1
|
Abstract
Transfer RNAs (tRNAs) are intermediate-sized non-coding RNAs found in all organisms that help translate messenger RNA into protein. Recently, the number of sequenced plant genomes has increased dramatically. The availability of this extensive data greatly accelerates the study of tRNAs on a large scale. Here, 8,768,261 scaffolds/chromosomes containing 229,093 giga-base pairs representing whole-genome sequences of 256 plant species were analyzed to identify tRNA genes. As a result, 331,242 nuclear, 3,216 chloroplast, and 1,467 mitochondrial tRNA genes were identified. The nuclear tRNA genes include 275,134 tRNAs decoding 20 standard amino acids, 1,325 suppressor tRNAs, 6,273 tRNAs with unknown isotypes, 48,475 predicted pseudogenes, and 37,873 tRNAs with introns. Efforts also extended to the creation of PltRNAdb (https://bioinformatics.um6p.ma/PltRNAdb/index.php), a data source for tRNA genes from 256 plant species. PltRNAdb website allows researchers to search, browse, visualize, BLAST, and download predicted tRNA genes. PltRNAdb will help improve our understanding of plant tRNAs and open the door to discovering the unknown regulatory roles of tRNAs in plant genomes.
Collapse
Affiliation(s)
- Morad M. Mokhtar
- African Genome Center, University Mohammed VI Polytechnic, Benguerir, Morocco
- * E-mail: (AE); (MMM)
| | - Achraf EL Allali
- African Genome Center, University Mohammed VI Polytechnic, Benguerir, Morocco
- * E-mail: (AE); (MMM)
| |
Collapse
|
2
|
Sadik N, Cruz L, Gurtner A, Rodosthenous RS, Dusoswa SA, Ziegler O, Van Solinge TS, Wei Z, Salvador-Garicano AM, Gyorgy B, Broekman M, Balaj L. Extracellular RNAs: A New Awareness of Old Perspectives. Methods Mol Biol 2019; 1740:1-15. [PMID: 29388131 DOI: 10.1007/978-1-4939-7652-2_1] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Extracellular RNA (exRNA) has recently expanded as a highly important area of study in biomarker discovery and cancer therapeutics. exRNA consists of diverse RNA subpopulations that are normally protected from degradation by incorporation into membranous vesicles or by lipid/protein association. They are found circulating in biofluids, and have proven highly promising for minimally invasive diagnostic and prognostic purposes, particularly in oncology. Recent work has made progress in our understanding of exRNAs-from their biogenesis, compartmentalization, and vesicle packaging to their various applications as biomarkers and therapeutics, as well as the new challenges that arise in isolation and purification for accurate and reproducible analysis. Here we review the most recent advancements in exRNA research.
Collapse
Affiliation(s)
- Noah Sadik
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Lilian Cruz
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Alessandra Gurtner
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Rodosthenis S Rodosthenous
- Cardiovascular Division of the Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Sophie A Dusoswa
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Department of Molecular Cell Biology and Immunology, VU University Medical Center, Amsterdam, The Netherlands.,Amsterdam Infection & Immunity Institute, VU University Medical Center, Amsterdam, The Netherlands.,Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Olivia Ziegler
- Cardiovascular Division of the Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Thomas Sebastiaan Van Solinge
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,NeuroDiscovery Center, Harvard Medical School, Boston, MA, USA.,Department of Neurosurgery, VU University Medical Center, Amsterdam, The Netherlands
| | - Zhiyun Wei
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Bence Gyorgy
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Marike Broekman
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Department of Neurosurgery, Brain Center Rudolf Magnus University Medical Center Utrecht, Utrecht, The Netherlands
| | - Leonora Balaj
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
3
|
Alves CS, Vicentini R, Duarte GT, Pinoti VF, Vincentz M, Nogueira FTS. Genome-wide identification and characterization of tRNA-derived RNA fragments in land plants. PLANT MOLECULAR BIOLOGY 2017; 93:35-48. [PMID: 27681945 DOI: 10.1007/s11103-016-0545-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 09/19/2016] [Indexed: 05/06/2023]
Abstract
