51
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Engel KL, Arora A, Goering R, Lo HYG, Taliaferro JM. Mechanisms and consequences of subcellular RNA localization across diverse cell types. Traffic 2020; 21:404-418. [PMID: 32291836 PMCID: PMC7304542 DOI: 10.1111/tra.12730] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/26/2020] [Accepted: 03/30/2020] [Indexed: 02/07/2023]
Abstract
Essentially all cells contain a variety of spatially restricted regions that are important for carrying out specialized functions. Often, these regions contain specialized transcriptomes that facilitate these functions by providing transcripts for localized translation. These transcripts play a functional role in maintaining cell physiology by enabling a quick response to changes in the cellular environment. Here, we review how RNA molecules are trafficked within cells, with a focus on the subcellular locations to which they are trafficked, mechanisms that regulate their transport and clinical disorders associated with misregulation of the process.
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Affiliation(s)
- Krysta L Engel
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Ankita Arora
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Raeann Goering
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Hei-Yong G Lo
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - J Matthew Taliaferro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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52
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Bruzzone L, Argüelles C, Sanial M, Miled S, Alvisi G, Gonçalves-Antunes M, Qasrawi F, Holmgren RA, Smibert CA, Lipshitz HD, Boccaccio GL, Plessis A, Bécam I. Regulation of the RNA-binding protein Smaug by the GPCR Smoothened via the kinase Fused. EMBO Rep 2020; 21:e48425. [PMID: 32383557 DOI: 10.15252/embr.201948425] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 03/17/2020] [Accepted: 04/14/2020] [Indexed: 12/13/2022] Open
Abstract
From fly to mammals, the Smaug/Samd4 family of prion-like RNA-binding proteins control gene expression by destabilizing and/or repressing the translation of numerous target transcripts. However, the regulation of its activity remains poorly understood. We show that Smaug's protein levels and mRNA repressive activity are downregulated by Hedgehog signaling in tissue culture cells. These effects rely on the interaction of Smaug with the G-protein coupled receptor Smoothened, which promotes the phosphorylation of Smaug by recruiting the kinase Fused. The activation of Fused and its binding to Smaug are sufficient to suppress its ability to form cytosolic bodies and to antagonize its negative effects on endogenous targets. Importantly, we demonstrate in vivo that HH reduces the levels of smaug mRNA and increases the level of several mRNAs downregulated by Smaug. Finally, we show that Smaug acts as a positive regulator of Hedgehog signaling during wing morphogenesis. These data constitute the first evidence for a post-translational regulation of Smaug and reveal that the fate of several mRNAs bound to Smaug is modulated by a major signaling pathway.
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Affiliation(s)
- Lucia Bruzzone
- CNRS, Institut Jacques Monod, Université de Paris, Paris, France
| | | | - Matthieu Sanial
- CNRS, Institut Jacques Monod, Université de Paris, Paris, France
| | - Samia Miled
- CNRS, Institut Jacques Monod, Université de Paris, Paris, France
| | - Giorgia Alvisi
- CNRS, Institut Jacques Monod, Université de Paris, Paris, France
| | | | - Fairouz Qasrawi
- CNRS, Institut Jacques Monod, Université de Paris, Paris, France
| | - Robert A Holmgren
- Department of Mol. Biosci., Northwestern University, Evanston, IL, USA
| | - Craig A Smibert
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Howard D Lipshitz
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Graciela L Boccaccio
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas Buenos Aires-Consejo Nacional de Investigaciones Científicas y Tecnológicas, Facultad de Ciencias Exactas y Naturales, University of Buenos Aires, Buenos Aires, Argentina
| | - Anne Plessis
- CNRS, Institut Jacques Monod, Université de Paris, Paris, France
| | - Isabelle Bécam
- CNRS, Institut Jacques Monod, Université de Paris, Paris, France
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53
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Denninger JK, Chen X, Turkoglu AM, Sarchet P, Volk AR, Rieskamp JD, Yan P, Kirby ED. Defining the adult hippocampal neural stem cell secretome: In vivo versus in vitro transcriptomic differences and their correlation to secreted protein levels. Brain Res 2020; 1735:146717. [PMID: 32035887 DOI: 10.1016/j.brainres.2020.146717] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 02/03/2020] [Accepted: 02/05/2020] [Indexed: 01/08/2023]
Abstract
Adult hippocampal neural stem and progenitor cells (NSPCs) secrete a variety of proteins that affect tissue function. Though several individual NSPC-derived proteins have been shown to impact key cellular processes, a broad characterization is lacking. Secretome profiling of low abundance stem cell populations is typically achieved via proteomic characterization of in vitro, isolated cells. Here, we identified hundreds of secreted proteins in conditioned media from in vitro adult mouse hippocampal NSPCs using an antibody array and mass spectrometry. Comparison of protein abundance between antibody array and mass spectrometry plus quantification of several key secreted proteins by ELISA revealed notable disconnect between methods in what proteins were identified as being high versus low abundance, suggesting that data from antibody arrays in particular should be approached with caution. We next assessed the NSPC secretome on a transcriptional level with single cell and bulk RNA sequencing (RNAseq) of cultured NSPCs. Comparison of RNAseq transcript levels of highly secreted proteins revealed that quantification of gene expression did not necessarily predict relative protein abundance. Interestingly, comparing our in vitro NSPC gene expression data with similar data from freshly isolated, in vivo hippocampal NSPCs revealed strong correlations in global gene expression between in vitro and in vivo NSPCs. Understanding the components and functions of the NSPC secretome is essential to understanding how these cells may modulate the hippocampal neurogenic niche. Cumulatively, our data emphasize the importance of using proteomics in conjunction with transcriptomics and highlights the need for better methods of unbiased secretome profiling.
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Affiliation(s)
- Jiyeon K Denninger
- Department of Psychology, College of Arts and Sciences, The Ohio State University, United States
| | - Xi Chen
- Comprehensive Cancer Center, The Ohio State University, United States
| | - Altan M Turkoglu
- College of Arts and Sciences, The Ohio State University, United States
| | - Patricia Sarchet
- Comprehensive Cancer Center, The Ohio State University, United States
| | - Abby R Volk
- College of Arts and Sciences, The Ohio State University, United States
| | - Joshua D Rieskamp
- Neuroscience Graduate Program, The Ohio State University, United States
| | - Pearlly Yan
- Comprehensive Cancer Center, The Ohio State University, United States; Division of Hematology, Department of Internal Medicine, College of Medicine, The Ohio State University, United States
| | - Elizabeth D Kirby
- Department of Psychology, College of Arts and Sciences, The Ohio State University, United States; Department of Neuroscience, The Ohio State University, United States; Chronic Brain Injury Initiative, The Ohio State University, United States.
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54
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Pushpalatha KV, Besse F. Local Translation in Axons: When Membraneless RNP Granules Meet Membrane-Bound Organelles. Front Mol Biosci 2019; 6:129. [PMID: 31824961 PMCID: PMC6882739 DOI: 10.3389/fmolb.2019.00129] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 11/06/2019] [Indexed: 12/14/2022] Open
Abstract
Eukaryotic cell compartmentalization relies on long-known membrane-delimited organelles, as well as on more recently discovered membraneless macromolecular condensates. How these two types of organelles interact to regulate cellular functions is still largely unclear. In this review, we highlight how membraneless ribonucleoprotein (RNP) organelles, enriched in RNAs and associated regulatory proteins, cooperate with membrane-bound organelles for tight spatio-temporal control of gene expression in the axons of neuronal cells. Specifically, we present recent evidence that motile membrane-bound organelles are used as vehicles by RNP cargoes, promoting the long-range transport of mRNA molecules to distal axons. As demonstrated by recent work, membrane-bound organelles also promote local protein synthesis, by serving as platforms for the local translation of mRNAs recruited to their outer surface. Furthermore, dynamic and specific association between RNP cargoes and membrane-bound organelles is mediated by bi-partite adapter molecules that interact with both types of organelles selectively, in a regulated-manner. Maintaining such a dynamic interplay is critical, as alterations in this process are linked to neurodegenerative diseases. Together, emerging studies thus point to the coordination of membrane-bound and membraneless organelles as an organizing principle underlying local cellular responses.
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Affiliation(s)
| | - Florence Besse
- Université Côte d'Azur, CNRS, Inserm, Institut de Biology Valrose, Nice, France
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55
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Greenblatt EJ, Obniski R, Mical C, Spradling AC. Prolonged ovarian storage of mature Drosophila oocytes dramatically increases meiotic spindle instability. eLife 2019; 8:49455. [PMID: 31755866 PMCID: PMC6905857 DOI: 10.7554/elife.49455] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 11/17/2019] [Indexed: 12/21/2022] Open
Abstract
Human oocytes frequently generate aneuploid embryos that subsequently miscarry. In contrast, Drosophila oocytes from outbred laboratory stocks develop fully regardless of maternal age. Since mature Drosophila oocytes are not extensively stored in the ovary under laboratory conditions like they are in the wild, we developed a system to investigate how storage affects oocyte quality. The developmental capacity of stored mature Drosophila oocytes decays in a precise manner over 14 days at 25°C. These oocytes are transcriptionally inactive and persist using ongoing translation of stored mRNAs. Ribosome profiling revealed a progressive 2.3-fold decline in average translational efficiency during storage that correlates with oocyte functional decay. Although normal bipolar meiotic spindles predominate during the first week, oocytes stored for longer periods increasingly show tripolar, monopolar and other spindle defects, and give rise to embryos that fail to develop due to aneuploidy. Thus, meiotic chromosome segregation in mature Drosophila oocytes is uniquely sensitive to prolonged storage. Our work suggests the chromosome instability of human embryos could be mitigated by reducing the period of time mature human oocytes are stored in the ovary prior to ovulation.
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Affiliation(s)
- Ethan J Greenblatt
- Department of Embryology, Howard Hughes Medical Institute Research Laboratories, Carnegie Institution for Science, Baltimore, United States
| | - Rebecca Obniski
- Department of Embryology, Howard Hughes Medical Institute Research Laboratories, Carnegie Institution for Science, Baltimore, United States
| | - Claire Mical
- Department of Embryology, Howard Hughes Medical Institute Research Laboratories, Carnegie Institution for Science, Baltimore, United States
| | - Allan C Spradling
- Department of Embryology, Howard Hughes Medical Institute Research Laboratories, Carnegie Institution for Science, Baltimore, United States
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56
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Designing and Modeling of Multi-epitope Proteins for Diagnosis of Toxocara canis Infection. Int J Pept Res Ther 2019. [DOI: 10.1007/s10989-019-09940-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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57
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Wippich F, Ephrussi A. Transcript specific mRNP capture from Drosophila egg-chambers for proteomic analysis. Methods 2019; 178:83-88. [PMID: 31493515 DOI: 10.1016/j.ymeth.2019.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 09/02/2019] [Accepted: 09/02/2019] [Indexed: 01/23/2023] Open
Abstract
mRNA binding proteins (RBPs) play a major role in post-transcriptional control of gene expression. To understand the complex regulatory processes regulating a specific mRNA during its life-time, a comprehensive view of the bound RBPs is essential. Here, we describe a method for transcript-specific isolation of endogenous ribonucleoprotein complexes (RNPs) from Drosophila egg-chambers. The method, which is based on in-solution hybridization of short biotinylated antisense DNA oligonucleotide probes to multiple segments of a transcript of interest allows unbiased identification of associated proteins by quantitative proteomics.
