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Retrovirus-Like Elements in Plants
Research Signpost 37/661 (2), Fort P.O., Trivandrum-695 023, Kerala, India Recent Res. Devel. Plant Sci., 3(2005): ISBN: 81-7736-245-3 Retrovirus-like elements in plants Antonio Marco and Ignacio Marín Departamento de Genética, Universidad de Valencia, Calle Doctor Moliner, 50 46100 Burjassot (Valencia), Spain Abstract LTR retrotransposons with structures that are identical to those found in simple vertebrate retroviruses, including a putative env gene, have been discovered in plants. Those potential plant retroviruses can be classified into two classes. The first one is formed by the Arabidopsis thaliana Athila elements and many other closely related env- containing elements. All of them belong to the Ty3/Gypsy group of LTR retrotransposons. The second class, in which the best-known element was first found in soybean and called SIRE1, belongs to the Ty1/Copia group. Thus, two distantly related lineages have convergent features that suggest that the transition between intracellular and infective ways of life may have occurred several times independently. Correspondence/Reprint request: Dr. Ignacio Marín, Departamento de Genética, Universidad de Valencia Calle Doctor Moliner, 50, 46100 Burjassot (Valencia), Spain. E-mail: [email protected] 2 Antonio Marco & Ignacio Marín Introduction First discovered in maize by Barbara McClintock and later recognized in all types of organisms, transposable elements are ubiquitous components of plant genomes. Eukaryotic transposable elements are generally divided into two classes. Class II elements or DNA transposons do not require an intermediate RNA. Class I elements however, require an intermediate RNA and cannot complete its replicative cycle without the use of the enzyme reverse transcriptase (RT), able to generate DNA molecules from RNA templates. -
The Primer Binding Site on the RNA Genome of Human and Simian Immunodeficiency Viruses Is Flanked by an Upstream Hairpin Structure Benjamin Berkhout
1997 Oxford University Press Nucleic Acids Research, 1997, Vol. 25, No. 20 4013–4017 The primer binding site on the RNA genome of human and simian immunodeficiency viruses is flanked by an upstream hairpin structure Benjamin Berkhout Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, PO Box 22700, 1100 DE Amsterdam, The Netherlands Received July 16, 1997; Revised and Accepted August 26, 1997 ABSTRACT PBS site. Such additional contacts were originally proposed for Rous sarcoma virus (2–4), but similar interactions have been Reverse transcription of retroviral genomes is primed reported for human immunodeficiency virus type 1 (HIV-1) (5), by a tRNA molecule that anneals to an 18 nt primer HIV-2 (6) and several retrotransposon elements (7–9). Consistent binding site (PBS) on the viral RNA genome. Additional with the idea that regions of the viral genome outside the PBS base pair interactions between the tRNA primer and sequence participate in selective tRNA primer usage is the the viral RNA have been proposed. In particular, base observation that retroviruses mutated in the PBS are genetically pairing was proposed between the anticodon loop of unstable, as they revert to the wild-type PBS sequence after a few tRNALys3 and the ‘A-rich’ loop of a hairpin located passages in cell culture (10–13). On the other hand, reasonable immediately upstream of the PBS site in HIV-1 RNA. In transduction efficiencies were obtained with murine leukemia order to judge the importance of this sequence/structure virus vectors that use an unnatural or genetically engineered motif, we performed an extensive phylogenetic tRNA primer (14,15). -
2007Murciaphd.Pdf
https://theses.gla.ac.uk/ Theses Digitisation: https://www.gla.ac.uk/myglasgow/research/enlighten/theses/digitisation/ This is a digitised version of the original print thesis. Copyright and moral rights for this work are retained by the author A copy can be downloaded for personal non-commercial research or study, without prior permission or charge This work cannot be reproduced or quoted extensively from without first obtaining permission in writing from the author The content must not be changed in any way or sold commercially in any format or medium without the formal permission of the author When referring to this work, full bibliographic details including the author, title, awarding institution and date of the thesis must be given Enlighten: Theses https://theses.gla.ac.uk/ [email protected] LATE RESTRICTION INDUCED BY AN ENDOGENOUS RETROVIRUS Pablo Ramiro Murcia August 2007 Thesis presented to the School of Veterinary Medicine at the University of Glasgow for the degree of Doctor of Philosophy Institute of Comparative Medicine 464 Bearsden Road Glasgow G61 IQH ©Pablo Murcia ProQuest Number: 10390741 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. uest ProQuest 10390741 Published by ProQuest LLO (2017). Copyright of the Dissertation is held by the Author. All rights reserved. This work is protected against unauthorized copying under Title 17, United States Code Microform Edition © ProQuest LLO. -
Role of Reverse Transcriptase and APOBEC3G in Survival of Human