The manuscript by Alves et al. entitled "Genome-wide identification and characterization of tRNA-derived RNA fragments in land plants" describes the identification and characterization of tRNAderived sRNA fragments in plants. By combining bioinformatic analysis and genetic and molecular approaches, we show that tRF biogenesis does not rely on canonical microRNA/siRNA processing machinery (i.e., independent of DICER-LIKE proteins). Moreover, we provide evidences that the Arabidopsis S-like Ribonuclease 1 (RNS1) might be involved in the biogenesis of tRFs. Detailed analyses showed that plant tRFs are sorted into different types of ARGONAUTE proteins and that they have potential target candidate genes. Our work advances the understanding of the tRF biology in plants by providing evidences that plant and animal tRFs shared common features and raising the hypothesis that an interplay between tRFs and other sRNAs might be important to fine-tune gene expression and protein biosynthesis in plant cells. Small RNA (sRNA) fragments derived from tRNAs (3'-loop, 5'-loop, anti-codon loop), named tRFs, have been reported in several organisms, including humans and plants. Although they may interfere with gene expression, their biogenesis and biological functions in plants remain poorly understood. Here, we capitalized on small RNA sequencing data from distinct species such as Arabidopsis thaliana, Oryza sativa, and Physcomitrella patens to examine the diversity of plant tRFs and provide insight into their properties. In silico analyzes of 19 to 25-nt tRFs derived from 5' (tRF-5s) and 3'CCA (tRF-3s) tRNA loops in these three evolutionary distant species showed that they are conserved and their abundance did not correlate with the number of genomic copies of the parental tRNAs. Moreover, tRF-5 is the most abundant variant in all three species. In silico and in vivo expression analyses unraveled differential accumulation of tRFs in Arabidopsis tissues/organs, suggesting that they are not byproducts of tRNA degradation. We also verified that the biogenesis of most Arabidopsis 19-25 nt tRF-5s and tRF-3s is not primarily dependent on DICER-LIKE proteins, though they seem to be associated with ARGONAUTE proteins and have few potential targets. Finally, we provide evidence that Arabidopsis ribonuclease RNS1 might be involved in the processing and/or degradation of tRFs. Our data support the notion that an interplay between tRFs and other sRNAs might be important to fine tune gene expression and protein biosynthesis in plant cells.
Collapse
Affiliation(s)
- Cristiane S Alves
- Departamento de Genetica, Instituto de Biociencias, Universidade Estadual Paulista (UNESP), Distrito de Rubião Jr., s/n, Botucatu, SP, 18618-970, Brazil
- Laboratorio de Genetica Molecular do Desenvolvimento Vegetal, Departamento de Ciencias Biologicas, ESALQ/USP, Avenida Pádua Dias s/n, 11, Piracicaba, SP, 13418-900, Brazil
| | - Renato Vicentini
- Laboratorio de Bioinformatica e Biologia de Sistemas, Departamento de Genetica, Evoluçao e Bioagentes, Universidade Estadual de Campinas (Unicamp), Campinas, SP, Brazil
| | - Gustavo T Duarte
- Centro de Biologia Molecular e Engenharia Genetica (CBMEG), Universidade Estadual de Campinas (Unicamp), Campinas, SP, Brazil
| | - Vitor F Pinoti
- Departamento de Genetica, Instituto de Biociencias, Universidade Estadual Paulista (UNESP), Distrito de Rubião Jr., s/n, Botucatu, SP, 18618-970, Brazil
| | - Michel Vincentz
- Centro de Biologia Molecular e Engenharia Genetica (CBMEG), Universidade Estadual de Campinas (Unicamp), Campinas, SP, Brazil
| | - Fabio T S Nogueira
- Laboratorio de Genetica Molecular do Desenvolvimento Vegetal, Departamento de Ciencias Biologicas, ESALQ/USP, Avenida Pádua Dias s/n, 11, Piracicaba, SP, 13418-900, Brazil.
| |
Collapse
|
4
|
Quek C, Bellingham SA, Jung CH, Scicluna BJ, Shambrook MC, Sharples RA, Cheng L, Hill AF. Defining the purity of exosomes required for diagnostic profiling of small RNA suitable for biomarker discovery. RNA Biol 2016; 14:245-258. [PMID: 28005467 PMCID: PMC5324750 DOI: 10.1080/15476286.2016.1270005] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Small non-coding RNAs (ncRNA), including microRNAs (miRNA), enclosed in exosomes are being utilised for biomarker discovery in disease. Two common exosome isolation methods involve differential ultracentrifugation or differential ultracentrifugation coupled with Optiprep gradient fractionation. Generally, the incorporation of an Optiprep gradient provides better separation and increased purity of exosomes. The question of whether increased purity of exosomes is required for small ncRNA profiling, particularly in diagnostic and biomarker purposes, has not been addressed and highly debated. Utilizing an established neuronal cell system, we used next-generation sequencing to comprehensively profile ncRNA in cells and exosomes isolated by these 2 isolation methods. By comparing ncRNA content in exosomes from these two methods, we found that exosomes from both isolation methods were enriched with miRNAs and contained a diverse range of rRNA, small nuclear RNA, small nucleolar RNA and piwi-interacting RNA as compared with their cellular counterparts. Additionally, tRNA fragments (30-55 nucleotides in length) were identified in exosomes and may act as potential modulators for repressing protein translation. Overall, the outcome of this study confirms that ultracentrifugation-based method as a feasible approach to identify ncRNA biomarkers in exosomes.
