overview of both lentiviral vectors and RNA silencing along with design considerations for generating lentiviral vectors capable of RNA silencing. We go on to describe the current preclinical data regarding lentiviral vector-mediated RNA silencing for CNS disorders and discuss the concerns of side effects associated with lentiviral vectors and small interfering RNAs and how these might be mitigated.
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Affiliation(s)
- Thomas H Hutson
- 1 Neurorestoration Group, Wolfson Centre for Age-Related Diseases, King's College London , Guy's Campus, London SE1 1UL, United Kingdom
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89
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Exploration of deleterious single nucleotide polymorphisms in the components of human P bodies: An in silico approach. Gene 2013; 528:360-3. [DOI: 10.1016/j.gene.2013.07.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2013] [Accepted: 07/14/2013] [Indexed: 11/22/2022]
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90
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Moving RNA moves RNA forward. SCIENCE CHINA-LIFE SCIENCES 2013; 56:914-20. [DOI: 10.1007/s11427-013-4545-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 08/23/2013] [Indexed: 12/11/2022]
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91
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Kubacka D, Kamenska A, Broomhead H, Minshall N, Darzynkiewicz E, Standart N. Investigating the consequences of eIF4E2 (4EHP) interaction with 4E-transporter on its cellular distribution in HeLa cells. PLoS One 2013; 8:e72761. [PMID: 23991149 PMCID: PMC3749138 DOI: 10.1371/journal.pone.0072761] [Citation(s) in RCA: 21] [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: 04/19/2013] [Accepted: 07/15/2013] [Indexed: 11/25/2022] Open
Abstract
In addition to the canonical eIF4E cap-binding protein, eukaryotes have evolved sequence–related variants with distinct features, some of which have been shown to negatively regulate translation of particular mRNAs, but which remain poorly characterised. Mammalian eIF4E proteins have been divided into three classes, with class I representing the canonical cap-binding protein eIF4E1. eIF4E1 binds eIF4G to initiate translation, and other eIF4E-binding proteins such as 4E-BPs and 4E-T prevent this interaction by binding eIF4E1 with the same consensus sequence YX 4Lϕ. We investigate here the interaction of human eIF4E2 (4EHP), a class II eIF4E protein, which binds the cap weakly, with eIF4E-transporter protein, 4E-T. We first show that ratios of eIF4E1:4E-T range from 50:1 to 15:1 in HeLa and HEK293 cells respectively, while those of eIF4E2:4E-T vary from 6:1 to 3:1. We next provide evidence that eIF4E2 binds 4E-T in the yeast two hybrid assay, as well as in pull-down assays and by recruitment to P-bodies in mammalian cells. We also show that while both eIF4E1 and eIF4E2 bind 4E-T via the canonical YX 4Lϕ sequence, nearby downstream sequences also influence eIF4E:4E-T interactions. Indirect immunofluorescence was used to demonstrate that eIF4E2, normally homogeneously localised in the cytoplasm, does not redistribute to stress granules in arsenite-treated cells, nor to P-bodies in Actinomycin D-treated cells, in contrast to eIF4E1. Moreover, eIF4E2 shuttles through nuclei in a Crm1-dependent manner, but in an 4E-T–independent manner, also unlike eIF4E1. Altogether we conclude that while both cap-binding proteins interact with 4E-T, and can be recruited by 4E-T to P-bodies, eIF4E2 functions are likely to be distinct from those of eIF4E1, both in the cytoplasm and nucleus, further extending our understanding of mammalian class I and II cap-binding proteins.