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Affiliation(s)
- Frank Wippich
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
| | - Anne Ephrussi
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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58
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Jung D, Seo JS, Nam J, Kim J. Functional association of Loc1 and Puf6 with RNA helicase Dhh1 in translational regulation of Saccharomyces cerevisiae Ste12. PLoS One 2019; 14:e0220137. [PMID: 31323064 PMCID: PMC6641207 DOI: 10.1371/journal.pone.0220137] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 07/09/2019] [Indexed: 12/14/2022] Open
Abstract
Loc1 and Puf6, which are localized predominantly to the nucleus, are required for the localization and translational repression of the ASH1 mRNA in the yeast, Saccharomyces cerevisiae. During its transport to the daughter cell, the ASH1 mRNA is translationally repressed via associations with She2, Loc1, and Puf6. Here, we investigated the roles of Loc1 and Puf6 in the translation of mRNAs other than that encoding ASH1. In loc1 or puf6 deletion strains, expression of the mating-specific transcription factor, Ste12, was significantly increased at the post-transcriptional level. These phenotypes required the 5’ untranslated region (UTR) of STE12, which carries the putative Puf6-binding sequences. The RNA helicase, Dhh1, which is a known positive regulator for the translation of STE12 mRNA, was found to be functionally connected with Loc1 and Puf6 in the context of Ste12 expression. Our results collectively show that the phosphorylation of the N-terminal Thr16 residue of Dhh1 affects the protein interactions of Dhh1 with Loc1 or Puf6, and consequently regulates Ste12 expression.
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Affiliation(s)
- Daehee Jung
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Jong Seok Seo
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Jayoung Nam
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Jinmi Kim
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
- * E-mail:
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59
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Moissoglu K, Yasuda K, Wang T, Chrisafis G, Mili S. Translational regulation of protrusion-localized RNAs involves silencing and clustering after transport. eLife 2019; 8:44752. [PMID: 31290739 PMCID: PMC6639073 DOI: 10.7554/elife.44752] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 07/08/2019] [Indexed: 02/06/2023] Open
Abstract
Localization of RNAs to various subcellular destinations is a widely used mechanism that regulates a large proportion of transcripts in polarized cells. In many cases, such localized transcripts mediate spatial control of gene expression by being translationally silent while in transit and locally activated at their destination. Here, we investigate the translation of RNAs localized at dynamic cellular protrusions of human and mouse, migrating, mesenchymal cells. In contrast to the model described above, we find that protrusion-localized RNAs are not locally activated solely at protrusions, but can be translated with similar efficiency in both internal and peripheral locations. Interestingly, protrusion-localized RNAs are translated at extending protrusions, they become translationally silenced in retracting protrusions and this silencing is accompanied by coalescence of single RNAs into larger heterogeneous RNA clusters. This work describes a distinct mode of translational regulation of localized RNAs, which we propose is used to regulate protein activities during dynamic cellular responses.
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Affiliation(s)
- Konstadinos Moissoglu
- Laboratory of Cellular and Molecular Biology,Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Kyota Yasuda
- Laboratory of Cellular and Molecular Biology,Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States.,Program of Mathematical and Life Sciences, Graduate School of Integrated Science for Life, Hiroshima University, Higashi-Hiroshima, Japan.,Laboratory for Comprehensive Bioimaging, RIKEN Center for Biosystems Dynamics Research, Suita, Japan
| | - Tianhong Wang
- Laboratory of Cellular and Molecular Biology,Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - George Chrisafis
- Laboratory of Cellular and Molecular Biology,Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Stavroula Mili
- Laboratory of Cellular and Molecular Biology,Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States
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60
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Regulation of Translationally Repressed mRNAs in Zebrafish and Mouse Oocytes. Results Probl Cell Differ 2019; 63:297-324. [PMID: 28779323 DOI: 10.1007/978-3-319-60855-6_13] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
From the beginning of oogenesis, oocytes accumulate tens of thousands of mRNAs for promoting oocyte growth and development. A large number of these mRNAs are translationally repressed and localized within the oocyte cytoplasm. Translational activation of these dormant mRNAs at specific sites and timings plays central roles in driving progression of the meiotic cell cycle, axis formation, mitotic cleavages, transcriptional initiation, and morphogenesis. Regulation of the localization and temporal translation of these mRNAs has been shown to rely on cis-acting elements in the mRNAs and trans-acting factors recognizing and binding to the elements. Recently, using model vertebrate zebrafish, localization itself and formation of physiological structures such as RNA granules have been shown to coordinate the accurate timings of translational activation of dormant mRNAs. This subcellular regulation of mRNAs is also utilized in other animals including mouse. In this chapter, we review fundamental roles of temporal regulation of mRNA translation in oogenesis and early development and then focus on the mechanisms of mRNA regulation in the oocyte cytoplasm by which the activation of dormant mRNAs at specific timings is achieved.
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61
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Vijayakumar J, Perrois C, Heim M, Bousset L, Alberti S, Besse F. The prion-like domain of Drosophila Imp promotes axonal transport of RNP granules in vivo. Nat Commun 2019; 10:2593. [PMID: 31197139 PMCID: PMC6565635 DOI: 10.1038/s41467-019-10554-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 05/15/2019] [Indexed: 01/29/2023] Open
Abstract
Prion-like domains (PLDs), defined by their low sequence complexity and intrinsic disorder, are present in hundreds of human proteins. Although gain-of-function mutations in the PLDs of neuronal RNA-binding proteins have been linked to neurodegenerative disease progression, the physiological role of PLDs and their range of molecular functions are still largely unknown. Here, we show that the PLD of Drosophila Imp, a conserved component of neuronal ribonucleoprotein (RNP) granules, is essential for the developmentally-controlled localization of Imp RNP granules to axons and regulates in vivo axonal remodeling. Furthermore, we demonstrate that Imp PLD restricts, rather than promotes, granule assembly, revealing a novel modulatory function for PLDs in RNP granule homeostasis. Swapping the position of Imp PLD compromises RNP granule dynamic assembly but not transport, suggesting that these two functions are uncoupled. Together, our study uncovers a physiological function for PLDs in the spatio-temporal control of neuronal RNP assemblies. The physiological role of prion-like domains (PLDs) within RNA-binding proteins is not well understood. Here, authors show in Drosophila that the PLD in the protein Imp is required for localization of ribonucleoprotein granules to axons and axonal remodelling.
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Affiliation(s)
| | | | - Marjorie Heim
- University Côte d'Azur, CNRS, Inserm, iBV, Nice, 06100, France
| | - Luc Bousset
- Paris-Saclay Institute of Neuroscience, Orsay, 91505, France
| | - Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307, Germany.,Center for Molecular and Cellular Bioengineering (CMCB), Biotechnology Center, Technische Universität Dresden, Dresden, 01307, Germany
| | - Florence Besse
- University Côte d'Azur, CNRS, Inserm, iBV, Nice, 06100, France.
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62
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Stueland M, Wang T, Park HY, Mili S. RDI Calculator: An Analysis Tool to Assess RNA Distributions in Cells. Sci Rep 2019; 9:8267. [PMID: 31164708 PMCID: PMC6547641 DOI: 10.1038/s41598-019-44783-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/20/2019] [Indexed: 11/17/2022] Open
Abstract
Localization of RNAs to various subcellular destinations has emerged as a widely used mechanism that regulates a large proportion of transcripts in polarized cells. A number of methodologies have been developed that allow detection and imaging of RNAs at single-molecule resolution. However, methodologies to quantitatively describe RNA distributions are limited. Such approaches usually rely on the identification of cytoplasmic and nuclear boundaries which are used as reference points. Here, we describe an automated, interactive image analysis program that facilitates the accurate generation of cellular outlines from single cells and the subsequent calculation of metrics that quantify how a population of RNA molecules is distributed in the cell cytoplasm. We apply this analysis to mRNAs in mouse and human cells to demonstrate how these metrics can highlight differences in the distribution patterns of distinct RNA species. We further discuss considerations for the practical use of this tool. This program provides a way to facilitate and expedite the analysis of subcellular RNA localization for mechanistic and functional studies.
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Affiliation(s)
- Michael Stueland
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Tianhong Wang
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Hye Yoon Park
- Department of Physics and Astronomy, Seoul National University, Seoul, Korea
| | - Stavroula Mili
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA.
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63
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Pizzinga M, Bates C, Lui J, Forte G, Morales-Polanco F, Linney E, Knotkova B, Wilson B, Solari CA, Berchowitz LE, Portela P, Ashe MP. Translation factor mRNA granules direct protein synthetic capacity to regions of polarized growth. J Cell Biol 2019; 218:1564-1581. [PMID: 30877141 PMCID: PMC6504908 DOI: 10.1083/jcb.201704019] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 11/12/2018] [Accepted: 02/28/2019] [Indexed: 12/22/2022] Open
Abstract
mRNA localization serves key functions in localized protein production, making it critical that the translation machinery itself is present at these locations. Here we show that translation factor mRNAs are localized to distinct granules within yeast cells. In contrast to many messenger RNP granules, such as processing bodies and stress granules, which contain translationally repressed mRNAs, these granules harbor translated mRNAs under active growth conditions. The granules require Pab1p for their integrity and are inherited by developing daughter cells in a She2p/She3p-dependent manner. These results point to a model where roughly half the mRNA for certain translation factors is specifically directed in granules or translation factories toward the tip of the developing daughter cell, where protein synthesis is most heavily required, which has particular implications for filamentous forms of growth. Such a feedforward mechanism would ensure adequate provision of the translation machinery where it is to be needed most over the coming growth cycle.
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Affiliation(s)
- Mariavittoria Pizzinga
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Christian Bates
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Jennifer Lui
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Gabriella Forte
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Fabián Morales-Polanco
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Emma Linney
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Barbora Knotkova
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Beverley Wilson
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Clara A Solari
- Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Luke E Berchowitz
- Department of Genetics and Development, Hammer Health Sciences Center, Columbia University Medical Center, New York, NY
| | - Paula Portela
- Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Mark P Ashe
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
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64
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Ding D, Enriquez-Algeciras M, Valdivia AO, Torres J, Pole C, Thompson JW, Chou TH, Perez-Pinzon M, Porciatti V, Udin S, Nestler E, Bhattacharya SK. The Role of Deimination in Regenerative Reprogramming of Neurons. Mol Neurobiol 2019; 56:2618-2639. [PMID: 30051351 PMCID: PMC6348056 DOI: 10.1007/s12035-018-1262-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 07/17/2018] [Indexed: 10/28/2022]
Abstract
Neurons from the adult central nervous system (CNS) demonstrate limited mRNA transport and localized protein synthesis versus developing neurons, correlating with lower regenerative capacity. We found that deimination (posttranslational conversion of protein-bound arginine into citrulline) undergoes upregulation during early neuronal development while declining to a low basal level in adults. This modification is associated with neuronal arborization from amphibians to mammals. The mRNA-binding proteins (ANP32a, REF), deiminated in neurons, have been implicated in local protein synthesis. Overexpression of the deiminating cytosolic enzyme peptidyl arginine deiminase 2 in nervous systems results in increased neuronal transport and neurite outgrowth. We further demonstrate that enriching deiminated proteins rescues transport deficiencies both in primary neurons and mouse optic nerve even in the presence of pharmacological transport blockers. We conclude that deimination promotes neuronal outgrowth via enhanced transport and local protein synthesis and represents a new avenue for neuronal regeneration in the adult CNS.