& My gy co lo lo ro g i y V Soni et al., Virol Mycol 2013, 3:1 Virology & Mycology DOI: 10.4172/2161-0517.1000125 ISSN: 2161-0517 Review Article Open Access Role of Reverse Transcriptase and APOBEC3G in Survival of Human Immune Deficiency Virus -1 Genome Raj Kumar Soni*, Amol Kanampalliwar and Archana Tiwari School of Biotechnology, Rajiv Gandhi Proudyogiki Vishwavidyalaya (State Technological University), Madhya Pradesh, India Abstract Development of an effective vaccine against HIV-1 is a major challenge for scientists at present. Rapid mutation and replication of the virus in patients contribute to the evolution of the virus, which makes it unconquerable. Hence a deep understanding of critical elements related to HIV-1 is necessary. Errors introduced during DNA synthesis by reverse transcriptase are the primary source of genetic variation within retroviral populations. Numerous current studies have shown that apolipo protein B mRNA-editing enzyme-catalytic polypeptide-like 3G (APOBEC3G) proteins mediated sub- lethal mutagenesis of HIV-1 proviral DNA contributes in viral fitness by accelerating human immunodeficiency virus-1 evolution. This results in the loss of the immunity and development of resistance against anti-viral drugs. This review focuses on the latest biological, biochemical, and structural studies in an attempt to discuss current ideas related to mutations initiated by reverse transcriptase and APOBEC3G. It also describes their effect on immunological diversity and retroviral restriction, and their overall effect on the viral genome respectively. A new procedure for eradication of HIV-1 has also been proposed based on the previous studies and proven facts. Keywords: HIV-1; Reverse transcriptase; Recombination; defined. -
Genomic Neighborhoods for Arabidopsisretrotransposons: a Role for Targeted Integration in the Distribution of the Metaviridae Brooke D
Statistics Publications Statistics 2004 Genomic neighborhoods for Arabidopsisretrotransposons: a role for targeted integration in the distribution of the Metaviridae Brooke D. Peterson-Burch U.S. Department of Agriculture Dan Nettleton Iowa State University, [email protected] Daniel F. Voytas Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/stat_las_pubs Part of the Applied Statistics Commons, Cell and Developmental Biology Commons, Genetics and Genomics Commons, and the Statistical Models Commons The ompc lete bibliographic information for this item can be found at https://lib.dr.iastate.edu/ stat_las_pubs/228. For information on how to cite this item, please visit http://lib.dr.iastate.edu/ howtocite.html. This Article is brought to you for free and open access by the Statistics at Iowa State University Digital Repository. It has been accepted for inclusion in Statistics Publications by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Genomic neighborhoods for Arabidopsisretrotransposons: a role for targeted integration in the distribution of the Metaviridae Abstract Background: Retrotransposons are an abundant component of eukaryotic genomes. The high quality of the Arabidopsis thaliana genome sequence makes it possible to comprehensively characterize retroelement populations and explore factors that contribute to their genomic distribution. Results: We identified the full complement of A. thaliana long terminal repeat (LTR) retroelements using RetroMap, a software tool that iteratively searches genome sequences for reverse transcriptases and then defines retroelement insertions. Relative ages of full-length elements were estimated by assessing sequence divergence between LTRs: the Pseudoviridae were significantly younger than the Metaviridae. -
Virus World As an Evolutionary Network of Viruses and Capsidless Selfish Elements
Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements Koonin, E. V., & Dolja, V. V. (2014). Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements. Microbiology and Molecular Biology Reviews, 78(2), 278-303. doi:10.1128/MMBR.00049-13 10.1128/MMBR.00049-13 American Society for Microbiology Version of Record http://cdss.library.oregonstate.edu/sa-termsofuse Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements Eugene V. Koonin,a Valerian V. Doljab National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USAa; Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, USAb Downloaded from SUMMARY ..................................................................................................................................................278 INTRODUCTION ............................................................................................................................................278 PREVALENCE OF REPLICATION SYSTEM COMPONENTS COMPARED TO CAPSID PROTEINS AMONG VIRUS HALLMARK GENES.......................279 CLASSIFICATION OF VIRUSES BY REPLICATION-EXPRESSION STRATEGY: TYPICAL VIRUSES AND CAPSIDLESS FORMS ................................279 EVOLUTIONARY RELATIONSHIPS BETWEEN VIRUSES AND CAPSIDLESS VIRUS-LIKE GENETIC ELEMENTS ..............................................280 Capsidless Derivatives of Positive-Strand RNA Viruses....................................................................................................280 -
Interactions Between APOBEC3 and Murine Retroviruses: Mechanisms of Restriction and Drug Resistance