Collapse
Affiliation(s)
- Camelia Quek
- a Department of Biochemistry and Molecular Biology , Bio21 Molecular Science and Biotechnology Institute, University of Melbourne , Melbourne , VIC , Australia.,b Department of Biochemistry and Genetics , La Trobe Institute for Molecular Science, La Trobe University , VIC , Australia
| | - Shayne A Bellingham
- a Department of Biochemistry and Molecular Biology , Bio21 Molecular Science and Biotechnology Institute, University of Melbourne , Melbourne , VIC , Australia
| | - Chol-Hee Jung
- c VLSCI Life Sciences Computation Centre, University of Melbourne , VIC , Australia
| | - Benjamin J Scicluna
- a Department of Biochemistry and Molecular Biology , Bio21 Molecular Science and Biotechnology Institute, University of Melbourne , Melbourne , VIC , Australia.,b Department of Biochemistry and Genetics , La Trobe Institute for Molecular Science, La Trobe University , VIC , Australia
| | - Mitch C Shambrook
- b Department of Biochemistry and Genetics , La Trobe Institute for Molecular Science, La Trobe University , VIC , Australia
| | - Robyn A Sharples
- a Department of Biochemistry and Molecular Biology , Bio21 Molecular Science and Biotechnology Institute, University of Melbourne , Melbourne , VIC , Australia
| | - Lesley Cheng
- b Department of Biochemistry and Genetics , La Trobe Institute for Molecular Science, La Trobe University , VIC , Australia
| | - Andrew F Hill
- b Department of Biochemistry and Genetics , La Trobe Institute for Molecular Science, La Trobe University , VIC , Australia
| |
Collapse
|
5
|
Zhang Y, Yuan C, Gao J, Liu Y, Wang Z. Testicular transcript responses in rare minnow Gobiocypris rarus following different concentrations bisphenol A exposure. CHEMOSPHERE 2016; 156:357-366. [PMID: 27183338 DOI: 10.1016/j.chemosphere.2016.05.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 04/30/2016] [Accepted: 05/04/2016] [Indexed: 06/05/2023]
Abstract
Bisphenol A (BPA) is widely spread in the environment. It can cause various reproductive disrupting effects on different organisms, including fish. To investigate the effect of BPA at different concentrations comprehensively, RNA-seq was performed on the testicular mRNA libraries of adult male rare minnow Gobiocypris rarus that exposed to 0, 1, 15 and 225 μg/L BPA for 7 days. Meanwhile, biological indicators and sex steroid hormone levels were investigated. Result showed that (1) BPA at all three concentrations affected the expression of genes related to testicular steroid hormone biosynthesis, blood-testis barrier, proteolysis, and lipid transport and metabolism. (2) BPA at 1 μg/L induced gene expression in renin-angiotensin system pathway and possibly initiate membrane form of estrogen receptor (mER); 1 and 15 μg/L BPA inhibited tRNA processing-related genes expression; 15 and 225 μg/L BPA decreased hemostasis and blood coagulation-related gene expression. The present study indicated that BPA did influence rare minnow testicular gene expressing, and the effect BPA effects varied with concentration.
Collapse
Affiliation(s)
- Yingying Zhang
- College of Animal Science and Technology, Northwest A&F University, 22 Xinong Road, Yangling, Shaanxi, 712100, China
| | - Cong Yuan
- College of Animal Science and Technology, Northwest A&F University, 22 Xinong Road, Yangling, Shaanxi, 712100, China
| | - Jiancao Gao
- College of Animal Science and Technology, Northwest A&F University, 22 Xinong Road, Yangling, Shaanxi, 712100, China
| | - Yan Liu
- College of Animal Science and Technology, Northwest A&F University, 22 Xinong Road, Yangling, Shaanxi, 712100, China
| | - Zaizhao Wang
- College of Animal Science and Technology, Northwest A&F University, 22 Xinong Road, Yangling, Shaanxi, 712100, China.
| |
Collapse
|
6
|
Jeltsch A, Ehrenhofer-Murray A, Jurkowski TP, Lyko F, Reuter G, Ankri S, Nellen W, Schaefer M, Helm M. Mechanism and biological role of Dnmt2 in Nucleic Acid Methylation. RNA Biol 2016; 14:1108-1123. [PMID: 27232191 PMCID: PMC5699548 DOI: 10.1080/15476286.2016.1191737] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
A group of homologous nucleic acid modification enzymes called Dnmt2, Trdmt1, Pmt1, DnmA, and Ehmet in different model organisms catalyze the transfer of a methyl group from the cofactor S-adenosyl-methionine (SAM) to the carbon-5 of cytosine residues. Originally considered as DNA MTases, these enzymes were shown to be tRNA methyltransferases about a decade ago. Between the presumed involvement in DNA modification-related epigenetics, and the recent foray into the RNA modification field, significant progress has characterized Dnmt2-related research. Here, we review this progress in its diverse facets including molecular evolution, structural biology, biochemistry, chemical biology, cell biology and epigenetics.
