RNA-Based Technologies for Engineering Plant Virus Resistance
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Two Independent Retrons with Highly Diverse Reverse Transcriptases In
Proc. Natl. Acad. Sci. USA Vol. 87, pp. 942-945, February 1990 Biochemistry Two independent retrons with highly diverse reverse transcriptases in Myxococcus xanthus (multicopy single-stranded DNA/2',5'-phosphodiester/codon usage/myxobacteria) SUMIKO INOUYE, PETER J. HERZER, AND MASAYORI INOUYE Department of Biochemistry, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, Piscataway, NJ 08854 Communicated by Russell F. Doolittle, November 27, 1989 (received for review September 29, 1989) ABSTRACT A reverse transcriptase (RT) was recently found that the Mx65 retron is highly diverse and independent found in Myxococcus xanthus, a Gram-negative soil bacterium. from the Mx162 retron and that RT associated with the Mx65 This RT has been shown to be associated with a chromosomal retron has only 47% identity with RT for the Mx162 retron. region designated a retron responsible for the synthesis of a peculiar extrachromosomal DNA called msDNA (multicopy single-stranded DNA). We demonstrate that M. xanthus con- MATERIALS AND METHODS tains two independent, unlinked retrons, one for the synthesis Materials. The clone of the 9.0-kilobase (kb) Pst I fragment of msDNA-Mxl62 and the other for msDNA-Mx65. The struc- containing the Mx65 retron was obtained (8). Restriction tural analysis of the retron for msDNA-Mx65 revealed that the enzymes were purchased from New England Biolabs and coding regions for msdRNA (msr) and msDNA (msd), and an Boehringer Mannheim. open reading frame (ORF) downstream of msr are arranged in A deletion mutant strain ofthe Mx162 retron, AmsSX, was the same manner as found for the Mx162 retron. -
RNA Epigenetics: Fine-Tuning Chromatin Plasticity and Transcriptional Regulation, and the Implications in Human Diseases
G C A T T A C G G C A T genes Review RNA Epigenetics: Fine-Tuning Chromatin Plasticity and Transcriptional Regulation, and the Implications in Human Diseases Amber Willbanks, Shaun Wood and Jason X. Cheng * Department of Pathology, Hematopathology Section, University of Chicago, Chicago, IL 60637, USA; [email protected] (A.W.); [email protected] (S.W.) * Correspondence: [email protected] Abstract: Chromatin structure plays an essential role in eukaryotic gene expression and cell identity. Traditionally, DNA and histone modifications have been the focus of chromatin regulation; however, recent molecular and imaging studies have revealed an intimate connection between RNA epigenetics and chromatin structure. Accumulating evidence suggests that RNA serves as the interplay between chromatin and the transcription and splicing machineries within the cell. Additionally, epigenetic modifications of nascent RNAs fine-tune these interactions to regulate gene expression at the co- and post-transcriptional levels in normal cell development and human diseases. This review will provide an overview of recent advances in the emerging field of RNA epigenetics, specifically the role of RNA modifications and RNA modifying proteins in chromatin remodeling, transcription activation and RNA processing, as well as translational implications in human diseases. Keywords: 5’ cap (5’ cap); 7-methylguanosine (m7G); R-loops; N6-methyladenosine (m6A); RNA editing; A-to-I; C-to-U; 2’-O-methylation (Nm); 5-methylcytosine (m5C); NOL1/NOP2/sun domain Citation: Willbanks, A.; Wood, S.; (NSUN); MYC Cheng, J.X. RNA Epigenetics: Fine-Tuning Chromatin Plasticity and Transcriptional Regulation, and the Implications in Human Diseases. Genes 2021, 12, 627. -
RNA Interference with Sirna
CANCER GENOMICS & PROTEOMICS 3: 127-136 (2006) Review RNA Interference with siRNA HELENA JOYCE*, ISABELLA BRAY* and MARTIN CLYNES National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin, Ireland Abstract. Over the last decade, RNA interference has RNAs (13). Twenty-one different gene products with emerged as an effective mechanism for silencing gene different functions and subcellular localizations were expression. This ancient cellular antiviral response can be used studied. Knockdown experiments, monitored by to allow specific inhibition of the function of any chosen target immunofluorescence and immunoblotting, showed that even gene, including those involved in diseases such as cancer, major cellular proteins such as actin and vimentin could be