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Affiliation(s)
- Di Ding
- Bascom Palmer Eye Institute, University of Miami, 1638 N.W. 10th Avenue, #706, Miami, FL, 33136, USA
- Department of Ophthalmology/Neuroscience Program, University of Miami, Miami, FL, 33136, USA
| | - Mabel Enriquez-Algeciras
- Bascom Palmer Eye Institute, University of Miami, 1638 N.W. 10th Avenue, #706, Miami, FL, 33136, USA
- Department of Ophthalmology/Neuroscience Program, University of Miami, Miami, FL, 33136, USA
| | - Anddre Osmar Valdivia
- Bascom Palmer Eye Institute, University of Miami, 1638 N.W. 10th Avenue, #706, Miami, FL, 33136, USA
- Department of Ophthalmology/Neuroscience Program, University of Miami, Miami, FL, 33136, USA
| | - Juan Torres
- Bascom Palmer Eye Institute, University of Miami, 1638 N.W. 10th Avenue, #706, Miami, FL, 33136, USA
- Department of Ophthalmology/Neuroscience Program, University of Miami, Miami, FL, 33136, USA
| | - Cameron Pole
- Department of Ophthalmology/Neuroscience Program, University of Miami, Miami, FL, 33136, USA
| | - John W Thompson
- Neurological Surgery, University of Miami, Miami, FL, 33136, USA
| | - Tsung-Han Chou
- Bascom Palmer Eye Institute, University of Miami, 1638 N.W. 10th Avenue, #706, Miami, FL, 33136, USA
- Department of Ophthalmology/Neuroscience Program, University of Miami, Miami, FL, 33136, USA
| | - Miguel Perez-Pinzon
- Department of Ophthalmology/Neuroscience Program, University of Miami, Miami, FL, 33136, USA
- Department of Neurology, University of Miami, Miami, FL, 33136, USA
| | - Vittorio Porciatti
- Bascom Palmer Eye Institute, University of Miami, 1638 N.W. 10th Avenue, #706, Miami, FL, 33136, USA
- Department of Ophthalmology/Neuroscience Program, University of Miami, Miami, FL, 33136, USA
| | - Susan Udin
- Department of Physiology and Biophysics, State University of New York, Buffalo, 553 Biomedical Res. Building, Buffalo, NY, 14214, USA
| | - Eric Nestler
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1065, New York, NY, 10029, USA
| | - Sanjoy K Bhattacharya
- Bascom Palmer Eye Institute, University of Miami, 1638 N.W. 10th Avenue, #706, Miami, FL, 33136, USA.
- Department of Ophthalmology/Neuroscience Program, University of Miami, Miami, FL, 33136, USA.
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65
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Almazán A, Ferrández-Roldán A, Albalat R, Cañestro C. Developmental atlas of appendicularian Oikopleura dioica actins provides new insights into the evolution of the notochord and the cardio-paraxial muscle in chordates. Dev Biol 2019; 448:260-270. [DOI: 10.1016/j.ydbio.2018.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 07/13/2018] [Accepted: 09/05/2018] [Indexed: 12/22/2022]
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66
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Mayya VK, Duchaine TF. Ciphers and Executioners: How 3'-Untranslated Regions Determine the Fate of Messenger RNAs. Front Genet 2019; 10:6. [PMID: 30740123 PMCID: PMC6357968 DOI: 10.3389/fgene.2019.00006] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 01/07/2019] [Indexed: 12/29/2022] Open
Abstract
The sequences and structures of 3'-untranslated regions (3'UTRs) of messenger RNAs govern their stability, localization, and expression. 3'UTR regulatory elements are recognized by a wide variety of trans-acting factors that include microRNAs (miRNAs), their associated machinery, and RNA-binding proteins (RBPs). In turn, these factors instigate common mechanistic strategies to execute the regulatory programs encoded by 3'UTRs. Here, we review classes of factors that recognize 3'UTR regulatory elements and the effector machineries they guide toward mRNAs to dictate their expression and fate. We outline illustrative examples of competitive, cooperative, and coordinated interplay such as mRNA localization and localized translation. We further review the recent advances in the study of mRNP granules and phase transition, and their possible significance for the functions of 3'UTRs. Finally, we highlight some of the most recent strategies aimed at deciphering the complexity of the regulatory codes of 3'UTRs, and identify some of the important remaining challenges.
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Affiliation(s)
| | - Thomas F. Duchaine
- Goodman Cancer Research Centre and Department of Biochemistry, McGill University, Montreal, QC, Canada
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67
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Chen YC, Chang YW, Huang YS. Dysregulated Translation in Neurodevelopmental Disorders: An Overview of Autism-Risk Genes Involved in Translation. Dev Neurobiol 2018; 79:60-74. [PMID: 30430754 DOI: 10.1002/dneu.22653] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 09/17/2018] [Accepted: 10/25/2018] [Indexed: 01/08/2023]
Abstract
Regulated local translation-whereby specific mRNAs are transported and localized in subcellular domains where they are translated in response to regional signals-allows for remote control of gene expression to concentrate proteins in subcellular compartments. Neurons are highly polarized cells with unique features favoring local control for axonal pathfinding and synaptic plasticity, which are key processes involved in constructing functional circuits in the developing brain. Neurodevelopmental disorders are caused by genetic or environmental factors that disturb the nervous system's development during prenatal and early childhood periods. The growing list of genetic mutations that affect mRNA translation raises the question of whether aberrant translatomes in individuals with neurodevelopmental disorders share common molecular features underlying their stereotypical phenotypes and, vice versa, cause a certain degree of phenotypic heterogeneity. Here, we briefly give an overview of the role of local translation during neuronal development. We take the autism-risk gene list and discuss the molecules that (perhaps) are involved in mRNA transport and translation. Both exaggerated and suppressed translation caused by mutations in those genes have been identified or suggested. Finally, we discuss some proof-of-principle regimens for use in autism mouse models to correct dysregulated translation.
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Affiliation(s)
- Yan-Chu Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Yu-Wei Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Yi-Shuian Huang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
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68
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Huang J, Liu P, Wang G. Regulation of mitochondrion-associated cytosolic ribosomes by mammalian mitochondrial ribonuclease T2 (RNASET2). J Biol Chem 2018; 293:19633-19644. [PMID: 30385512 PMCID: PMC6314140 DOI: 10.1074/jbc.ra118.005433] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 10/15/2018] [Indexed: 11/12/2022] Open
Abstract
Mitochondrial proteins are encoded in both mitochondrial and nuclear genomes. The expression levels of these two pools of mitochondrial genes are co-regulated and synchronized. Import and assembly of the nucleus-encoded oxidative phosphorylation (OXPHOS) subunits affect protein synthesis in the mitochondrial matrix by engaging the mitochondrial ribosomes. How the ribosomes at the outside of mitochondria are regulated by mitochondria, however, remains mostly unexplored. Here, using an array of biochemical assays and genetic knockdown and overexpression in HEK293 or mouse cells, we show that cytosolic rRNAs that are associated with the mitochondrial outer membrane have very different decay patterns from those of both endoplasmic reticulum–associated and –nonassociated cytosolic rRNAs. Mitochondrial intermembrane space RNase T2 (RNASET2), which has been previously shown to degrade mitochondrial RNAs, is also responsible for selective degradation of the cytosolic rRNAs on the outer membrane. We noted that the degradation activity also has a positive effect on nuclear transcription of rRNAs, suggesting a compensatory feedback mechanism, and affects protein translations in and out of mitochondria. These findings establish a mechanism for the co-regulation of gene expression programs inside and outside of mitochondria in mammalian cells.
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Affiliation(s)
- Jinliang Huang
- From the Ministry of Education Key Laboratory of Bioinformatics, Cell Biology and Development Center, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Peipei Liu
- From the Ministry of Education Key Laboratory of Bioinformatics, Cell Biology and Development Center, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Geng Wang
- From the Ministry of Education Key Laboratory of Bioinformatics, Cell Biology and Development Center, School of Life Sciences, Tsinghua University, Beijing 100084, China
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69
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Böhm BB, Fehrl Y, Janczi T, Schneider N, Burkhardt H. Cell adhesion-induced transient interaction of ADAM15 with poly(A) binding protein at the cell membrane colocalizes with mRNA translation. PLoS One 2018; 13:e0203847. [PMID: 30265671 PMCID: PMC6161846 DOI: 10.1371/journal.pone.0203847] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 08/28/2018] [Indexed: 12/15/2022] Open
Abstract
The regulation of temporo-spatial compartmentalization of protein synthesis is of crucial importance for a variety of physiologic cellular functions. Here, we demonstrate that the cell membrane-anchored disintegrin metalloproteinase ADAM15, upregulated in a variety of aggressively growing tumor cells, in the hyperproliferative synovial membrane of inflamed joints as well as in osteoarthritic chondrocytes, transiently binds to poly(A) binding protein 1 (PABP) in cells undergoing adhesion. The cytoplasmic domain of ADAM15 was shown to selectively interact with the proline-rich linker of PABP. Immunostainings of adhesion-triggered cells demonstrate an ADAM15-dependent recruitment of PABP to cell membrane foci coinciding with ongoing mRNA translation as visualized by the detection of puromycin-terminated polypeptides. Moreover, the increase in cell membrane-associated neosynthesis of puromycylated proteins upon induction of cell adhesion was proven linked to ADAM15 expression in HeLa and ADAM15-transfected chondrocytic cells. Thus, down regulation of ADAM15 by siRNA and/or the use of a cell line transfected with a mutant ADAM15-construct lacking the cytoplasmic tail resulted in a considerable reduction in the amount of cell membrane-associated puromycylated proteins formed during induced cell adhesion. These results provide first direct evidence for a regulatory role of ADAM15 on mRNA translation at the cell membrane that transiently emerges in response to triggering cell adhesion and might have potential implications under pathologic conditions of matrix remodeling associated with ADAM15 upregulation.