Collapse
Affiliation(s)
- Albert Jeltsch
- a Institute of Biochemistry , Stuttgart University , Stuttgart , Germany
| | | | - Tomasz P Jurkowski
- a Institute of Biochemistry , Stuttgart University , Stuttgart , Germany
| | - Frank Lyko
- c Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center , Heidelberg , Germany
| | - Gunter Reuter
- d Institute of Biology, Developmental Genetics, Martin Luther University Halle , Halle , Germany
| | - Serge Ankri
- e Department of Molecular Microbiology , The Bruce Rappaport Faculty of Medicine , Technion , Haifa , Israel
| | - Wolfgang Nellen
- f Abteilung für Genetik, Universität Kassel , Kassel , Germany
| | - Matthias Schaefer
- g Medical University of Vienna, Center for Anatomy & Cell Biology , Vienna , Austria
| | - Mark Helm
- h Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität Mainz , Mainz , Germany
| |
Collapse
|
7
|
Armengod ME, Meseguer S, Villarroya M, Prado S, Moukadiri I, Ruiz-Partida R, Garzón MJ, Navarro-González C, Martínez-Zamora A. Modification of the wobble uridine in bacterial and mitochondrial tRNAs reading NNA/NNG triplets of 2-codon boxes. RNA Biol 2015; 11:1495-507. [PMID: 25607529 DOI: 10.4161/15476286.2014.992269] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Posttranscriptional modification of the uridine located at the wobble position (U34) of tRNAs is crucial for optimization of translation. Defects in the U34 modification of mitochondrial-tRNAs are associated with a group of rare diseases collectively characterized by the impairment of the oxidative phosphorylation system. Retrograde signaling pathways from mitochondria to nucleus are involved in the pathophysiology of these diseases. These pathways may be triggered by not only the disturbance of the mitochondrial (mt) translation caused by hypomodification of tRNAs, but also as a result of nonconventional roles of mt-tRNAs and mt-tRNA-modifying enzymes. The evolutionary conservation of these enzymes supports their importance for cell and organismal functions. Interestingly, bacterial and eukaryotic cells respond to stress by altering the expression or activity of these tRNA-modifying enzymes, which leads to changes in the modification status of tRNAs. This review summarizes recent findings about these enzymes and sets them within the previous data context.
Collapse
Affiliation(s)
- M Eugenia Armengod
- a Laboratory of RNA Modification and Mitochondrial Diseases ; Centro de Investigación Príncipe Felipe ; Valencia , Spain
| | | | | | | | | | | | | | | | | |
Collapse
|
8
|
Weitzer S, Hanada T, Penninger JM, Martinez J. CLP1 as a novel player in linking tRNA splicing to neurodegenerative disorders. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 6:47-63. [DOI: 10.1002/wrna.1255] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 06/27/2014] [Accepted: 06/28/2014] [Indexed: 12/12/2022]
Affiliation(s)
- Stefan Weitzer
- IMBA; Institute of Molecular Biotechnology of the Academy of Sciences; Vienna Austria
| | - Toshikatsu Hanada
- TK Project, Medical Innovation Center; Kyoto University Graduate School of Medicine; Kyoto Japan
| | - Josef M. Penninger
- IMBA; Institute of Molecular Biotechnology of the Academy of Sciences; Vienna Austria
| | - Javier Martinez
- IMBA; Institute of Molecular Biotechnology of the Academy of Sciences; Vienna Austria
| |
Collapse
|
9
|
Abbott JA, Francklyn CS, Robey-Bond SM. Transfer RNA and human disease. Front Genet 2014; 5:158. [PMID: 24917879 PMCID: PMC4042891 DOI: 10.3389/fgene.2014.00158] [Citation(s) in RCA: 149] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 05/14/2014] [Indexed: 12/25/2022] Open
Abstract
Pathological mutations in tRNA genes and tRNA processing enzymes are numerous and result in very complicated clinical phenotypes. Mitochondrial tRNA (mt-tRNA) genes are “hotspots” for pathological mutations and over 200 mt-tRNA mutations have been linked to various disease states. Often these mutations prevent tRNA aminoacylation. Disrupting this primary function affects protein synthesis and the expression, folding, and function of oxidative phosphorylation enzymes. Mitochondrial tRNA mutations manifest in a wide panoply of diseases related to cellular energetics, including COX deficiency (cytochrome C oxidase), mitochondrial myopathy, MERRF (Myoclonic Epilepsy with Ragged Red Fibers), and MELAS (mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes). Diseases caused by mt-tRNA mutations can also affect very specific tissue types, as in the case of neurosensory non-syndromic hearing loss and pigmentary retinopathy, diabetes mellitus, and hypertrophic cardiomyopathy. Importantly, mitochondrial heteroplasmy plays a role in disease severity and age of onset as well. Not surprisingly, mutations in enzymes that modify cytoplasmic and mitochondrial tRNAs are also linked to a diverse range of clinical phenotypes. In addition to compromised aminoacylation of the tRNAs, mutated modifying enzymes can also impact tRNA expression and abundance, tRNA modifications, tRNA folding, and even tRNA maturation (e.g., splicing). Some of these pathological mutations in tRNAs and processing enzymes are likely to affect non-canonical tRNA functions, and contribute to the diseases without significantly impacting on translation. This chapter will review recent literature on the relation of mitochondrial and cytoplasmic tRNA, and enzymes that process tRNAs, to human disease. We explore the mechanisms involved in the clinical presentation of these various diseases with an emphasis on neurological disease.