University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2013 Interactions Between APOBEC3 and Murine Retroviruses: Mechanisms of Restriction and Drug Resistance Alyssa Lea MacMillan University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Virology Commons Recommended Citation MacMillan, Alyssa Lea, "Interactions Between APOBEC3 and Murine Retroviruses: Mechanisms of Restriction and Drug Resistance" (2013). Publicly Accessible Penn Dissertations. 894. https://repository.upenn.edu/edissertations/894 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/894 For more information, please contact [email protected]. Interactions Between APOBEC3 and Murine Retroviruses: Mechanisms of Restriction and Drug Resistance Abstract APOBEC3 proteins are important for antiretroviral defense in mammals. The activity of these factors has been well characterized in vitro, identifying cytidine deamination as an active source of viral restriction leading to hypermutation of viral DNA synthesized during reverse transcription. These mutations can result in viral lethality via disruption of critical genes, but in some cases is insufficiento t completely obstruct viral replication. This sublethal level of mutagenesis could aid in viral evolution. A cytidine deaminase-independent mechanism of restriction has also been identified, as catalytically inactive proteins are still able to inhibit infection in vitro. Murine retroviruses do not exhibit characteristics of hypermutation by mouse APOBEC3 in vivo. However, human APOBEC3G protein expressed in transgenic mice maintains antiviral restriction and actively deaminates viral genomes. The mechanism by which endogenous APOBEC3 proteins function is unclear. The mouse provides a system amenable to studying the interaction of APOBEC3 and retroviral targets in vivo. -
Criteria for Reverse Transcription Primer Binding
Criteria For Reverse Transcription Primer Binding Husain liquesce his calentures explores zealously, but tubuliflorous Markos never reft so inconvertibly. Irreproducible burgeonsGerome speeds out-of-bounds supernormally and snooze or swallows his Hounslow. illiberally when Wright is amphibrachic. Equine and sporocystic Urban always Transfer the plates to stop thermal cycler block. Reverse transcriptase activities and mechanism of action. DNA controlsequence from the soy lectin gene, however is expressed in both GM and unmodifiedsoy. This means that the reaction was established cell cycle of transcription primer. RT and PCR temperatures and times. In reverse transcription, transcripts were only and ic amplicons in cerebrospinal fluid from. Xeno Substrate. Dna for reverse transcription pcr system of microbiology community college of multiple forward primer. Method described as these transcription as well as when designing effective primer for sharing this sometimes leads to bind and biomedical laboratories starting amount can emerge in yeast. The truth is then cleaved by the polymerase enzyme during the reaction. Luna Universal qPCR & RT-qPCR NEB. Relative simplicity and structure of some of rt reaction buffer and labgown, which makes it is fully denatured proteins. In background amplification ofthe product into a nick, and assists with pcr include fever, such as chrome or specimens may vary widely reported primers. Relative quantitation of known target against common internal standard is particularly useful for control expression measurements. Transcription start site not long-range enhancers in the FK506 binding protein 5. PCR products can be detected using either fluorescent dyes that stray to. Oh of thereaction products which is a way to each standard deviation of cells participating in each primer hybridizes to study will enable reverse primer binding protein functions. -
Designing Lentiviral Vectors for Gene Therapy of Genetic Diseases
viruses Review Designing Lentiviral Vectors for Gene Therapy of Genetic Diseases Valentina Poletti 1,2,3,* and Fulvio Mavilio 4 1 Department of Woman and Child Health, University of Padua, 35128 Padua, Italy 2 Harvard Medical School, Harvard University, Boston, MA 02115, USA 3 Pediatric Research Institute City of Hope, 35128 Padua, Italy 4 Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; [email protected] * Correspondence: [email protected] Abstract: Lentiviral vectors are the most frequently used tool to stably transfer and express genes in the context of gene therapy for monogenic diseases. The vast majority of clinical applications involves an ex vivo modality whereby lentiviral vectors are used to transduce autologous somatic cells, ob- tained from patients and re-delivered to patients after transduction. Examples are hematopoietic stem cells used in gene therapy for hematological or neurometabolic diseases or T cells for immunotherapy of cancer. We review the design and use of lentiviral vectors in gene therapy of monogenic diseases, with a focus on controlling gene expression by transcriptional or post-transcriptional mechanisms in the context of vectors that have already entered a clinical development phase. Keywords: lentiviral vectors; transcriptional regulation; post-transcriptional regulation; miRNA; promoters; retroviral integration; ex vivo gene therapy Citation: Poletti, V.; Mavilio, F. 1. Introduction Designing Lentiviral Vectors for Gene Therapy of Genetic Diseases. -