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Affiliation(s)
- Beate B. Böhm
- Division of Rheumatology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Yuliya Fehrl
- Division of Rheumatology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Tomasz Janczi
- Division of Rheumatology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Nadine Schneider
- Project Group Translational Medicine & Pharmacology TMP, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Frankfurt am Main, Germany
| | - Harald Burkhardt
- Division of Rheumatology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
- Project Group Translational Medicine & Pharmacology TMP, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Frankfurt am Main, Germany
- * E-mail:
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70
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Suter B. RNA localization and transport. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:938-951. [PMID: 30496039 DOI: 10.1016/j.bbagrm.2018.08.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 08/23/2018] [Accepted: 08/23/2018] [Indexed: 12/30/2022]
Abstract
RNA localization serves numerous purposes from controlling development and differentiation to supporting the physiological activities of cells and organisms. After a brief introduction into the history of the study of mRNA localization I will focus on animal systems, describing in which cellular compartments and in which cell types mRNA localization was observed and studied. In recent years numerous novel localization patterns have been described, and countless mRNAs have been documented to accumulate in specific subcellular compartments. These fascinating revelations prompted speculations about the purpose of localizing all these mRNAs. In recent years experimental evidence for an unexpected variety of different functions has started to emerge. Aside from focusing on the functional aspects, I will discuss various ways of localizing mRNAs with a focus on the mechanism of active and directed transport on cytoskeletal tracks. Structural studies combined with imaging of transport and biochemical studies have contributed to the enormous recent progress, particularly in understanding how dynein/dynactin/BicD (DDB) dependent transport on microtubules works. This transport process actively localizes diverse cargo in similar ways to the minus end of microtubules and, at least in flies, also individual mRNA molecules. A sophisticated mechanism ensures that cargo loading licenses processive transport.
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Affiliation(s)
- Beat Suter
- Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland.
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71
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Gallagher C, Ramos A. Joining the dots - protein-RNA interactions mediating local mRNA translation in neurons. FEBS Lett 2018; 592:2932-2947. [PMID: 29856909 DOI: 10.1002/1873-3468.13121] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 05/24/2018] [Accepted: 05/30/2018] [Indexed: 01/26/2023]
Abstract
Establishing and maintaining the complex network of connections required for neuronal communication requires the transport and in situ translation of large groups of mRNAs to create local proteomes. In this Review, we discuss the regulation of local mRNA translation in neurons and the RNA-binding proteins that recognise RNA zipcode elements and connect the mRNAs to the cellular transport networks, as well as regulate their translation control. However, mRNA recognition by the regulatory proteins is mediated by the combinatorial action of multiple RNA-binding domains. This increases the specificity and affinity of the interaction, while allowing the protein to recognise a diverse set of targets and mediate a range of mechanisms for translational regulation. The structural and molecular understanding of the interactions can be used together with novel microscopy and transcriptome-wide data to build a mechanistic framework for the regulation of local mRNA translation.
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Affiliation(s)
- Christopher Gallagher
- Institute of Structural and Molecular Biology, University College London, UK.,The Francis Crick Institute, London, UK
| | - Andres Ramos
- Institute of Structural and Molecular Biology, University College London, UK
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72
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Zampa F, Bicker S, Schratt G. Activity-Dependent Pre-miR-134 Dendritic Localization Is Required for Hippocampal Neuron Dendritogenesis. Front Mol Neurosci 2018; 11:171. [PMID: 29942249 PMCID: PMC6004952 DOI: 10.3389/fnmol.2018.00171] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 05/07/2018] [Indexed: 01/15/2023] Open
Abstract
microRNAs (miRNAs) have emerged as critical regulators of neuronal dendrite development. Specific precursor (pre-)miRNAs are actively transported to dendrites, but whether this process is regulated by neuronal activity and involved in activity-dependent dendritogenesis is unknown. Here we show that BDNF, a neurotrophin that is released in response to increased neuronal activity, promotes dendritic accumulation of pre-miR-134. Dendritic accumulation, but not transcription of pre-miR-134, is abrogated by treatment of neurons with the NMDA receptor (NMDAR) antagonist APV. Furthermore, APV interferes with BDNF-mediated repression of the known miR-134 target Pumilio 2 (Pum2) in a miR-134 binding site-specific manner. At the functional level, both APV treatment and knockdown of the pre-miR-134 transport protein DHX36 antagonize BDNF-induced dendritogenesis. These effects are likely mediated by reduced dendritic miR-134 activity, since both transfection of a synthetic miR-134 duplex or of a dendritically targeted pre-miR-134-181a chimera rescues BDNF-dependent dendritogenesis in the presence of APV. In conclusion, we have identified a novel NMDAR-dependent mechanism involved in the activity-dependent control of miRNA function during neuronal development.
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Affiliation(s)
- Federico Zampa
- Institute of Physiological Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Silvia Bicker
- Institute of Physiological Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Gerhard Schratt
- Institute of Physiological Chemistry, Philipps-University Marburg, Marburg, Germany
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73
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Battling for Ribosomes: Translational Control at the Forefront of the Antiviral Response. J Mol Biol 2018; 430:1965-1992. [PMID: 29746850 DOI: 10.1016/j.jmb.2018.04.040] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 04/24/2018] [Accepted: 04/27/2018] [Indexed: 01/05/2023]
Abstract
In the early stages of infection, gaining control of the cellular protein synthesis machinery including its ribosomes is the ultimate combat objective for a virus. To successfully replicate, viruses unequivocally need to usurp and redeploy this machinery for translation of their own mRNA. In response, the host triggers global shutdown of translation while paradoxically allowing swift synthesis of antiviral proteins as a strategy to limit collateral damage. This fundamental conflict at the level of translational control defines the outcome of infection. As part of this special issue on molecular mechanisms of early virus-host cell interactions, we review the current state of knowledge regarding translational control during viral infection with specific emphasis on protein kinase RNA-activated and mammalian target of rapamycin-mediated mechanisms. We also describe recent technological advances that will allow unprecedented insight into how viruses and host cells battle for ribosomes.
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74
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Hao L, Yang Z, Lei J. Underlying Mechanisms of Cooperativity, Input Specificity, and Associativity of Long-Term Potentiation Through a Positive Feedback of Local Protein Synthesis. Front Comput Neurosci 2018; 12:25. [PMID: 29765314 PMCID: PMC5938377 DOI: 10.3389/fncom.2018.00025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 03/28/2018] [Indexed: 12/20/2022] Open
Abstract
Long-term potentiation (LTP) is a specific form of activity-dependent synaptic plasticity that is a leading mechanism of learning and memory in mammals. The properties of cooperativity, input specificity, and associativity are essential for LTP; however, the underlying mechanisms are unclear. Here, based on experimentally observed phenomena, we introduce a computational model of synaptic plasticity in a pyramidal cell to explore the mechanisms responsible for the cooperativity, input specificity, and associativity of LTP. The model is based on molecular processes involved in synaptic plasticity and integrates gene expression involved in the regulation of neuronal activity. In the model, we introduce a local positive feedback loop of protein synthesis at each synapse, which is essential for bimodal response and synapse specificity. Bifurcation analysis of the local positive feedback loop of brain-derived neurotrophic factor (BDNF) signaling illustrates the existence of bistability, which is the basis of LTP induction. The local bifurcation diagram provides guidance for the realization of LTP, and the projection of whole system trajectories onto the two-parameter bifurcation diagram confirms the predictions obtained from bifurcation analysis. Moreover, model analysis shows that pre- and postsynaptic components are required to achieve the three properties of LTP. This study provides insights into the mechanisms underlying the cooperativity, input specificity, and associativity of LTP, and the further construction of neural networks for learning and memory.
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Affiliation(s)
- Lijie Hao
- School of Mathematics and Systems Science, Key Laboratory of Mathematics, Informatics and Behavioral Semantics, Ministry of Education, Beihang University, Beijing, China
| | - Zhuoqin Yang
- School of Mathematics and Systems Science, Key Laboratory of Mathematics, Informatics and Behavioral Semantics, Ministry of Education, Beihang University, Beijing, China
| | - Jinzhi Lei
- Zhou Pei-Yuan Center for Applied Mathematics, MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
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75
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Neuronal RNP granules: from physiological to pathological assemblies. Biol Chem 2018; 399:623-635. [DOI: 10.1515/hsz-2018-0141] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 03/30/2018] [Indexed: 12/11/2022]
Abstract
Abstract
Neuronal cells rely on macro- and micro-cellular compartmentalization to rapidly process information, and respond locally to external stimuli. Such a cellular organization is achieved via the assembly of neuronal ribonucleoprotein (RNP) granules, dynamic membrane-less organelles enriched in RNAs and associated regulatory proteins. In this review, we discuss how these high-order structures transport mRNAs to dendrites and axons, and how they contribute to the spatio-temporal regulation of localized mRNA translation. We also highlight how recent biophysical studies have shed light on the mechanisms underlying neuronal RNP granule dynamic assembly, remodeling and maturation, in both physiological and pathological contexts.
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76
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Shirokikh NE, Preiss T. Translation initiation by cap-dependent ribosome recruitment: Recent insights and open questions. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1473. [PMID: 29624880 DOI: 10.1002/wrna.1473] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 02/02/2018] [Accepted: 02/14/2018] [Indexed: 12/14/2022]
Abstract
Gene expression universally relies on protein synthesis, where ribosomes recognize and decode the messenger RNA template by cycling through translation initiation, elongation, and termination phases. All aspects of translation have been studied for decades using the tools of biochemistry and molecular biology available at the time. Here, we focus on the mechanism of translation initiation in eukaryotes, which is remarkably more complex than prokaryotic initiation and is the target of multiple types of regulatory intervention. The "consensus" model, featuring cap-dependent ribosome entry and scanning of mRNA leader sequences, represents the predominantly utilized initiation pathway across eukaryotes, although several variations of the model and alternative initiation mechanisms are also known. Recent advances in structural biology techniques have enabled remarkable molecular-level insights into the functional states of eukaryotic ribosomes, including a range of ribosomal complexes with different combinations of translation initiation factors that are thought to represent bona fide intermediates of the initiation process. Similarly, high-throughput sequencing-based ribosome profiling or "footprinting" approaches have allowed much progress in understanding the elongation phase of translation, and variants of them are beginning to reveal the remaining mysteries of initiation, as well as aspects of translation termination and ribosomal recycling. A current view on the eukaryotic initiation mechanism is presented here with an emphasis on how recent structural and footprinting results underpin axioms of the consensus model. Along the way, we further outline some contested mechanistic issues and major open questions still to be addressed. This article is categorized under: Translation > Translation Mechanisms Translation > Translation Regulation RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Nikolay E Shirokikh
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia
| | - Thomas Preiss
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia
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77
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Yamashita A, Takeuchi O. Translational control of mRNAs by 3'-Untranslated region binding proteins. BMB Rep 2018; 50:194-200. [PMID: 28287067 PMCID: PMC5437963 DOI: 10.5483/bmbrep.2017.50.4.040] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Indexed: 12/31/2022] Open
Abstract
Eukaryotic gene expression is precisely regulated at all points between transcription and translation. In this review, we focus on translational control mediated by the 3′-untranslated regions (UTRs) of mRNAs. mRNA 3′-UTRs contain cis-acting elements that function in the regulation of protein translation or mRNA decay. Each RNA binding protein that binds to these cis-acting elements regulates mRNA translation via various mechanisms targeting the mRNA cap structure, the eukaryotic initiation factor 4E (eIF4E)-eIF4G complex, ribosomes, and the poly (A) tail. We also discuss translation-mediated regulation of mRNA fate.