Collapse
Affiliation(s)
- Jamie A Abbott
- Department of Biochemistry, College of Medicine, University of Vermont Burlington, VT, USA
| | | | - Susan M Robey-Bond
- Department of Biochemistry, College of Medicine, University of Vermont Burlington, VT, USA
| |
Collapse
|
10
|
Vojtech L, Woo S, Hughes S, Levy C, Ballweber L, Sauteraud RP, Strobl J, Westerberg K, Gottardo R, Tewari M, Hladik F. Exosomes in human semen carry a distinctive repertoire of small non-coding RNAs with potential regulatory functions. Nucleic Acids Res 2014; 42:7290-304. [PMID: 24838567 PMCID: PMC4066774 DOI: 10.1093/nar/gku347] [Citation(s) in RCA: 409] [Impact Index Per Article: 40.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 04/01/2014] [Accepted: 04/11/2014] [Indexed: 12/21/2022] Open
Abstract
Semen contains relatively ill-defined regulatory components that likely aid fertilization, but which could also interfere with defense against infection. Each ejaculate contains trillions of exosomes, membrane-enclosed subcellular microvesicles, which have immunosuppressive effects on cells important in the genital mucosa. Exosomes in general are believed to mediate inter-cellular communication, possibly by transferring small RNA molecules. We found that seminal exosome (SE) preparations contain a substantial amount of RNA from 20 to 100 nucleotides (nts) in length. We sequenced 20-40 and 40-100 nt fractions of SE RNA separately from six semen donors. We found various classes of small non-coding RNA, including microRNA (21.7% of the RNA in the 20-40 nt fraction) as well as abundant Y RNAs and tRNAs present in both fractions. Specific RNAs were consistently present in all donors. For example, 10 (of ∼2600 known) microRNAs constituted over 40% of mature microRNA in SE. Additionally, tRNA fragments were strongly enriched for 5'-ends of 18-19 or 30-34 nts in length; such tRNA fragments repress translation. Thus, SE could potentially deliver regulatory signals to the recipient mucosa via transfer of small RNA molecules.
Collapse
Affiliation(s)
- Lucia Vojtech
- Department of Obstetrics and Gynecology, University of Washington, Seattle, USA
| | - Sangsoon Woo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Sean Hughes
- Department of Obstetrics and Gynecology, University of Washington, Seattle, USA
| | - Claire Levy
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Lamar Ballweber
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Renan P Sauteraud
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Johanna Strobl
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Katharine Westerberg
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Raphael Gottardo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, USA Department of Medicine, University of Washington, Seattle, USA
| | - Muneesh Tewari
- Department of Medicine, University of Washington, Seattle, USA Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Florian Hladik
- Department of Obstetrics and Gynecology, University of Washington, Seattle, USA Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, USA Department of Medicine, University of Washington, Seattle, USA
| |
Collapse
|
11
|
Ramesh A, Winkler WC. Metabolite-binding ribozymes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:989-994. [PMID: 24769284 DOI: 10.1016/j.bbagrm.2014.04.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 04/08/2014] [Accepted: 04/13/2014] [Indexed: 12/22/2022]
Abstract
Catalysis in the biological context was largely thought to be a protein-based phenomenon until the discovery of RNA catalysts called ribozymes. These discoveries demonstrated that many RNA molecules exhibit remarkable structural and functional versatility. By virtue of these features, naturally occurring ribozymes have been found to be involved in catalyzing reactions for fundamentally important cellular processes such as translation and RNA processing. Another class of RNAs called riboswitches directly binds ligands to control downstream gene expression. Most riboswitches regulate downstream gene expression by controlling premature transcription termination or by affecting the efficiency of translation initiation. However, one riboswitch class couples ligand-sensing to ribozyme activity. Specifically, the glmS riboswitch is a nucleolytic ribozyme, whose self-cleavage activity is triggered by the binding of GlcN6P. The products of this self-cleavage reaction are then targeted by cellular RNases for rapid degradation, thereby reducing glmS expression under conditions of sufficient GlcN6P. Since the discovery of the glmS ribozyme, other metabolite-binding ribozymes have been identified. Together, these discoveries have expanded the general understanding of noncoding RNAs and provided insights that will assist future development of synthetic riboswitch-ribozymes. A very broad overview of natural and synthetic ribozymes is presented herein with an emphasis on the structure and function of the glmS ribozyme as a paradigm for metabolite-binding ribozymes that control gene expression. This article is part of a Special Issue entitled: Riboswitches.