AIDS and hepatitis. It has become an invaluable research tool silenced efficiently. Previous work had discovered that these to aid in the identification of novel genes involved in disease 22-nucleotide sequences served as guide sequences that processes. It has advanced from the use of synthetic RNA for instruct a multicomponent nuclease, RNA-induced silencing the endogenous production of small hairpin RNA by plasmid complex (RISC), to destroy specific messenger RNAs (7). and viral vectors, and from transient inhibition in vitro to It was then found that, in response to dsRNA, cells trigger longer-lasting effects in vivo. However, as with antisense and a two-step reaction. In the first step, long dsRNA is ribozymes, the efficient delivery of siRNA into cells is currently processed by a ribonuclease (RNase) III enzyme, called the limiting factor to successful gene expression inhibition in Dicer, into small interfering RNAs (siRNAs); these vivo. This review gives an overview of the mechanism of action subsequently serve as the sequence determinants of the of siRNA and its use in cancer research. -
RNA Interference in the Nucleus: Roles for Small Rnas in Transcription, Epigenetics and Beyond
REVIEWS NON-CODING RNA RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond Stephane E. Castel1 and Robert A. Martienssen1,2 Abstract | A growing number of functions are emerging for RNA interference (RNAi) in the nucleus, in addition to well-characterized roles in post-transcriptional gene silencing in the cytoplasm. Epigenetic modifications directed by small RNAs have been shown to cause transcriptional repression in plants, fungi and animals. Additionally, increasing evidence indicates that RNAi regulates transcription through interaction with transcriptional machinery. Nuclear small RNAs include small interfering RNAs (siRNAs) and PIWI-interacting RNAs (piRNAs) and are implicated in nuclear processes such as transposon regulation, heterochromatin formation, developmental gene regulation and genome stability. RNA interference Since the discovery that double-stranded RNAs (dsRNAs) have revealed a conserved nuclear role for RNAi in (RNAi). Silencing at both the can robustly silence genes in Caenorhabditis elegans and transcriptional gene silencing (TGS). Because it occurs post-transcriptional and plants, RNA interference (RNAi) has become a new para- in the germ line, TGS can lead to transgenerational transcriptional levels that is digm for understanding gene regulation. The mecha- inheritance in the absence of the initiating RNA, but directed by small RNA molecules. nism is well-conserved across model organisms and it is dependent on endogenously produced small RNA. uses short antisense RNA to inhibit translation or to Such epigenetic inheritance is familiar in plants but has Post-transcriptional gene degrade cytoplasmic mRNA by post-transcriptional gene only recently been described in metazoans. silencing silencing (PTGS). PTGS protects against viral infection, In this Review, we cover the broad range of nuclear (PTGS). -
Producing Vaccines Against Enveloped Viruses in Plants: Making the Impossible, Difficult
Review Producing Vaccines against Enveloped Viruses in Plants: Making the Impossible, Difficult Hadrien Peyret , John F. C. Steele † , Jae-Wan Jung, Eva C. Thuenemann , Yulia Meshcheriakova and George P. Lomonossoff * Department of Biochemistry and Metabolism, John Innes Centre, Norwich NR4 7UH, UK; [email protected] (H.P.); [email protected] (J.F.C.S.); [email protected] (J.-W.J.); [email protected] (E.C.T.); [email protected] (Y.M.) * Correspondence: [email protected] † Current address: Piramal Healthcare UK Ltd., Piramal Pharma Solutions, Northumberland NE61 3YA, UK. Abstract: The past 30 years have seen the growth of plant molecular farming as an approach to the production of recombinant proteins for pharmaceutical and biotechnological uses. Much of this effort has focused on producing vaccine candidates against viral diseases, including those caused by enveloped viruses. These represent a particular challenge given the difficulties associated with expressing and purifying membrane-bound proteins and achieving correct assembly. Despite this, there have been notable successes both from a biochemical and a clinical perspective, with a number of clinical trials showing great promise. This review will explore the history and current status of plant-produced vaccine candidates against enveloped viruses to date, with a particular focus on virus-like particles (VLPs), which mimic authentic virus structures but do not contain infectious genetic material. Citation: Peyret, H.; Steele, J.F.C.; Jung, J.-W.; Thuenemann, E.C.; Keywords: alphavirus; Bunyavirales; coronavirus; Flaviviridae; hepatitis B virus; human immunode- Meshcheriakova, Y.; Lomonossoff, ficiency virus; Influenza virus; newcastle disease virus; plant molecular farming; plant-produced G.P. -