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Affiliation(s)
- Akio Yamashita
- Department of Molecular Biology, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
| | - Osamu Takeuchi
- Laboratory of Infection and Prevention, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
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78
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Wang DO, Ninomiya K, Mori C, Koyama A, Haan M, Kitabatake M, Hagiwara M, Chida K, Takahashi SI, Ohno M, Kataoka N. Transport Granules Bound with Nuclear Cap Binding Protein and Exon Junction Complex Are Associated with Microtubules and Spatially Separated from eIF4E Granules and P Bodies in Human Neuronal Processes. Front Mol Biosci 2017; 4:93. [PMID: 29312956 PMCID: PMC5744441 DOI: 10.3389/fmolb.2017.00093] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 12/15/2017] [Indexed: 02/05/2023] Open
Abstract
RNA transport and regulated local translation play critically important roles in spatially restricting gene expression in neurons. Heterogeneous population of RNA granules serve as motile units to translocate, store, translate, and degrade mRNAs in the dendrites contain cis-elements and trans-acting factors such as RNA-binding proteins and microRNAs to convey stimulus-, transcript-specific local translation. Here we report a class of mRNA granules in human neuronal processes that are enriched in the nuclear cap-binding protein complex (CBC) and exon junction complex (EJC) core components, Y14 and eIF4AIII. These granules are physically associated with stabilized microtubules and are spatially segregated from eIF4E-enriched granules and P-bodies. The existence of mRNAs retaining both nuclear cap binding protein and EJC in the distal sites of neuronal processes suggests that some localized mRNAs have not yet undergone the “very first translation,” which contribute to the spatio-temporal regulation of gene expression.
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Affiliation(s)
- Dan O Wang
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto, Japan.,K-CONNEX (Keihanshin Consortium for Fostering Next Generation of Global Leaders in Research), Kyoto, Japan
| | - Kensuke Ninomiya
- Institute for Virus research, Kyoto University, Kyoto, Japan.,Laboratory of Anatomy and Developmental Biology, Kyoto University School of Medicine, Kyoto, Japan
| | - Chihiro Mori
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto, Japan
| | - Ayako Koyama
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto, Japan
| | - Martine Haan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto, Japan
| | | | - Masatoshi Hagiwara
- Laboratory of Anatomy and Developmental Biology, Kyoto University School of Medicine, Kyoto, Japan
| | - Kazuhiro Chida
- Laboratory of Cell Regulation, Departments of Applied Animal Sciences and Applied Biological Chemistry Graduate School of Agriculture and Life Sciences, The University of Tokyo, Kyoto, Japan
| | - Shin-Ichiro Takahashi
- Laboratory of Cell Regulation, Departments of Applied Animal Sciences and Applied Biological Chemistry Graduate School of Agriculture and Life Sciences, The University of Tokyo, Kyoto, Japan
| | - Mutsuhito Ohno
- Institute for Virus research, Kyoto University, Kyoto, Japan
| | - Naoyuki Kataoka
- Institute for Virus research, Kyoto University, Kyoto, Japan.,Laboratory of Anatomy and Developmental Biology, Kyoto University School of Medicine, Kyoto, Japan.,Laboratory of Cell Regulation, Departments of Applied Animal Sciences and Applied Biological Chemistry Graduate School of Agriculture and Life Sciences, The University of Tokyo, Kyoto, Japan.,Medical Innovation Center, Laboratory for Malignancy Control Research, Kyoto University Graduate School of Medicine, Kyoto, Japan.,Medical Top Track Program, Medical Research Institute, Tokyo Dental and Medical University, Tokyo, Japan
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79
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Hassan MA, Vasquez JJ, Guo-Liang C, Meissner M, Nicolai Siegel T. Comparative ribosome profiling uncovers a dominant role for translational control in Toxoplasma gondii. BMC Genomics 2017; 18:961. [PMID: 29228904 PMCID: PMC5725899 DOI: 10.1186/s12864-017-4362-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 12/01/2017] [Indexed: 11/17/2022] Open
Abstract
Background The lytic cycle of the protozoan parasite Toxoplasma gondii, which involves a brief sojourn in the extracellular space, is characterized by defined transcriptional profiles. For an obligate intracellular parasite that is shielded from the cytosolic host immune factors by a parasitophorous vacuole, the brief entry into the extracellular space is likely to exert enormous stress. Due to its role in cellular stress response, we hypothesize that translational control plays an important role in regulating gene expression in Toxoplasma during the lytic cycle. Unlike transcriptional profiles, insights into genome-wide translational profiles of Toxoplasma gondii are lacking. Methods We have performed genome-wide ribosome profiling, coupled with high throughput RNA sequencing, in intracellular and extracellular Toxoplasma gondii parasites to investigate translational control during the lytic cycle. Results Although differences in transcript abundance were mostly mirrored at the translational level, we observed significant differences in the abundance of ribosome footprints between the two parasite stages. Furthermore, our data suggest that mRNA translation in the parasite is potentially regulated by mRNA secondary structure and upstream open reading frames. Conclusion We show that most of the Toxoplasma genes that are dysregulated during the lytic cycle are translationally regulated. Electronic supplementary material The online version of this article (10.1186/s12864-017-4362-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Musa A Hassan
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Edinburgh, UK. .,The Centre for Tropical Livestock Genetics and Health, The Roslin Institute, University of Edinburgh, Edinburgh, UK.
| | - Juan J Vasquez
- Research Centre for Infectious Diseases, University of Wuerzburg, Wuerzburg, 97080, Germany.,Present address: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Chew Guo-Liang
- Computational Biology Program, Basic Sciences and Public Health Sciences Division, Fred Hutchinson Cancer Research Centre, Seattle, WA, 98105, USA
| | - Markus Meissner
- Wellcome Centre for Molecular Parasitology, University of Glasgow, Glasgow, UK.,Department of Veterinary Sciences, Experimental Parasitology, Ludwig-Maximilians-Universität, München, 80802, Munich, Germany
| | - T Nicolai Siegel
- Research Centre for Infectious Diseases, University of Wuerzburg, Wuerzburg, 97080, Germany.,Department of Veterinary Sciences, Experimental Parasitology, Ludwig-Maximilians-Universität, München, 80802, Munich, Germany.,Biomedical Center Munich, Physiological Chemistry, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 82152, Germany
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80
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The devil is in the domain: understanding protein recognition of multiple RNA targets. Biochem Soc Trans 2017; 45:1305-1311. [DOI: 10.1042/bst20160362] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 10/22/2017] [Accepted: 10/23/2017] [Indexed: 11/17/2022]
Abstract
RNA regulation provides a finely tuned and highly co-ordinated control of gene expression. Regulation is mediated by hundreds to thousands of multi-functional RNA-binding proteins which often interact with large sets of RNAs. In this brief review, we focus on a recent work that highlights how the proteins use multiple RNA-binding domains to interact selectively with the different RNA targets. Deconvoluting the molecular complexity of the RNA regulatory network is essential to understanding cell differentiation and function, and requires accurate models for protein–RNA recognition and protein target selectivity. We discuss that the structural and molecular understanding of the key determinant of recognition, together with the availability of methods to examine protein–RNA interactions at the transcriptome level, may provide an avenue to establish these models.
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81
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Extracellular matrix stiffness and cell contractility control RNA localization to promote cell migration. Nat Commun 2017; 8:896. [PMID: 29026081 PMCID: PMC5638855 DOI: 10.1038/s41467-017-00884-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 08/02/2017] [Indexed: 01/13/2023] Open
Abstract
Numerous RNAs are enriched within cellular protrusions, but the underlying mechanisms are largely unknown. We had shown that the APC (adenomatous polyposis coli) protein controls localization of some RNAs at protrusions. Here, using protrusion-isolation schemes and RNA-Seq, we find that RNAs localized in protrusions of migrating fibroblasts can be distinguished in two groups, which are differentially enriched in distinct types of protrusions, and are additionally differentially dependent on APC. APC-dependent RNAs become enriched in high-contractility protrusions and, accordingly, their localization is promoted by increasing stiffness of the extracellular matrix. Dissecting the underlying mechanism, we show that actomyosin contractility activates a RhoA-mDia1 signaling pathway that leads to formation of a detyrosinated-microtubule network, which in turn is required for localization of APC-dependent RNAs. Importantly, a competition-based approach to specifically mislocalize APC-dependent RNAs suggests that localization of the APC-dependent RNA subgroup is functionally important for cell migration.Adenomatous polyposis coli (APC) regulates the localization of some mRNAs at cellular protrusions but the underlying mechanisms and functional roles are not known. Here the authors show that APC-dependent RNAs are enriched in contractile protrusions, via detyrosinated microtubules, and enhance cell migration.
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82
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Abstract
Translation is a fundamental biological process by which ribosomes decode genetic information into proteins. The regulation of this process plays a key role in tuning protein levels, allowing cells to respond rapidly to changes in the environment and to synthesize proteins with precise timing and at specific subcellular locations. Despite detailed biochemical and structural insight into the mechanism of protein synthesis, translational dynamics and localization in a cellular context are less well understood. Here, we summarize recent efforts to quantify and visualize translation, focusing on four publications (Morisaki et al., 2016; Wang et al., 2016; Wu et al., 2016; Yan et al., 2016) describing novel approaches to imaging in real time the synthesis of nascent peptides from individual mRNAs in living cells.
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Affiliation(s)
- Marina Chekulaeva
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany.
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany.
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83
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Moor AE, Golan M, Massasa EE, Lemze D, Weizman T, Shenhav R, Baydatch S, Mizrahi O, Winkler R, Golani O, Stern-Ginossar N, Itzkovitz S. Global mRNA polarization regulates translation efficiency in the intestinal epithelium. Science 2017; 357:1299-1303. [PMID: 28798045 DOI: 10.1126/science.aan2399] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 07/03/2017] [Accepted: 08/01/2017] [Indexed: 12/19/2022]
Abstract
Asymmetric messenger RNA (mRNA) localization facilitates efficient translation in cells such as neurons and fibroblasts. However, the extent and importance of mRNA polarization in epithelial tissues are unclear. Here, we used single-molecule transcript imaging and subcellular transcriptomics to uncover global apical-basal intracellular polarization of mRNA in the mouse intestinal epithelium. The localization of mRNAs did not generally overlap protein localization. Instead, ribosomes were more abundant on the apical sides, and apical transcripts were consequently more efficiently translated. Refeeding of fasted mice elicited a basal-to-apical shift in polarization of mRNAs encoding ribosomal proteins, which was associated with a specific boost in their translation. This led to increased protein production, required for efficient nutrient absorption. These findings reveal a posttranscriptional regulatory mechanism involving dynamic polarization of mRNA and polarized translation.