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Affiliation(s)
- Dorota Kubacka
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Anastasiia Kamenska
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Helen Broomhead
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Nicola Minshall
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Edward Darzynkiewicz
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Nancy Standart
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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92
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MicroRNAs: Critical Regulators of mRNA Traffic and Translational Control with Promising Biotech and Therapeutic Applications. IRANIAN JOURNAL OF BIOTECHNOLOGY 2013. [DOI: 10.5812/ijb.11081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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93
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Sharif H, Ozgur S, Sharma K, Basquin C, Urlaub H, Conti E. Structural analysis of the yeast Dhh1-Pat1 complex reveals how Dhh1 engages Pat1, Edc3 and RNA in mutually exclusive interactions. Nucleic Acids Res 2013; 41:8377-90. [PMID: 23851565 PMCID: PMC3783180 DOI: 10.1093/nar/gkt600] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Translational repression and deadenylation of eukaryotic mRNAs result either in the sequestration of the transcripts in a nontranslatable pool or in their degradation. Removal of the 5′ cap structure is a crucial step that commits deadenylated mRNAs to 5′-to-3′ degradation. Pat1, Edc3 and the DEAD-box protein Dhh1 are evolutionary conserved factors known to participate in both translational repression and decapping, but their interplay is currently unclear. We report the 2.8 Å resolution structure of yeast Dhh1 bound to the N-terminal domain of Pat1. The structure shows how Pat1 wraps around the C-terminal RecA domain of Dhh1, docking onto the Phe-Asp-Phe (FDF) binding site. The FDF-binding site of Dhh1 also recognizes Edc3, revealing why the binding of Pat1 and Edc3 on Dhh1 are mutually exclusive events. Using co-immunoprecipitation assays and structure-based mutants, we demonstrate that the mode of Dhh1-Pat1 recognition is conserved in humans. Pat1 and Edc3 also interfere and compete with the RNA-binding properties of Dhh1. Mapping the RNA-binding sites on Dhh1 with a crosslinking–mass spectrometry approach shows a large RNA-binding surface around the C-terminal RecA domain, including the FDF-binding pocket. The results suggest a model for how Dhh1-containing messenger ribonucleoprotein particles might be remodeled upon Pat1 and Edc3 binding.
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Affiliation(s)
- Humayun Sharif
- Structural Cell Biology Department, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried/Munich, D-82152 Germany and Cellular Biochemistry Department, Max Planck Institute of Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen, Germany
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94
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Jones CI, Grima DP, Waldron JA, Jones S, Parker HN, Newbury SF. The 5'-3' exoribonuclease Pacman (Xrn1) regulates expression of the heat shock protein Hsp67Bc and the microRNA miR-277-3p in Drosophila wing imaginal discs. RNA Biol 2013; 10:1345-55. [PMID: 23792537 PMCID: PMC3817156 DOI: 10.4161/rna.25354] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Pacman/Xrn1 is a highly conserved exoribonuclease known to play a critical role in gene regulatory events such as control of mRNA stability, RNA interference and regulation via miRNAs. Although Pacman has been well studied in Drosophila tissue culture cells, the biologically relevant cellular pathways controlled by Pacman in natural tissues are unknown. This study shows that a hypomorphic mutation in pacman (pcm5) results in smaller wing imaginal discs. These tissues, found in the larva, are known to grow and differentiate to form wing and thorax structures in the adult fly. Using microarray analysis, followed by quantitative RT-PCR, we show that eight mRNAs were increased in level by > 2-fold in the pcm5 mutant wing discs compared with the control. The levels of pre-mRNAs were tested for five of these mRNAs; four did not increase in the pcm5 mutant, showing that they are regulated at the post-transcriptional level and, therefore, could be directly affected by Pacman. These transcripts include one that encodes the heat shock protein Hsp67Bc, which is upregulated 11.9-fold at the post-transcriptional level and 2.3-fold at the protein level. One miRNA, miR-277-3p, is 5.6-fold downregulated at the post-transcriptional level in mutant discs, suggesting that Pacman affects its processing in this tissue. Together, these data show that a relatively small number of mRNAs and miRNAs substantially change in abundance in pacman mutant wing imaginal discs. Since Hsp67Bc is known to regulate autophagy and protein synthesis, it is possible that Pacman may control the growth of wing imaginal discs by regulating these processes.