Collapse
Affiliation(s)
- Arati Ramesh
- The University of Texas Southwestern Medical Center, Department of Biophysics, 6001 Forest Park Rd, Dallas, USA.
| | - Wade C Winkler
- The University of Maryland, Department of Cell Biology and Molecular Genetics, 3112 Biosciences Research Building, College Park, MD, USA.
| |
Collapse
|
12
|
The Mitochondrial Aminoacyl tRNA Synthetases: Genes and Syndromes. Int J Cell Biol 2014; 2014:787956. [PMID: 24639874 PMCID: PMC3932222 DOI: 10.1155/2014/787956] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 12/01/2013] [Indexed: 02/05/2023] Open
Abstract
Mitochondrial respiratory chain (RC) disorders are a group of genetically and clinically heterogeneous diseases. This is because protein components of the RC are encoded by both mitochondrial and nuclear genomes and are essential in all cells. In addition, the biogenesis and maintenance of mitochondria, including mitochondrial DNA (mtDNA) replication, transcription, and translation, require nuclear-encoded genes. In the past decade, a growing number of syndromes associated with dysfunction of mtDNA translation have been reported. This paper reviews the current knowledge of mutations affecting mitochondrial aminoacyl tRNAs synthetases and their role in the pathogenic mechanisms underlying the different clinical presentations.
Collapse
|
13
|
Kramer S. RNA in development: how ribonucleoprotein granules regulate the life cycles of pathogenic protozoa. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 5:263-84. [PMID: 24339376 DOI: 10.1002/wrna.1207] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Revised: 10/22/2013] [Accepted: 10/29/2013] [Indexed: 12/11/2022]
Abstract
Ribonucleoprotein (RNP) granules are important posttranscriptional regulators of messenger RNA (mRNA) fate. Several types of RNP granules specifically regulate gene expression during development of multicellular organisms and are commonly referred to as germ granules. The function of germ granules is not entirely understood and probably diverse, but it is generally agreed that one main function is posttranscriptional regulation of gene expression during early development, when transcription is silent. One example is the translational repression of maternally derived mRNAs in oocytes. Here, I hope to show that the need for regulation of gene expression by RNP granules is not restricted to animal development, but plays an equally important role during the development of pathogenic protozoa. Apicomplexa and Trypanosomatidae have complex life cycles with frequent host changes. The need to quickly adapt gene expression to a new environment as well as the ability to suppress translation to survive latencies is critical for successful completion of life cycles. Posttranscriptional gene regulation is not necessarily simpler in protozoa. Apicomplexa surprise with the presence of micro RNA (miRNAs) and upstream open reading frames (µORFs). Trypanosomes have an unusually large repertoire of different RNP granule types. A better understanding of RNP granules in protozoa may help to gain insight into the evolutionary origin of RNP granules: Trypanosomes for example have two types of granules with interesting similarities to animal germ granules.
Collapse
Affiliation(s)
- Susanne Kramer
- Lehrstuhl für Zell- und Entwicklungsbiologie, Biozentrum, Universität Würzburg, Würzburg, Germany
| |
Collapse
|
14
|
Nowacka M, Strozycki PM, Jackowiak P, Hojka-Osinska A, Szymanski M, Figlerowicz M. Identification of stable, high copy number, medium-sized RNA degradation intermediates that accumulate in plants under non-stress conditions. PLANT MOLECULAR BIOLOGY 2013; 83:191-204. [PMID: 23708952 PMCID: PMC3777163 DOI: 10.1007/s11103-013-0079-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 05/15/2013] [Indexed: 05/22/2023]
Abstract
It is becoming increasingly evident that the RNA degradome is a crucial component of the total cellular RNA pool. Here, we present an analysis of the medium-sized RNAs (midi RNAs) that form in Arabidopsis thaliana. Our analyses revealed that the midi RNA fraction contained mostly 20-70-nt-long fragments derived from various RNA species, including tRNA, rRNA, mRNA and snRNA. The majority of these fragments could be classified as stable RNA degradation intermediates (RNA degradants). Using two dimensional polyacrylamide gel electrophoresis, we demonstrated that high copy number RNA (hcn RNA) degradants appear in plant cells not only during stress, as it was earlier suggested. They are continuously produced also under physiological conditions. The data collected indicated that the accumulation pattern of the hcn RNA degradants is organ-specific and can be affected by various endogenous and exogenous factors. In addition, we demonstrated that selected degradants efficiently inhibit translation in vitro. Thus, the results of our studies suggest that hcn RNA degradants are likely to be involved in the regulation of gene expression in plants.