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Affiliation(s)
- Andreas E Moor
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Matan Golan
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Efi E Massasa
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Doron Lemze
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Tomer Weizman
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Rom Shenhav
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Shaked Baydatch
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Orel Mizrahi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Roni Winkler
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ofra Golani
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Noam Stern-Ginossar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Shalev Itzkovitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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84
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Abstract
Asymmetric localization of mRNAs is a widespread gene regulatory mechanism that is crucial for many cellular processes. The localization of a transcript involves multiple steps and requires several protein factors to mediate transport, anchoring and translational repression of the mRNA. Specific recognition of the localizing transcript is a key step that depends on linear or structured localization signals, which are bound by RNA-binding proteins. Genetic studies have identified many components involved in mRNA localization. However, mechanistic aspects of the pathway are still poorly understood. Here we provide an overview of structural studies that contributed to our understanding of the mechanisms underlying mRNA localization, highlighting open questions and future challenges.
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Affiliation(s)
| | - Fulvia Bono
- a Max Planck Institute for Developmental Biology , Tübingen , Germany
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85
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Chorghade S, Seimetz J, Emmons R, Yang J, Bresson SM, Lisio MD, Parise G, Conrad NK, Kalsotra A. Poly(A) tail length regulates PABPC1 expression to tune translation in the heart. eLife 2017; 6. [PMID: 28653618 PMCID: PMC5487213 DOI: 10.7554/elife.24139] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 05/18/2017] [Indexed: 12/13/2022] Open
Abstract
The rate of protein synthesis in the adult heart is one of the lowest in mammalian tissues, but it increases substantially in response to stress and hypertrophic stimuli through largely obscure mechanisms. Here, we demonstrate that regulated expression of cytosolic poly(A)-binding protein 1 (PABPC1) modulates protein synthetic capacity of the mammalian heart. We uncover a poly(A) tail-based regulatory mechanism that dynamically controls PABPC1 protein synthesis in cardiomyocytes and thereby titrates cellular translation in response to developmental and hypertrophic cues. Our findings identify PABPC1 as a direct regulator of cardiac hypertrophy and define a new paradigm of gene regulation in the heart, where controlled changes in poly(A) tail length influence mRNA translation. DOI:http://dx.doi.org/10.7554/eLife.24139.001 Hundreds of thousands of different proteins are needed to build and maintain the cells in the human body. All proteins are produced when copies of genetic information in the form of molecules of messenger RNA (mRNAs) are translated by the ribosome. The rate at which proteins are made varies widely between different tissues and at different times. In particular, the adult heart has one of the lowest rates of protein production, though this rate can increase markedly during exercise and heart disease. The mechanisms that drive this kind of dynamic change in protein production remain unclear. A better understanding of this process would tell scientists more about how and why cells regulate the translation of mRNAs in general, and might uncover new ways for treating heart disease. Molecules of mRNA are composed of smaller building blocks called nucleotides. All mature mRNAs in humans have a long stretch at one end that contains the nucleotide adenosine – commonly referred to as A for short – repeated 200 to 300 times. This sequence is called the poly(A) tail, and specific proteins can bind to this tail and determine the final fate of the mRNA, such as how efficiently it is translated. One such poly(A) binding protein, called PABPC1, is known to promote mRNA translation. Now, Chorghade, Seimetz et al. examine how PABPC1 regulates protein production in mice and human cells. The experiments reveal that, before birth, ample amounts of PABPC1 are found in the heart, but that this protein is undetectable in the hearts of adults. Further experiments showed that the levels of the mRNA for PABPC1 in the heart are the same before birth and in adulthood. So why is the mRNA for PABPC1 translated inefficiently in adult hearts? In general, mRNAs with long tails tend to be translated more efficiently compared to those with short tails, and it turns out that the mRNA for PABPC1 has a substantially shorter poly(A) tail in the adult heart. This tail shortening limits the translation of this specific mRNA, which leads to reduced protein production. Chorghade, Seimetz et al. also showed that the length of the poly(A) tail on the mRNA and the levels of the PABPC1 protein are restored in adult hearts during a condition known as hypertrophy. This state of hypertrophy can be triggered by exercise or heart disease and is marked by an increase in the size of individual heart cells and enhanced protein production. Finally, Chorghade, Seimetz et al. found that experimentally raising the levels of PABPC1 in adult hearts could, by itself, make the heart cells produce more protein and the heart grow more. Further studies will explore if other mRNAs in the heart also undergo similar changes and whether this is a general mechanism for controlling protein production. DOI:http://dx.doi.org/10.7554/eLife.24139.002
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Affiliation(s)
- Sandip Chorghade
- Department of Biochemistry, University of Illinois, Illinois, United States
| | - Joseph Seimetz
- Department of Biochemistry, University of Illinois, Illinois, United States
| | - Russell Emmons
- Department of Kinesiology and Community Health, University of Illinois, Illinois, United States
| | - Jing Yang
- Department of Comparative Biosciences, University of Illinois, Illinois, United States
| | - Stefan M Bresson
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Michael De Lisio
- Department of Kinesiology and Community Health, University of Illinois, Illinois, United States.,School of Human Kinetics, University of Ottawa, Ottawa, Canada
| | - Gianni Parise
- Department of Kinesiology, McMaster University, Hamilton, Canada
| | - Nicholas K Conrad
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Auinash Kalsotra
- Department of Biochemistry, University of Illinois, Illinois, United States.,Carl R. Woese Institute of Genomic Biology, University of Illinois, Illinois, United States
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86
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Das S, Parker JM, Guven C, Wang W, Kriebel PW, Losert W, Larson DR, Parent CA. Adenylyl cyclase mRNA localizes to the posterior of polarized DICTYOSTELIUM cells during chemotaxis. BMC Cell Biol 2017; 18:23. [PMID: 28545392 PMCID: PMC5445419 DOI: 10.1186/s12860-017-0139-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 05/09/2017] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND In Dictyostelium discoideum, vesicular transport of the adenylyl cyclase A (ACA) to the posterior of polarized cells is essential to relay exogenous 3',5'-cyclic adenosine monophosphate (cAMP) signals during chemotaxis and for the collective migration of cells in head-to-tail arrangements called streams. RESULTS Using fluorescence in situ hybridization (FISH), we discovered that the ACA mRNA is asymmetrically distributed at the posterior of polarized cells. Using both standard estimators and Monte Carlo simulation methods, we found that the ACA mRNA enrichment depends on the position of the cell within a stream, with the posterior localization of ACA mRNA being strongest for cells at the end of a stream. By monitoring the recovery of ACA-YFP after cycloheximide (CHX) treatment, we observed that ACA mRNA and newly synthesized ACA-YFP first emerge as fluorescent punctae that later accumulate to the posterior of cells. We also found that the ACA mRNA localization requires 3' ACA cis-acting elements. CONCLUSIONS Together, our findings suggest that the asymmetric distribution of ACA mRNA allows the local translation and accumulation of ACA protein at the posterior of cells. These data represent a novel functional role for localized translation in the relay of chemotactic signal during chemotaxis.
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Affiliation(s)
- Satarupa Das
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, 37 Convent Drive, Bldg.37/Rm2066, NCI, NIH, Bethesda, MD, 20892-4256, USA.,Institute for Physical Science and Technology, Department of Physics, University of Maryland, College Park, MD, 20742, USA
| | - Joshua M Parker
- Institute for Physical Science and Technology, Department of Physics, University of Maryland, College Park, MD, 20742, USA
| | - Can Guven
- Institute for Physical Science and Technology, Department of Physics, University of Maryland, College Park, MD, 20742, USA
| | - Weiye Wang
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, 37 Convent Drive, Bldg.37/Rm2066, NCI, NIH, Bethesda, MD, 20892-4256, USA
| | - Paul W Kriebel
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, 37 Convent Drive, Bldg.37/Rm2066, NCI, NIH, Bethesda, MD, 20892-4256, USA
| | - Wolfgang Losert
- Institute for Physical Science and Technology, Department of Physics, University of Maryland, College Park, MD, 20742, USA
| | - Daniel R Larson
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, NCI, NIH, Bethesda, MD, 20892, USA
| | - Carole A Parent
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, 37 Convent Drive, Bldg.37/Rm2066, NCI, NIH, Bethesda, MD, 20892-4256, USA. .,Institute for Physical Science and Technology, Department of Physics, University of Maryland, College Park, MD, 20742, USA.
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87
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Huang Y, Fang C, Shi JW, Wen Y, Liu D. Identification of hMex-3A and its effect on human bladder cancer cell proliferation. Oncotarget 2017; 8:61215-61225. [PMID: 28977858 PMCID: PMC5617418 DOI: 10.18632/oncotarget.18050] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 04/25/2017] [Indexed: 11/25/2022] Open
Abstract
In this study, hMex-3A was selected from TCGA database as a research object to observe the effects of small interfering RNA (siRNA) targeting hMex-3A on the biological activities of human bladder cancer and explore its mechanism for the first time. In this study, there were 2 groups including negative control group and hMex-3A-siRNA-transfected cells group for 5637 and T24 cell lines, respectively. After bladder cancer cells were transfected with the interference RNA sequence, proliferation of transfected cells were assessed by Celigo Cell Counting, and apoptosis were detected by flow cytometry. The knockdown rate of hMex-3A was 74% in 5637 cells and 68% in T24 cells after RNA interference. In addition, Celigo Cell Counting indicated that cell viability was significantly lower in hMex-3A-siRNA-transfected cells group (2196/well) than in negative control group (6777/well) (P < 0.05), but T24 cells did not show statistical significance between hMex-3A-siRNA-transfected cells group (5799/well) and negative control group (7899/well) (P >0.05). Flow cytometer showed that apoptosis was the highest and cells were significantly blocked after cells were transfected in hMex-3A-siRNA-transfected cells group in 5 days later (P < 0.05). Mex-3A protein was detected in bladder carcinoma sections with a mean staining intensity of 7.06±2.60. Mex-3A protein expression was significantly higher in cancerous tissue than in para-cancerous tissue (P <0.05). Our study suggested that siRNA targeting hMex-3A could markedly inhibit cell proliferation and promote apoptosis in 5637 cells. These might have significant implications to bladder carcinogenesis and serve as a potential target for the treatment of bladder cancer.