Sequences and Phylogenies of Plant Pararetroviruses, Viruses and Transposable Elements
Hansen and Heslop-Harrison. 2004. Adv.Bot.Res. 41: 165-193. Page 1 of 34. FROM: 231. Hansen CN, Heslop-Harrison JS. 2004 . Sequences and phylogenies of plant pararetroviruses, viruses and transposable elements. Advances in Botanical Research 41 : 165-193. Sequences and Phylogenies of 5 Plant Pararetroviruses, Viruses and Transposable Elements CELIA HANSEN AND JS HESLOP-HARRISON* DEPARTMENT OF BIOLOGY 10 UNIVERSITY OF LEICESTER LEICESTER LE1 7RH, UK *AUTHOR FOR CORRESPONDENCE E-MAIL: [email protected] 15 WEBSITE: WWW.MOLCYT.COM I. Introduction ............................................................................................................2 A. Plant genome organization................................................................................2 20 B. Retroelements in the genome ............................................................................3 C. Reverse transcriptase.........................................................................................4 D. Viruses ..............................................................................................................5 II. Retroelements........................................................................................................5 A. Viral retroelements – Retrovirales....................................................................6 25 B. Non-viral retroelements – Retrales ...................................................................7 III. Viral and non-viral elements................................................................................7 -
RNA Interference in the Age of CRISPR: Will CRISPR Interfere with Rnai?
International Journal of Molecular Sciences Review RNA Interference in the Age of CRISPR: Will CRISPR Interfere with RNAi? Unnikrishnan Unniyampurath 1, Rajendra Pilankatta 2 and Manoj N. Krishnan 1,* 1 Program on Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore; [email protected] 2 Department of Biochemistry and Molecular Biology, School of Biological Sciences, Central University of Kerala, Nileshwar 671328, India; [email protected] * Correspondence: [email protected]; Tel.: +65-6516-2666 Academic Editor: Michael Ladomery Received: 2 November 2015; Accepted: 15 February 2016; Published: 26 February 2016 Abstract: The recent emergence of multiple technologies for modifying gene structure has revolutionized mammalian biomedical research and enhanced the promises of gene therapy. Over the past decade, RNA interference (RNAi) based technologies widely dominated various research applications involving experimental modulation of gene expression at the post-transcriptional level. Recently, a new gene editing technology, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and the CRISPR-associated protein 9 (Cas9) (CRISPR/Cas9) system, has received unprecedented acceptance in the scientific community for a variety of genetic applications. Unlike RNAi, the CRISPR/Cas9 system is bestowed with the ability to introduce heritable precision insertions and deletions in the eukaryotic genome. The combination of popularity and superior capabilities of CRISPR/Cas9 system raises the possibility that this technology may occupy the roles currently served by RNAi and may even make RNAi obsolete. We performed a comparative analysis of the technical aspects and applications of the CRISPR/Cas9 system and RNAi in mammalian systems, with the purpose of charting out a predictive picture on whether the CRISPR/Cas9 system will eclipse the existence and future of RNAi. -
Reverse Transcriptase Genes Are Highly Abundant and Transcriptionally Active in Marine Plankton Assemblages