Collapse
Affiliation(s)
- Martyna Nowacka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
- Present Address: Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, 02-109 Warsaw, Poland
| | - Pawel M. Strozycki
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Paulina Jackowiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Anna Hojka-Osinska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Maciej Szymanski
- Computational Genomics Laboratory, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, Piotrowo 3A, 60-965 Poznan, Poland
| |
Collapse
|
15
|
Durdevic Z, Mobin M, Hanna K, Lyko F, Schaefer M. The RNA Methyltransferase Dnmt2 Is Required for Efficient Dicer-2-Dependent siRNA Pathway Activity in Drosophila. Cell Rep 2013; 4:931-7. [DOI: 10.1016/j.celrep.2013.07.046] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 04/24/2013] [Accepted: 07/31/2013] [Indexed: 12/20/2022] Open
|
16
|
Taft RJ, Vanderver A, Leventer RJ, Damiani SA, Simons C, Grimmond SM, Miller D, Schmidt J, Lockhart PJ, Pope K, Ru K, Crawford J, Rosser T, de Coo IFM, Juneja M, Verma IC, Prabhakar P, Blaser S, Raiman J, Pouwels PJW, Bevova MR, Abbink TEM, van der Knaap MS, Wolf NI. Mutations in DARS cause hypomyelination with brain stem and spinal cord involvement and leg spasticity. Am J Hum Genet 2013; 92:774-80. [PMID: 23643384 DOI: 10.1016/j.ajhg.2013.04.006] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 04/01/2013] [Accepted: 04/08/2013] [Indexed: 02/03/2023] Open
Abstract
Inherited white-matter disorders are a broad class of diseases for which treatment and classification are both challenging. Indeed, nearly half of the children presenting with a leukoencephalopathy remain without a specific diagnosis. Here, we report on the application of high-throughput genome and exome sequencing to a cohort of ten individuals with a leukoencephalopathy of unknown etiology and clinically characterized by hypomyelination with brain stem and spinal cord involvement and leg spasticity (HBSL), as well as the identification of compound-heterozygous and homozygous mutations in cytoplasmic aspartyl-tRNA synthetase (DARS). These mutations cause nonsynonymous changes to seven highly conserved amino acids, five of which are unchanged between yeast and man, in the DARS C-terminal lobe adjacent to, or within, the active-site pocket. Intriguingly, HBSL bears a striking resemblance to leukoencephalopathy with brain stem and spinal cord involvement and elevated lactate (LBSL), which is caused by mutations in the mitochondria-specific DARS2, suggesting that these two diseases might share a common underlying molecular pathology. These findings add to the growing body of evidence that mutations in tRNA synthetases can cause a broad range of neurologic disorders.
Collapse
Affiliation(s)
- Ryan J Taft
- Institute for Molecular Bioscience, University of Queensland, St. Lucia, Queensland 4072, Australia.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Galizi R, Spano F, Giubilei MA, Capuccini B, Magini A, Urbanelli L, Ogawa T, Dubey JP, Spaccapelo R, Emiliani C, Di Cristina M. Evidence of tRNA cleavage in apicomplexan parasites: Half-tRNAs as new potential regulatory molecules of Toxoplasma gondii and Plasmodium berghei. Mol Biochem Parasitol 2013; 188:99-108. [DOI: 10.1016/j.molbiopara.2013.03.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 03/12/2013] [Accepted: 03/24/2013] [Indexed: 12/11/2022]
|
18
|
Hanada T, Weitzer S, Mair B, Bernreuther C, Wainger BJ, Ichida J, Hanada R, Orthofer M, Cronin SJ, Komnenovic V, Minis A, Sato F, Mimata H, Yoshimura A, Tamir I, Rainer J, Kofler R, Yaron A, Eggan KC, Woolf CJ, Glatzel M, Herbst R, Martinez J, Penninger JM. CLP1 links tRNA metabolism to progressive motor-neuron loss. Nature 2013; 495:474-80. [PMID: 23474986 DOI: 10.1038/nature11923] [Citation(s) in RCA: 189] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Accepted: 01/18/2013] [Indexed: 12/21/2022]
Abstract
CLP1 was the first mammalian RNA kinase to be identified. However, determining its in vivo function has been elusive. Here we generated kinase-dead Clp1 (Clp1(K/K)) mice that show a progressive loss of spinal motor neurons associated with axonal degeneration in the peripheral nerves and denervation of neuromuscular junctions, resulting in impaired motor function, muscle weakness, paralysis and fatal respiratory failure. Transgenic rescue experiments show that CLP1 functions in motor neurons. Mechanistically, loss of CLP1 activity results in accumulation of a novel set of small RNA fragments, derived from aberrant processing of tyrosine pre-transfer RNA. These tRNA fragments sensitize cells to oxidative-stress-induced p53 (also known as TRP53) activation and p53-dependent cell death. Genetic inactivation of p53 rescues Clp1(K/K) mice from the motor neuron loss, muscle denervation and respiratory failure. Our experiments uncover a mechanistic link between tRNA processing, formation of a new RNA species and progressive loss of lower motor neurons regulated by p53.