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Affiliation(s)
- Ying Huang
- Department of Ultrasound, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Chao Fang
- Department of Ultrasound, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Jing-Wen Shi
- Department of Ultrasound, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Yu Wen
- Department of Histoembryology, China Medical University, Shenyang 110000, China
| | - Da Liu
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang 110004, China
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88
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Calabrese F, Brivio P, Gruca P, Lason-Tyburkiewicz M, Papp M, Riva MA. Chronic Mild Stress-Induced Alterations of Local Protein Synthesis: A Role for Cognitive Impairment. ACS Chem Neurosci 2017; 8:817-825. [PMID: 28094500 DOI: 10.1021/acschemneuro.6b00392] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Depression, a major cause of disability worldwide, is characterized by a complex and heterogeneous symptomatology. With this respect, cognitive deterioration represents a major problem that has a strong impact on a patient's function. Thus, within the context of a depressive phenotype, it is important to characterize the mechanisms that sustain cognitive dysfunctions and may represent an important target for pharmacological intervention. Here, using the chronic mild stress (CMS) paradigm of depression, we found that, independently from the anhedonic phenotype, CMS rats showed a deficit in the novel object recognition (NOR) test, which is associated with an inability to phosphorylate GluN2B subunit on Ser1303 and to activate the mTOR pathway. In agreement with the role of these systems in the control of local protein synthesis, we observed an increase phosphorylated eukaryotic elongation factor 2 (eEF2) in the crude synaptosomal fraction after the NOR test specifically in control animals. Since it has been demonstrated that peEF2 leads to the translation of specific mRNAs, we investigated if the gene-specific translational control depends on the presence of upstream open reading frame (uORF). Interestingly, we found a significant increase of oligophrenin-1 (2 uORFs) and of Bmal1 (7 uORFs) protein levels specifically in the control animals exposed to the NOR test. Our results demonstrated that the cognitive decline associated with stress exposure might be due to alterations in local protein translation of specific mRNAs, suggesting that a pharmacological intervention able to correct these defects might be useful in the improvement of deteriorated functions in patients with major depression and stress-related disorders.
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Affiliation(s)
- Francesca Calabrese
- Department
of Pharmacological and Biomolecular Sciences, University of Milan, 20133 Milan, Italy
| | - Paola Brivio
- Department
of Pharmacological and Biomolecular Sciences, University of Milan, 20133 Milan, Italy
| | - Piotr Gruca
- Institute
of Pharmacology, Polish Academy of Sciences, 31-343 Krakow, Poland
| | | | - Mariusz Papp
- Institute
of Pharmacology, Polish Academy of Sciences, 31-343 Krakow, Poland
| | - Marco A. Riva
- Department
of Pharmacological and Biomolecular Sciences, University of Milan, 20133 Milan, Italy
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89
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Mamon LA, Ginanova VR, Kliver SF, Yakimova AO, Atsapkina AA, Golubkova EV. RNA-binding proteins of the NXF (nuclear export factor) family and their connection with the cytoskeleton. Cytoskeleton (Hoboken) 2017; 74:161-169. [PMID: 28296067 DOI: 10.1002/cm.21362] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 03/04/2017] [Accepted: 03/08/2017] [Indexed: 02/05/2023]
Abstract
The mutual relationship between mRNA and the cytoskeleton can be seen from two points of view. On the one hand, the cytoskeleton is necessary for mRNA trafficking and anchoring to subcellular domains. On the other hand, cytoskeletal growth and rearrangement require the translation of mRNAs that are connected to the cytoskeleton. β-actin mRNA localization may influence dynamic changes in the actin cytoskeleton. In the cytoplasm, long-lived mRNAs exist in the form of RNP (ribonucleoprotein) complexes, where they interact with RNA-binding proteins, including NXF (Nuclear eXport Factor). Dm NXF1 is an evolutionarily conserved protein in Drosophila melanogaster that has orthologs in different animals. The universal function of nxf1 genes is the nuclear export of different mRNAs in various organisms. In this mini-review, we briefly discuss the evidence demonstrating that Dm NXF1 fulfils not only universal but also specialized cytoplasmic functions. This protein is detected not only in the nucleus but also in the cytoplasm. It is a component of neuronal granules. Dm NXF1 marks nuclear division spindles during early embryogenesis and the dense body on one side of the elongated spermatid nuclei. The characteristic features of sbr mutants (sbr10 and sbr5 ) are impairment of chromosome segregation and spindle formation anomalies during female meiosis. sbr12 mutant sterile males with immobile spermatozoa exhibit disturbances in the axoneme, mitochondrial derivatives and cytokinesis. These data allow us to propose that the Dm NXF1 proteins transport certain mRNAs in neurites and interact with localized mRNAs that are necessary for dynamic changes of the cytoskeleton.
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Affiliation(s)
- L A Mamon
- Department of Genetics and Biotechnology, Faculty of Biology, St Petersburg State University Universitetskaya nab. 7-9, Saint-Petersburg, 199034, Russia
| | - V R Ginanova
- Department of Genetics and Biotechnology, Faculty of Biology, St Petersburg State University Universitetskaya nab. 7-9, Saint-Petersburg, 199034, Russia
| | - S F Kliver
- Department of Genetics and Biotechnology, Faculty of Biology, St Petersburg State University Universitetskaya nab. 7-9, Saint-Petersburg, 199034, Russia
| | - A O Yakimova
- Department of Genetics and Biotechnology, Faculty of Biology, St Petersburg State University Universitetskaya nab. 7-9, Saint-Petersburg, 199034, Russia
| | - A A Atsapkina
- Department of Genetics and Biotechnology, Faculty of Biology, St Petersburg State University Universitetskaya nab. 7-9, Saint-Petersburg, 199034, Russia
| | - E V Golubkova
- Department of Genetics and Biotechnology, Faculty of Biology, St Petersburg State University Universitetskaya nab. 7-9, Saint-Petersburg, 199034, Russia
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90
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Abdolvahab RH. Chaperone-driven polymer translocation through nanopore: Spatial distribution and binding energy. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2017; 40:41. [PMID: 28389823 DOI: 10.1140/epje/i2017-11528-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 03/10/2017] [Indexed: 06/07/2023]
Abstract
Chaperones are binding proteins working as a driving force in biopolymer translocation. They bind to the biopolymer near the pore and prevent its backsliding. Chaperones may have different spatial distributions. Recently, we showed the importance of their spatial distribution in translocation and its effects on the sequence dependency of the translocation time. Here we focus on homopolymers and exponential distribution. Because of the exponential distribution of chaperones, the energy dependency of the translocation time will change. Here we find a minimum in translocation time versus binding effective energy (EBE) curve. The same trend can be seen in the scaling exponent of time versus polymer length, [Formula: see text] ([Formula: see text]), when plotted against EBE. Interestingly in some special cases, e.g. chaperones of size [Formula: see text] and with an exponential distribution rate of [Formula: see text], the minimum even reaches to an amount of less than 1 ([Formula: see text]). We explain the possibility of this rare result. Moreover, based on a theoretical discussion we show that, by taking into account the velocity dependency of the translocation on polymer length, one can truly predict the value of this minimum.
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91
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Rotem N, Magen I, Ionescu A, Gershoni-Emek N, Altman T, Costa CJ, Gradus T, Pasmanik-Chor M, Willis DE, Ben-Dov IZ, Hornstein E, Perlson E. ALS Along the Axons - Expression of Coding and Noncoding RNA Differs in Axons of ALS models. Sci Rep 2017; 7:44500. [PMID: 28300211 PMCID: PMC5353576 DOI: 10.1038/srep44500] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 02/08/2017] [Indexed: 12/18/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a multifactorial lethal motor neuron disease with no known treatment. Although the basic mechanism of its degenerative pathogenesis remains poorly understood, a subcellular spatial alteration in RNA metabolism is thought to play a key role. The nature of these RNAs remains elusive, and a comprehensive characterization of the axonal RNAs involved in maintaining neuronal health has yet to be described. Here, using cultured spinal cord (SC) neurons grown using a compartmented platform followed by next-generation sequencing (NGS) technology, we find that RNA expression differs between the somatic and axonal compartments of the neuron, for both mRNA and microRNA (miRNA). Further, the introduction of SOD1G93A and TDP43A315T, established ALS-related mutations, changed the subcellular expression and localization of RNAs within the neurons, showing a spatial specificity to either the soma or the axon. Altogether, we provide here the first combined inclusive profile of mRNA and miRNA expression in two ALS models at the subcellular level. These data provide an important resource for studies on the roles of local protein synthesis and axon degeneration in ALS and can serve as a possible target pool for ALS treatment.
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Affiliation(s)
- Nimrod Rotem
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, and the Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Iddo Magen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ariel Ionescu
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, and the Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Noga Gershoni-Emek
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, and the Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Topaz Altman
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, and the Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Christopher J Costa
- Brain and Mind Research Institute, Weill Cornell Medicine, Burke Medical Research Institute, White Plains, NY, USA
| | - Tal Gradus
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, and the Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | | | - Dianna E Willis
- Brain and Mind Research Institute, Weill Cornell Medicine, Burke Medical Research Institute, White Plains, NY, USA
| | - Iddo Z Ben-Dov
- Department of Nephrology and Hypertension, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Eran Hornstein
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Perlson
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, and the Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
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92
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Golani-Armon A, Arava Y. Localization of Nuclear-Encoded mRNAs to Mitochondria Outer Surface. BIOCHEMISTRY (MOSCOW) 2017; 81:1038-1043. [PMID: 27908229 DOI: 10.1134/s0006297916100023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The diverse functions of mitochondria depend on hundreds of different proteins. The vast majority of these proteins is encoded in the nucleus, translated in the cytosol, and must be imported into the organelle. Import was shown to occur after complete synthesis of the protein, with the assistance of cytosolic chaperones that maintain it in an unfolded state and target it to the mitochondrial translocase of the outer membrane (TOM complex). Recent studies, however, identified many mRNAs encoding mitochondrial proteins near the outer membrane of mitochondria. Translation studies suggest that many of these mRNAs are translated locally, presumably allowing cotranslational import into mitochondria. Herein we review these data and discuss its relevance for local protein synthesis. We also suggest alternative roles for mRNA localization to mitochondria. Finally, we suggest future research directions, including revealing the significance of localization to mitochondria physiology and the molecular players that regulate it.
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Affiliation(s)
- A Golani-Armon
- Technion - Israel Institute of Technology, Faculty of Biology, Haifa, 32000, Israel.
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93
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Liu Y, Beyer A, Aebersold R. On the Dependency of Cellular Protein Levels on mRNA Abundance. Cell 2016; 165:535-50. [PMID: 27104977 DOI: 10.1016/j.cell.2016.03.014] [Citation(s) in RCA: 1811] [Impact Index Per Article: 226.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Indexed: 12/30/2022]
Abstract
The question of how genomic information is expressed to determine phenotypes is of central importance for basic and translational life science research and has been studied by transcriptomic and proteomic profiling. Here, we review the relationship between protein and mRNA levels under various scenarios, such as steady state, long-term state changes, and short-term adaptation, demonstrating the complexity of gene expression regulation, especially during dynamic transitions. The spatial and temporal variations of mRNAs, as well as the local availability of resources for protein biosynthesis, strongly influence the relationship between protein levels and their coding transcripts. We further discuss the buffering of mRNA fluctuations at the level of protein concentrations. We conclude that transcript levels by themselves are not sufficient to predict protein levels in many scenarios and to thus explain genotype-phenotype relationships and that high-quality data quantifying different levels of gene expression are indispensable for the complete understanding of biological processes.
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Affiliation(s)
- Yansheng Liu
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Andreas Beyer
- Cellular Networks and Systems Biology, University of Cologne, CECAD, Joseph-Stelzmann-Strasse 26, Cologne 50931, Germany.
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland; Faculty of Science, University of Zurich, 8057 Zurich, Switzerland.
