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Regulation of retrotransposition in Arabidopsis. Biochem Soc Trans 2021; 49:2241-2251. [PMID: 34495315 DOI: 10.1042/bst20210337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/10/2021] [Accepted: 08/12/2021] [Indexed: 01/01/2023]
Abstract
Plant genomes are largely comprised of retrotransposons which can replicate through 'copy and paste' mechanisms. Long terminal repeat (LTR) retrotransposons are the major class of retrotransposons in plant species, and importantly they broadly affect the expression of nearby genes. Although most LTR retrotransposons are non-functional, active retrotranspositions have been reported in plant species or mutants under normal growth condition and environmental stresses. With the well-defined reference genome and numerous mutant alleles, Arabidopsis studies have significantly expanded our understanding of retrotransposon regulation. Active LTR retrotransposon loci produce virus-like particles to perform reverse transcription, and their complementary DNA can be inserted into new genomic loci. Due to the detrimental consequences of retrotransposition, plants like animals, have developed transcriptional and post-transcriptional silencing mechanisms. Recently several different genome-wide techniques have been developed to understand LTR retrotransposition in Arabidopsis and different plant species. Transposome, methylome, transcriptome, translatome and small RNA sequencing data have revealed how host silencing mechanisms can affect multiple steps of retrotransposition. These recent advances shed light on future mechanistic studies of retrotransposition as well as retrotransposon diversity.
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Tokan V, Lorenzo JLR, Jedlicka P, Kejnovska I, Hobza R, Kejnovsky E. Quadruplex-Forming Motif Inserted into 3'UTR of Ty1his3-AI Retrotransposon Inhibits Retrotransposition in Yeast. BIOLOGY 2021; 10:347. [PMID: 33924086 PMCID: PMC8074290 DOI: 10.3390/biology10040347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/09/2021] [Accepted: 04/15/2021] [Indexed: 11/20/2022]
Abstract
Guanine quadruplexes (G4s) serve as regulators of replication, recombination and gene expression. G4 motifs have been recently identified in LTR retrotransposons, but their role in the retrotransposon life-cycle is yet to be understood. Therefore, we inserted G4s into the 3'UTR of Ty1his3-AI retrotransposon and measured the frequency of retrotransposition in yeast strains BY4741, Y00509 (without Pif1 helicase) and with G4-stabilization by N-methyl mesoporphyrin IX (NMM) treatment. We evaluated the impact of G4s on mRNA levels by RT-qPCR and products of reverse transcription by Southern blot analysis. We found that the presence of G4 inhibited Ty1his3-AI retrotransposition. The effect was stronger when G4s were on a transcription template strand which leads to reverse transcription interruption. Both NMM and Pif1p deficiency reduced the retrotransposition irrespective of the presence of a G4 motif in the Ty1his3-AI element. Quantity of mRNA and products of reverse transcription did not fully explain the impact of G4s on Ty1his3-AI retrotransposition indicating that G4s probably affect some other steps of the retrotransposon life-cycle (e.g., translation, VLP formation, integration). Our results suggest that G4 DNA conformation can tune the activity of mobile genetic elements that in turn contribute to shaping the eukaryotic genomes.
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Affiliation(s)
- Viktor Tokan
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 61200 Brno, Czech Republic; (V.T.); (J.L.R.L.); (P.J.); (R.H.)
| | - Jose Luis Rodriguez Lorenzo
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 61200 Brno, Czech Republic; (V.T.); (J.L.R.L.); (P.J.); (R.H.)
| | - Pavel Jedlicka
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 61200 Brno, Czech Republic; (V.T.); (J.L.R.L.); (P.J.); (R.H.)
| | - Iva Kejnovska
- Department of Biophysics of Nucleic Acids, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 61200 Brno, Czech Republic;
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 61200 Brno, Czech Republic; (V.T.); (J.L.R.L.); (P.J.); (R.H.)
| | - Eduard Kejnovsky
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 61200 Brno, Czech Republic; (V.T.); (J.L.R.L.); (P.J.); (R.H.)
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Meers C, Keskin H, Banyai G, Mazina O, Yang T, Gombolay AL, Mukherjee K, Kaparos EI, Newnam G, Mazin A, Storici F. Genetic Characterization of Three Distinct Mechanisms Supporting RNA-Driven DNA Repair and Modification Reveals Major Role of DNA Polymerase ζ. Mol Cell 2020; 79:1037-1050.e5. [PMID: 32882183 DOI: 10.1016/j.molcel.2020.08.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 06/30/2020] [Accepted: 08/12/2020] [Indexed: 01/08/2023]
Abstract
DNA double-stranded breaks (DSBs) are dangerous lesions threatening genomic stability. Fidelity of DSB repair is best achieved by recombination with a homologous template sequence. In yeast, transcript RNA was shown to template DSB repair of DNA. However, molecular pathways of RNA-driven repair processes remain obscure. Utilizing assays of RNA-DNA recombination with and without an induced DSB in yeast DNA, we characterize three forms of RNA-mediated genomic modifications: RNA- and cDNA-templated DSB repair (R-TDR and c-TDR) using an RNA transcript or a DNA copy of the RNA transcript for DSB repair, respectively, and a new mechanism of RNA-templated DNA modification (R-TDM) induced by spontaneous or mutagen-induced breaks. While c-TDR requires reverse transcriptase, translesion DNA polymerase ζ (Pol ζ) plays a major role in R-TDR, and it is essential for R-TDM. This study characterizes mechanisms of RNA-DNA recombination, uncovering a role of Pol ζ in transferring genetic information from transcript RNA to DNA.