Collapse
Affiliation(s)
- Toshikatsu Hanada
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna 1030, Austria
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Cognat V, Pawlak G, Duchêne AM, Daujat M, Gigant A, Salinas T, Michaud M, Gutmann B, Giegé P, Gobert A, Maréchal-Drouard L. PlantRNA, a database for tRNAs of photosynthetic eukaryotes. Nucleic Acids Res 2013; 41:D273-9. [PMID: 23066098 PMCID: PMC3531208 DOI: 10.1093/nar/gks935] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 09/06/2012] [Accepted: 09/16/2012] [Indexed: 12/17/2022] Open
Abstract
PlantRNA database (http://plantrna.ibmp.cnrs.fr/) compiles transfer RNA (tRNA) gene sequences retrieved from fully annotated plant nuclear, plastidial and mitochondrial genomes. The set of annotated tRNA gene sequences has been manually curated for maximum quality and confidence. The novelty of this database resides in the inclusion of biological information relevant to the function of all the tRNAs entered in the library. This includes 5'- and 3'-flanking sequences, A and B box sequences, region of transcription initiation and poly(T) transcription termination stretches, tRNA intron sequences, aminoacyl-tRNA synthetases and enzymes responsible for tRNA maturation and modification. Finally, data on mitochondrial import of nuclear-encoded tRNAs as well as the bibliome for the respective tRNAs and tRNA-binding proteins are also included. The current annotation concerns complete genomes from 11 organisms: five flowering plants (Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Medicago truncatula and Brachypodium distachyon), a moss (Physcomitrella patens), two green algae (Chlamydomonas reinhardtii and Ostreococcus tauri), one glaucophyte (Cyanophora paradoxa), one brown alga (Ectocarpus siliculosus) and a pennate diatom (Phaeodactylum tricornutum). The database will be regularly updated and implemented with new plant genome annotations so as to provide extensive information on tRNA biology to the research community.
Collapse
MESH Headings
- Bryopsida/genetics
- Chlorophyta/genetics
- Cyanophora/genetics
- Databases, Nucleic Acid
- Diatoms/genetics
- Enzymes/genetics
- Enzymes/metabolism
- Genome, Mitochondrial
- Genome, Plant
- Genome, Plastid
- Internet
- Magnoliopsida/genetics
- Phaeophyceae/genetics
- Photosynthesis/genetics
- Plants/genetics
- RNA, Plant/chemistry
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Stramenopiles/genetics
- User-Computer Interface
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Laurence Maréchal-Drouard
- Institut de Biologie Moléculaire des Plantes, UPR 2357-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg Cedex, France
| |
Collapse
|
20
|
Nolte-'t Hoen ENM, Buermans HPJ, Waasdorp M, Stoorvogel W, Wauben MHM, 't Hoen PAC. Deep sequencing of RNA from immune cell-derived vesicles uncovers the selective incorporation of small non-coding RNA biotypes with potential regulatory functions. Nucleic Acids Res 2012; 40:9272-85. [PMID: 22821563 PMCID: PMC3467056 DOI: 10.1093/nar/gks658] [Citation(s) in RCA: 537] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Cells release RNA-carrying vesicles and membrane-free RNA/protein complexes into the extracellular milieu. Horizontal vesicle-mediated transfer of such shuttle RNA between cells allows dissemination of genetically encoded messages, which may modify the function of target cells. Other studies used array analysis to establish the presence of microRNAs and mRNA in cell-derived vesicles from many sources. Here, we used an unbiased approach by deep sequencing of small RNA released by immune cells. We found a large variety of small non-coding RNA species representing pervasive transcripts or RNA cleavage products overlapping with protein coding regions, repeat sequences or structural RNAs. Many of these RNAs were enriched relative to cellular RNA, indicating that cells destine specific RNAs for extracellular release. Among the most abundant small RNAs in shuttle RNA were sequences derived from vault RNA, Y-RNA and specific tRNAs. Many of the highly abundant small non-coding transcripts in shuttle RNA are evolutionary well-conserved and have previously been associated to gene regulatory functions. These findings allude to a wider range of biological effects that could be mediated by shuttle RNA than previously expected. Moreover, the data present leads for unraveling how cells modify the function of other cells via transfer of specific non-coding RNA species.
Collapse
Affiliation(s)
- Esther N M Nolte-'t Hoen
- Department of Biochemistry & Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584 CM Utrecht, The Netherlands.
| | | | | | | | | | | |
Collapse
|