The ISME Journal (2016) 10, 1134–1146 © 2016 International Society for Microbial Ecology All rights reserved 1751-7362/16 OPEN www.nature.com/ismej ORIGINAL ARTICLE Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages Magali Lescot1, Pascal Hingamp1, Kenji K Kojima2, Emilie Villar1, Sarah Romac3,4, Alaguraj Veluchamy5,11, Martine Boccara5, Olivier Jaillon6,7,8, Daniele Iudicone9, Chris Bowler5, Patrick Wincker6,7,8, Jean-Michel Claverie1 and Hiroyuki Ogata10 1Information Génomique et Structurale, UMR7256, CNRS, Aix-Marseille Université, Institut de Microbiologie de la Méditerranée (FR3479), Parc Scientifique de Luminy, Marseille, France; 2Genetic Information Research Institute, Los Altos, CA, USA; 3CNRS, UMR 7144, team EPEP, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France; 4Sorbonne Universités, UPMC Univ Paris 06, Station Biologique de Roscoff, Place Georges Teissier, FR-Roscoff, France; 5Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Paris, France; 6CEA-Institut de Génomique, GENOSCOPE, Centre National de Séquençage, Evry Cedex, France; 7Université d’Evry, Evry Cedex, France; 8Centre National de la Recherche Scientifique (CNRS), Evry Cedex, France; 9Laboratory of Ecology and Evolution of Plankton, Stazione Zoologica Anton Dohrn, Naples, Italy and 10Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, Japan Genes encoding reverse transcriptases (RTs) are found in most eukaryotes, often as a component of retrotransposons, as well as in retroviruses and in prokaryotic retroelements. We investigated the abundance, classification and transcriptional status of RTs based on Tara Oceans marine metagenomes and metatranscriptomes encompassing a wide organism size range. Our analyses revealed that RTs predominate large-size fraction metagenomes (45 μm), where they reached a maximum of 13.5% of the total gene abundance. -
The Interactions of Plant Viruses with the Phloem Svetlana Y
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by St Andrews Research Repository Hitchhikers, highway tolls and roadworks: the interactions of plant viruses with the phloem Svetlana Y. Folimonova1, Jens Tilsner2,3 1University of Florida, Plant Pathology Department, Gainesville, FL 32611, USA 2Biomedical Sciences Research Complex, University of St Andrews, BMS Building, North Haugh, St Andrews, Fife KY16 9ST, United Kingdom 3Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom [email protected] [email protected] Abstract The phloem is of central importance to plant viruses, providing the route by which they spread throughout their host. Compared with virus movement in non-vascular tissue, phloem entry, exit, and long-distance translocation usually involve additional viral factors and complex virus-host interactions, probably, because the phloem has evolved additional protection against these molecular ‘hitchhikers’. Recent progress in understanding phloem trafficking of endogenous mRNAs along with observations of membranous viral replication ‘factories’ in sieve elements challenge existing conceptions of virus long-distance transport. At the same time, the central role of the phloem in plant defences against viruses and the sophisticated viral manipulation of this host tissue are beginning to emerge. Introduction For plant-infecting viruses, the phloem is of particular importance, as it provides the fastest way to spread throughout the host in a race against systemic defence responses, in order to optimize viral load and reach tissues favoring host-to-host transmission [1;2]. Perhaps because it is a gatekeeper to systemic infection, the phloem appears to be specially protected against viruses, as its successful invasion often requires additional viral proteins compared with non-vascular movement. -
Aphid Transmission of Potyvirus: the Largest Plant-Infecting RNA Virus Genus
Supplementary Aphid Transmission of Potyvirus: The Largest Plant-Infecting RNA Virus Genus Kiran R. Gadhave 1,2,*,†, Saurabh Gautam 3,†, David A. Rasmussen 2 and Rajagopalbabu Srinivasan 3 1 Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA 2 Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27606, USA; [email protected] 3 Department of Entomology, University of Georgia, 1109 Experiment Street, Griffin, GA 30223, USA; [email protected] * Correspondence: [email protected]. † Authors contributed equally. Received: 13 May 2020; Accepted: 15 July 2020; Published: date Abstract: Potyviruses are the largest group of plant infecting RNA viruses that cause significant losses in a wide range of crops across the globe. The majority of viruses in the genus Potyvirus are transmitted by aphids in a non-persistent, non-circulative manner and have been extensively studied vis-à-vis their structure, taxonomy, evolution, diagnosis, transmission