Arabidopsis Retrotransposon Virus-Like Particles and Their Regulation by Epigenetically Activated Small RNA
Downloaded from genome.cshlp.org on October 5, 2021 - Published by Cold Spring Harbor Laboratory Press Research Arabidopsis retrotransposon virus-like particles and their regulation by epigenetically activated small RNA Seung Cho Lee,1,3 Evan Ernst,1,3 Benjamin Berube,2 Filipe Borges,1 Jean-Sebastien Parent,1 Paul Ledon,2 Andrea Schorn,2 and Robert A. Martienssen1,2 1Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; 2Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA In Arabidopsis, LTR retrotransposons are activated by mutations in the chromatin gene DECREASE in DNA METHYLATION 1 (DDM1), giving rise to 21- to 22-nt epigenetically activated siRNA (easiRNA) that depend on RNA DEPENDENT RNA POLYMERASE 6 (RDR6). We purified virus-like particles (VLPs) from ddm1 and ddm1rdr6 mutants in which genomic RNA is reverse transcribed into complementary DNA. High-throughput short-read and long-read sequencing of VLP DNA (VLP DNA-seq) revealed a comprehensive catalog of active LTR retrotransposons without the need for mapping transpo- sition, as well as independent of genomic copy number. Linear replication intermediates of the functionally intact COPIA element EVADE revealed multiple central polypurine tracts (cPPTs), a feature shared with HIV in which cPPTs promote nu- clear localization. For one member of the ATCOPIA52 subfamily (SISYPHUS), cPPT intermediates were not observed, but abundant circular DNA indicated transposon “suicide” by auto-integration within the VLP. easiRNA targeted EVADE geno- mic RNA, polysome association of GYPSY (ATHILA) subgenomic RNA, and transcription via histone H3 lysine-9 dimethy- lation. VLP DNA-seq provides a comprehensive landscape of LTR retrotransposons and their control at transcriptional, post-transcriptional, and reverse transcriptional levels. -
Genome Walking with 2- to 4-Kb Steps Using Panhandle PCR
Downloaded from genome.cshlp.org on October 4, 2021 - Published by Cold Spring Harbor Laboratory Press Genome Walking with 2- to 4-kb Steps Using Panhandle PCR Douglas H. Jones and Stanley C. Winistorfer Department of Pediatrics, University of Iowa College of Medicine, Iowa City, Iowa 52242-1083 Panhandle PCR is a method that per- The PCR permits the highly specific trastrand annealing, those single strands mits the rapid retrieval of DNA seg- amplification of DNA sequences, but re- of genomic DNA that contain the com- ments flanking a known DNA se- quires knowledge of the sequences that plement to the 3' ends wil! form a stem- quence. This method extends the flank both ends of the sequence of inter- loop structure with a recessed 3' end. application of PCR to the retrieval of est. ~1-3~ Several methods have been de- Therefore, the ligated oligonucleotide DNA where only one end of the DNA veloped to permit the PCR amplification can prime template-directed DNA poly- sequence is known, so that one can of unknown DNA that flanks one end of merization on those strands that contain use PCR to walk along an uncharac- a known sequence. (4-23) The number the known sequence, resulting in known terized stretch of DNA. In this report, and variety of methods developed to am- DNA being attached to the uncharacter- we demonstrate that this method can plify DNA flanking a known sequence at- ized end of the unknown DNA (Fig. 1, be applied to the highly specific re- test to the scientific need for an effective step 3). -
Participation of Multifunctional RNA in Replication, Recombination and Regulation of Endogenous Plant Pararetroviruses (Eprvs)
fpls-12-689307 June 18, 2021 Time: 16:5 # 1 MINI REVIEW published: 21 June 2021 doi: 10.3389/fpls.2021.689307 Participation of Multifunctional RNA in Replication, Recombination and Regulation of Endogenous Plant Pararetroviruses (EPRVs) Katja R. Richert-Pöggeler1*, Kitty Vijverberg2,3, Osamah Alisawi4, Gilbert N. Chofong1, J. S. (Pat) Heslop-Harrison5,6 and Trude Schwarzacher5,6 1 Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany, 2 Naturalis Biodiversity Center, Evolutionary Ecology Group, Leiden, Netherlands, 3 Radboud University, Institute for Water and Wetland Research (IWWR), Nijmegen, Netherlands, 4 Department of Plant Protection, Faculty of Agriculture, University of Kufa, Najaf, Iraq, 5 Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom, 6 Key Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China Edited by: Jens Staal, Pararetroviruses, taxon Caulimoviridae, are typical of retroelements with reverse Ghent University, Belgium transcriptase and share a common origin with retroviruses and LTR retrotransposons, Reviewed by: Jie Cui, presumably dating back 1.6 billion years and illustrating the transition from an RNA Institut Pasteur of Shanghai (CAS), to a DNA world. After transcription of the viral genome in the host nucleus, viral DNA China Marco Catoni, synthesis occurs in the cytoplasm on the generated terminally redundant RNA including University of Birmingham, inter- and intra-molecule recombination steps rather than relying on nuclear DNA United Kingdom replication. RNA recombination events between an ancestral genomic retroelement with *Correspondence: exogenous RNA viruses were seminal in pararetrovirus evolution resulting in horizontal Katja R.