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Affiliation(s)
- Christopher I Jones
- Brighton and Sussex Medical School; Medical Research Building; University of Sussex; Falmer, Brighton, UK
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95
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Pattnaik AK, Dinh PX. Manipulation of cellular processing bodies and their constituents by viruses. DNA Cell Biol 2013; 32:286-91. [PMID: 23617258 PMCID: PMC3665300 DOI: 10.1089/dna.2013.2054] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 03/29/2013] [Indexed: 01/19/2023] Open
Abstract
The processing bodies (PBs) are a form of cytoplasmic aggregates that house the cellular RNA decay machinery as well as many RNA-binding proteins and mRNAs. The PBs are constitutively present in eukaryotic cells and are involved in maintaining cellular homeostasis by regulating RNA metabolism, cell signaling, and survival. Virus infections result in modification of the PBs and their constituents. Many viruses induce compositionally altered PBs, while many others use specific components of the PBs for their replication. PB constituents are also known to restrict virus replication by a variety of mechanisms. Further, continuing studies in this rapidly emerging field of PB-virus interactions will undoubtedly provide important clues to the understanding of the role of PBs in cellular homeostasis as well as their role in virus infections and innate immune signaling.
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Affiliation(s)
- Asit K Pattnaik
- School of Veterinary Medicine and Biomedical Sciences and the Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583-0900, USA.
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96
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Nagarajan VK, Jones CI, Newbury SF, Green PJ. XRN 5'→3' exoribonucleases: structure, mechanisms and functions. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1829:590-603. [PMID: 23517755 PMCID: PMC3742305 DOI: 10.1016/j.bbagrm.2013.03.005] [Citation(s) in RCA: 247] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2012] [Revised: 03/08/2013] [Accepted: 03/11/2013] [Indexed: 01/11/2023]
Abstract
The XRN family of 5'→3' exoribonucleases is critical for ensuring the fidelity of cellular RNA turnover in eukaryotes. Highly conserved across species, the family is typically represented by one cytoplasmic enzyme (XRN1/PACMAN or XRN4) and one or more nuclear enzymes (XRN2/RAT1 and XRN3). Cytoplasmic and/or nuclear XRNs have proven to be essential in all organisms tested, and deficiencies can have severe developmental phenotypes, demonstrating that XRNs are indispensable in fungi, plants and animals. XRNs degrade diverse RNA substrates during general RNA decay and function in specialized processes integral to RNA metabolism, such as nonsense-mediated decay (NMD), gene silencing, rRNA maturation, and transcription termination. Here, we review current knowledge of XRNs, highlighting recent work of high impact and future potential. One example is the breakthrough in our understanding of how XRN1 processively degrades 5' monophosphorylated RNA, revealed by its crystal structure and mutational analysis. The expanding knowledge of XRN substrates and interacting partners is outlined and the functions of XRNs are interpreted at the organismal level using available mutant phenotypes. Finally, three case studies are discussed in more detail to underscore a few of the most exciting areas of research on XRN function: XRN4 involvement in small RNA-associated processes in plants, the roles of XRN1/PACMAN in Drosophila development, and the function of human XRN2 in nuclear transcriptional quality control. This article is part of a Special Issue entitled: RNA Decay mechanisms.
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Affiliation(s)
- Vinay K. Nagarajan
- Delaware Biotechnology Institute, Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19711, USA
| | - Christopher I. Jones
- Medical Research Building, Brighton and Sussex Medical School, University of Sussex, Falmer, Brighton BN1 9PS, UK
| | - Sarah F. Newbury
- Medical Research Building, Brighton and Sussex Medical School, University of Sussex, Falmer, Brighton BN1 9PS, UK
| | - Pamela J. Green
- Delaware Biotechnology Institute, Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19711, USA
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97
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Vlachakis D, Tsiliki G, Pavlopoulou A, Roubelakis MG, Tsaniras SC, Kossida S. Antiviral Stratagems Against HIV-1 Using RNA Interference (RNAi) Technology. Evol Bioinform Online 2013; 9:203-13. [PMID: 23761954 PMCID: PMC3662398 DOI: 10.4137/ebo.s11412] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The versatility of human immunodeficiency virus (HIV)-1 and its evolutionary potential to elude antiretroviral agents by mutating may be its most invincible weapon. Viruses, including HIV, in order to adapt and survive in their environment evolve at extremely fast rates. Given that conventional approaches which have been applied against HIV have failed, novel and more promising approaches must be employed. Recent studies advocate RNA interference (RNAi) as a promising therapeutic tool against HIV. In this regard, targeting multiple HIV sites in the context of a combinatorial RNAi-based approach may efficiently stop viral propagation at an early stage. Moreover, large high-throughput RNAi screens are widely used in the fields of drug development and reverse genetics. Computer-based algorithms, bioinformatics, and biostatistical approaches have been employed in traditional medicinal chemistry discovery protocols for low molecular weight compounds. However, the diversity and complexity of RNAi screens cannot be efficiently addressed by these outdated approaches. Herein, a series of novel workflows for both wet- and dry-lab strategies are presented in an effort to provide an updated review of state-of-the-art RNAi technologies, which may enable adequate progress in the fight against the HIV-1 virus.