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94
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Schieweck R, Popper B, Kiebler MA. Co-Translational Folding: A Novel Modulator of Local Protein Expression in Mammalian Neurons? Trends Genet 2016; 32:788-800. [DOI: 10.1016/j.tig.2016.10.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 10/04/2016] [Accepted: 10/11/2016] [Indexed: 01/15/2023]
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95
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Abstract
Localized mRNA translation is a widespread mechanism for targeting protein synthesis, important for cell fate, motility and pathogenesis. In Drosophila, the spatiotemporal control of gurken/TGF-α mRNA translation is required for establishing the embryonic body axes. A number of recent studies have highlighted key aspects of the mechanism of gurken mRNA translational control at the dorsoanterior corner of the mid-stage oocyte. Orb/CPEB and Wispy/GLD-2 are required for polyadenylation of gurken mRNA, but unlocalized gurken mRNA in the oocyte is not fully polyadenylated. 1 At the dorsoanterior corner, Orb and gurken mRNA have been shown to be enriched at the edge of Processing bodies, where translation occurs. 2 Over-expression of Orb in the adjacent nurse cells, where gurken mRNA is transcribed, is sufficient to cause mis-expression of Gurken protein. 3 In orb mutant egg chambers, reducing the activity of CK2, a Serine/Threonine protein kinase, enhances the ventralized phenotype, consistent with perturbation of gurken translation. 4 Here we show that sites phosphorylated by CK2 overlap with active Orb and with Gurken protein expression. Together with our new findings we consolidate the literature into a working model for gurken mRNA translational control and review the role of kinases, cell cycle factors and polyadenylation machinery highlighting a multitude of conserved factors and mechanisms in the Drosophila egg chamber.
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Affiliation(s)
| | - Timothy T Weil
- a Department of Zoology , University of Cambridge , Cambridge , UK
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96
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Rajamanickam GD, Kastelic JP, Thundathil JC. Content of testis-specific isoform of Na/K-ATPase (ATP1A4) is increased during bovine sperm capacitation through translation in mitochondrial ribosomes. Cell Tissue Res 2016; 368:187-200. [PMID: 27807702 DOI: 10.1007/s00441-016-2514-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 09/16/2016] [Indexed: 01/30/2023]
Abstract
Capacitation comprises a series of structural and functional modifications of sperm that confer fertilizing ability. We previously reported that the testis-specific isoform of Na/K-ATPase (ATP1A4) regulated bovine sperm capacitation through signaling mechanisms involving kinases. During subsequent investigations to elucidate mechanisms by which ATP1A4 regulates sperm capacitation, we observed that ATP1A4 was localised in both raft and non-raft fractions of the sperm plasma membrane and that its total content was increased in both membrane fractions during capacitation. The objective of the present study was to investigate mechanism(s) of capacitation-associated increase in the content of ATP1A4. Despite the widely accepted dogma of transcriptional/translational quiescence, incubation of sperm with either ouabain (specific ligand for ATP1A4) or heparin increased ATP1A4 content in raft and non-raft sperm membrane fractions, total sperm protein extracts (immunoblotting) and fixed sperm (flow cytometry), with a concurrent increase in Na/K-ATPase enzyme activity. This capacitation-associated increase in ATP1A4 content was partially decreased by chloramphenicol (mitochondrial translation inhibitor) but not affected by actinomycin D (transcription inhibitor). To demonstrate de novo ATP1A4 synthesis, we evaluated incorporation of bodipy conjugated lysine in this protein during capacitation. A partial decrease in bodipy-lysine incorporation occurred in ATP1A4 from sperm capacitated in the presence of chloramphenicol. Therefore, increased ATP1A4 content during capacitation was attributed to mitochondrial translation of ATP1A4 mRNA present in ejaculated sperm, rather than gene transcription. To our knowledge, this is the first report demonstrating ATP1A4 synthesis during bovine sperm capacitation.
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Affiliation(s)
- Gayathri D Rajamanickam
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Heritage Medical Research Building RM 400, Calgary, AB, T2N4N1, Canada
| | - John P Kastelic
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Heritage Medical Research Building RM 400, Calgary, AB, T2N4N1, Canada
| | - Jacob C Thundathil
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Heritage Medical Research Building RM 400, Calgary, AB, T2N4N1, Canada.
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97
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Stubenvoll MD, Medley JC, Irwin M, Song MH. ATX-2, the C. elegans Ortholog of Human Ataxin-2, Regulates Centrosome Size and Microtubule Dynamics. PLoS Genet 2016; 12:e1006370. [PMID: 27689799 PMCID: PMC5045193 DOI: 10.1371/journal.pgen.1006370] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 09/16/2016] [Indexed: 11/26/2022] Open
Abstract
Centrosomes are critical sites for orchestrating microtubule dynamics, and exhibit dynamic changes in size during the cell cycle. As cells progress to mitosis, centrosomes recruit more microtubules (MT) to form mitotic bipolar spindles that ensure proper chromosome segregation. We report a new role for ATX-2, a C. elegans ortholog of Human Ataxin-2, in regulating centrosome size and MT dynamics. ATX-2, an RNA-binding protein, forms a complex with SZY-20 in an RNA-independent fashion. Depleting ATX-2 results in embryonic lethality and cytokinesis failure, and restores centrosome duplication to zyg-1 mutants. In this pathway, SZY-20 promotes ATX-2 abundance, which inversely correlates with centrosome size. Centrosomes depleted of ATX-2 exhibit elevated levels of centrosome factors (ZYG-1, SPD-5, γ-Tubulin), increasing MT nucleating activity but impeding MT growth. We show that ATX-2 influences MT behavior through γ-Tubulin at the centrosome. Our data suggest that RNA-binding proteins play an active role in controlling MT dynamics and provide insight into the control of proper centrosome size and MT dynamics. The microtubule (MT) cytoskeleton undergoes dynamic rearrangements during the cell cycle. As the primary microtubule-organizing center, centrosomes orchestrate MT dynamics and play a key role in establishing bipolar spindles in mitosis. Errors in centrosome assembly lead to missegregation of genomic content and aneuploidy. Thus, stringent regulation of centrosome assembly is of vital importance for the fidelity of cell division and survival. Using the nematode Caenorhabditis elegans (C. elegans) as a model, we study the role of the RNA-binding protein, ATX-2, a C. elegans homolog of Human Ataxin-2 in early cell division. A number of RNAs and RNA-binding proteins are shown to be associated with centrosomes and MTs, and influence the assembly of mitotic spindles. In C. elegans, the RNA-binding role of SZY-20 is implicated in regulating centrosome size. We show that ATX-2 functions together with SZY-20 in centrosome size and MT behavior. SZY-20 promotes ATX-2 protein levels, and the amount of ATX-2 influences centrosome size and subsequent MT dynamics. Our work provides evidence that RNA-binding proteins have an active role in controlling MT dynamics.
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Affiliation(s)
- Michael D. Stubenvoll
- Department of Biological Sciences, Oakland University, Rochester, Michigan, United States of America
| | - Jeffrey C. Medley
- Department of Biological Sciences, Oakland University, Rochester, Michigan, United States of America
| | - Miranda Irwin
- Department of Biological Sciences, Oakland University, Rochester, Michigan, United States of America
| | - Mi Hye Song
- Department of Biological Sciences, Oakland University, Rochester, Michigan, United States of America
- * E-mail:
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98
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Ninomiya K, Ohno M, Kataoka N. Dendritic transport element of human arc mRNA confers RNA degradation activity in a translation-dependent manner. Genes Cells 2016; 21:1263-1269. [DOI: 10.1111/gtc.12439] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 08/22/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Kensuke Ninomiya
- Institute for Virus Research; Kyoto University; Shogo-in Kawaharacho 53 Sakyo-ku Kyoto 606-8507 Japan
- Institute for Genetic Medicine; Hokkaido University; Kita-15 Nishi-7 Kita-ku Sapporo 060-0815 Japan
| | - Mutsuhito Ohno
- Institute for Virus Research; Kyoto University; Shogo-in Kawaharacho 53 Sakyo-ku Kyoto 606-8507 Japan
| | - Naoyuki Kataoka
- Institute for Virus Research; Kyoto University; Shogo-in Kawaharacho 53 Sakyo-ku Kyoto 606-8507 Japan
- Medical Innovation Center; Laboratory for Malignancy Control Research; Kyoto University; Shogo-in Kawaharacho 53 Sakyo-ku Kyoto 606-8507 Japan
- Departments of Applied Animal Sciences and Applied Biological Chemistry; Laboratory of Cell Regulation; Graduate School of Agriculture and Life Sciences, The University of Tokyo; Yayoi 1-1-1 Bunkyo-ku Tokyo 113-8657 Japan
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99
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Boehm V, Gehring NH. Exon Junction Complexes: Supervising the Gene Expression Assembly Line. Trends Genet 2016; 32:724-735. [PMID: 27667727 DOI: 10.1016/j.tig.2016.09.003] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 08/23/2016] [Accepted: 09/01/2016] [Indexed: 12/16/2022]
Abstract
The exon junction complex (EJC) is an RNA-binding protein complex that is assembled and deposited onto mRNAs during splicing. The EJC comprises four core components that bind to not only canonical sites upstream of exon-exon junctions, but also to noncanonical sites at other positions in exons. EJC-associated proteins are recruited by the EJC at different steps of gene expression to execute the multiple functions of the EJC. Recently, new insights have been obtained into how EJCs stimulate pre-mRNA splicing, and mRNA export, translation, and degradation. Furthermore, mutations in EJC core components were shown to result in severe disorders in humans, demonstrating the critical physiological role of the EJC. Hence, the EJC has been identified as an important player in post-transcriptional gene regulation in metazoans.
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Affiliation(s)
- Volker Boehm
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany
| | - Niels H Gehring
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany.
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100
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Smethurst DGJ, Cooper KF. ER fatalities-The role of ER-mitochondrial contact sites in yeast life and death decisions. Mech Ageing Dev 2016; 161:225-233. [PMID: 27507669 DOI: 10.1016/j.mad.2016.07.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 06/22/2016] [Accepted: 07/19/2016] [Indexed: 12/22/2022]
Abstract
Following extracellular stress signals, all eukaryotic cells choose whether to elicit a pro-survival or pro-death response. The decision over which path to take is governed by the severity and duration of the damage. In response to mild stress, pro-survival programs are initiated (unfolded protein response, autophagy, mitophagy) whereas severe or chronic stress forces the cell to abandon these adaptive programs and shift towards regulated cell death to remove irreversibly damaged cells. Both pro-survival and pro-death programs involve regulated communication between the endoplasmic reticulum (ER) and mitochondria. In yeast, recent data suggest this inter-organelle contact is facilitated by the endoplasmic reticulum mitochondria encounter structure (ERMES). These membrane contacts are not only important for the exchange of cellular signals, but also play a role in mitochondrial tethering during mitophagy, mitochondrial fission and mitochondrial inheritance. This review focuses on recent findings in yeast that shed light on how ER-mitochondrial communication mediates critical cell fate decisions.
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Affiliation(s)
- Daniel G J Smethurst
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, NJ, 08055 USA
| | - Katrina F Cooper
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, NJ, 08055 USA.
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