and molecular interactions with hosts. This comprehensive review exclusively discusses potyviruses and their transmission by aphid vectors, specifically in the light of several virus, aphid and plant factors, and how their interplay influences potyviral binding in aphids, aphid behavior and fitness, host plant biochemistry, virus epidemics, and transmission bottlenecks. We present the heatmap of the global distribution of potyvirus species, variation in the potyviral coat protein gene, and top aphid vectors of potyviruses. Lastly, we examine how the fundamental understanding of these multi-partite interactions through multi-omics approaches is already contributing to, and can have future implications for, devising effective and sustainable management strategies against aphid- transmitted potyviruses to global agriculture. -
Small Hydrophobic Viral Proteins Involved in Intercellular Movement of Diverse Plant Virus Genomes Sergey Y
AIMS Microbiology, 6(3): 305–329. DOI: 10.3934/microbiol.2020019 Received: 23 July 2020 Accepted: 13 September 2020 Published: 21 September 2020 http://www.aimspress.com/journal/microbiology Review Small hydrophobic viral proteins involved in intercellular movement of diverse plant virus genomes Sergey Y. Morozov1,2,* and Andrey G. Solovyev1,2,3 1 A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia 2 Department of Virology, Biological Faculty, Moscow State University, Moscow, Russia 3 Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia * Correspondence: E-mail: [email protected]; Tel: +74959393198. Abstract: Most plant viruses code for movement proteins (MPs) targeting plasmodesmata to enable cell-to-cell and systemic spread in infected plants. Small membrane-embedded MPs have been first identified in two viral transport gene modules, triple gene block (TGB) coding for an RNA-binding helicase TGB1 and two small hydrophobic proteins TGB2 and TGB3 and double gene block (DGB) encoding two small polypeptides representing an RNA-binding protein and a membrane protein. These findings indicated that movement gene modules composed of two or more cistrons may encode the nucleic acid-binding protein and at least one membrane-bound movement protein. The same rule was revealed for small DNA-containing plant viruses, namely, viruses belonging to genus Mastrevirus (family Geminiviridae) and the family Nanoviridae. In multi-component transport modules the nucleic acid-binding MP can be viral capsid protein(s), as in RNA-containing viruses of the families Closteroviridae and Potyviridae. However, membrane proteins are always found among MPs of these multicomponent viral transport systems. -
Replication of Plant RNA Virus Genomes in a Cell-Free Extract of Evacuolated Plant Protoplasts
Replication of plant RNA virus genomes in a cell-free extract of evacuolated plant protoplasts Keisuke Komoda*, Satoshi Naito*, and Masayuki Ishikawa*†‡ *Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan; and †Core Research for Evolutional Science and Technology, Japan Science and Technology Corporation, Kawaguchi, Saitama 322-0012, Japan Edited by George Bruening, University of California, Davis, CA, and approved December 22, 2003 (received for review November 4, 2003) The replication of eukaryotic positive-strand RNA virus genomes here the development of a plant cell extract-based in vitro occurs through a complex process involving multiple viral and host translation-genome replication system applicable to multiple proteins and intracellular membranes. Here we report a cell-free plant positive-strand RNA viruses: ToMV and BMV that belong system that reproduces this process in vitro. This system uses a to the alpha-like virus supergroup, and TCV that belongs to the membrane-containing extract of uninfected plant protoplasts from carmo-like virus supergroup (5). which the vacuoles had been removed by Percoll gradient centrif- ugation. We demonstrate that the system supported translation, Materials and Methods negative-strand RNA synthesis, genomic RNA replication, and sub- Viruses. ToMV (formerly referred to as TMV-L; ref. 10), genomic RNA transcription of tomato mosaic virus and two other BMV-M1 (11, 12) and TCV-B (13) were used. ToMV is a plant positive-strand RNA viruses. The RNA synthesis, which de- tobamovirus closely related to tobacco mosaic virus. pended on translation of the genomic RNA, produced virus-related RNA species similar to those that are generated in vivo.