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Affiliation(s)
- Dimitrios Vlachakis
- Bioinformatics and Medical Informatics Team, Biomedical Research Foundation, Academy of Athens, Athens, Greece
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98
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Bentmann E, Haass C, Dormann D. Stress granules in neurodegeneration - lessons learnt from TAR DNA binding protein of 43 kDa and fused in sarcoma. FEBS J 2013; 280:4348-70. [DOI: 10.1111/febs.12287] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 03/28/2013] [Accepted: 04/08/2013] [Indexed: 12/12/2022]
Affiliation(s)
- Eva Bentmann
- Adolf Butenandt Institute; Department of Biochemistry; Ludwig Maximilians University; Munich Germany
| | - Christian Haass
- Adolf Butenandt Institute; Department of Biochemistry; Ludwig Maximilians University; Munich Germany
- German Center for Neurodegenerative Diseases (DZNE); Munich Germany
- Munich Cluster for Systems Neurology (SyNergy); Munich Germany
| | - Dorothee Dormann
- Adolf Butenandt Institute; Department of Biochemistry; Ludwig Maximilians University; Munich Germany
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99
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Abstract
lin-41 (lineage variant 41)/TRIM71 (tripartite motif 71) is well known for being a conserved target of the let-7 (lethal 7) microRNA (miRNA), a regulatory relationship found in animals evolutionarily as distant as Caenorhabditis elegans and humans. It has thus been studied extensively as a model for miRNA-mediated gene silencing. In contrast, the developmental and molecular functions of LIN41 have historically received less attention. However, LIN41 proteins are now emerging as important regulators of cell proliferation and differentiation in stem and progenitor cells. Moreover, LIN41's functions appear to involve two distinct molecular activities; namely, protein ubiquitylation and post-transcriptional silencing of mRNAs. Thus, LIN41 is ready for a scientific life of its own.
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Affiliation(s)
- Matyas Ecsedi
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
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100
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Watanabe K, Miyagawa R, Tomikawa C, Mizuno R, Takahashi A, Hori H, Ijiri K. Degradation of initiator tRNAMet by Xrn1/2 via its accumulation in the nucleus of heat-treated HeLa cells. Nucleic Acids Res 2013; 41:4671-85. [PMID: 23471000 PMCID: PMC3632136 DOI: 10.1093/nar/gkt153] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Stress response mechanisms that modulate the dynamics of tRNA degradation and accumulation from the cytoplasm to the nucleus have been studied in yeast, the rat hepatoma and human cells. In the current study, we investigated tRNA degradation and accumulation in HeLa cells under various forms of stress. We found that initiator tRNAMet (tRNA(iMet)) was specifically degraded under heat stress. Two exonucleases, Xrn1 and Xrn2, are involved in the degradation of tRNA(iMet) in the cytoplasm and the nucleus, respectively. In addition to degradation, we observed accumulation of tRNA(iMet) in the nucleus. We also found that the mammalian target of rapamycin (mTOR), which regulates tRNA trafficking in yeast, is partially phosphorylated at Ser2448 in the presence of rapamycin and/or during heat stress. Our results suggest phosphorylation of mTOR may correlate with accumulation of tRNA(iMet) in heat-treated HeLa cells.
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Affiliation(s)
- Kazunori Watanabe
- Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
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