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Affiliation(s)
- Chance Meers
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Havva Keskin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Gabor Banyai
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Olga Mazina
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Taehwan Yang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Alli L Gombolay
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Kuntal Mukherjee
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Efiyenia I Kaparos
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Gary Newnam
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Alexander Mazin
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Francesca Storici
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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Lee SC, Ernst E, Berube B, Borges F, Parent JS, Ledon P, Schorn A, Martienssen RA. Arabidopsis retrotransposon virus-like particles and their regulation by epigenetically activated small RNA. Genome Res 2020; 30:576-588. [PMID: 32303559 PMCID: PMC7197481 DOI: 10.1101/gr.259044.119] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 03/24/2020] [Indexed: 02/07/2023]
Abstract
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 transposition, 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 nuclear 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 genomic RNA, polysome association of GYPSY (ATHILA) subgenomic RNA, and transcription via histone H3 lysine-9 dimethylation. VLP DNA-seq provides a comprehensive landscape of LTR retrotransposons and their control at transcriptional, post-transcriptional, and reverse transcriptional levels.
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Affiliation(s)
- Seung Cho Lee
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Evan Ernst
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Benjamin Berube
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Filipe Borges
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Jean-Sebastien Parent
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Paul Ledon
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Andrea Schorn
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Robert A Martienssen
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.,Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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Determinants of Genomic RNA Encapsidation in the Saccharomyces cerevisiae Long Terminal Repeat Retrotransposons Ty1 and Ty3. Viruses 2016; 8:v8070193. [PMID: 27428991 PMCID: PMC4974528 DOI: 10.3390/v8070193] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 06/21/2016] [Accepted: 06/28/2016] [Indexed: 12/12/2022] Open
Abstract
Long-terminal repeat (LTR) retrotransposons are transposable genetic elements that replicate intracellularly, and can be considered progenitors of retroviruses. Ty1 and Ty3 are the most extensively characterized LTR retrotransposons whose RNA genomes provide the template for both protein translation and genomic RNA that is packaged into virus-like particles (VLPs) and reverse transcribed. Genomic RNAs are not divided into separate pools of translated and packaged RNAs, therefore their trafficking and packaging into VLPs requires an equilibrium between competing events. In this review, we focus on Ty1 and Ty3 genomic RNA trafficking and packaging as essential steps of retrotransposon propagation. We summarize the existing knowledge on genomic RNA sequences and structures essential to these processes, the role of Gag proteins in repression of genomic RNA translation, delivery to VLP assembly sites, and encapsidation.
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6
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Abstract
Long-terminal repeat (LTR)-retrotransposons generate a copy of their DNA (cDNA) by reverse transcription of their RNA genome in cytoplasmic nucleocapsids. They are widespread in the eukaryotic kingdom and are the evolutionary progenitors of retroviruses [1]. The Ty1 element of the budding yeast Saccharomyces cerevisiae was the first LTR-retrotransposon demonstrated to mobilize through an RNA intermediate, and not surprisingly, is the best studied. The depth of our knowledge of Ty1 biology stems not only from the predominance of active Ty1 elements in the S. cerevisiae genome but also the ease and breadth of genomic, biochemical and cell biology approaches available to study cellular processes in yeast. This review describes the basic structure of Ty1 and its gene products, the replication cycle, the rapidly expanding compendium of host co-factors known to influence retrotransposition and the nature of Ty1's elaborate symbiosis with its host. Our goal is to illuminate the value of Ty1 as a paradigm to explore the biology of LTR-retrotransposons in multicellular organisms, where the low frequency of retrotransposition events presents a formidable barrier to investigations of retrotransposon biology.
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Ty1 integrase overexpression leads to integration of non-Ty1 DNA fragments into the genome of Saccharomyces cerevisiae. Mol Genet Genomics 2010; 284:231-42. [PMID: 20677012 PMCID: PMC2939329 DOI: 10.1007/s00438-010-0561-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2010] [Accepted: 07/08/2010] [Indexed: 10/25/2022]
Abstract
The integrase of the Saccharomyces cerevisiae retrotransposon Ty1 integrates Ty1 cDNA into genomic DNA likely via a transesterification reaction. Little is known about the mechanisms ensuring that integrase does not integrate non-Ty DNA fragments. In an effort to elucidate the conditions under which Ty1 integrase accepts non-Ty DNA as substrate, PCR fragments encompassing a selectable marker gene were transformed into yeast strains overexpressing Ty1 integrase. These fragments do not exhibit similarity to Ty1 cDNA except for the presence of the conserved terminal dinucleotide 5'-TG-CA-3'. The frequency of fragment insertion events increased upon integrase overexpression. Characterization of insertion events by genomic sequencing revealed that most insertion events exhibited clear hallmarks of integrase-mediated reactions, such as 5 bp target site duplication and target site preferences. Alteration of the terminal dinucleotide abolished the suitability of the PCR fragments to serve as substrates. We hypothesize that substrate specificity under normal conditions is mainly due to compartmentalization of integrase and Ty cDNA, which meet in virus-like particles. In contrast, recombinant integrase, which is not confined to virus-like particles, is able to accept non-Ty DNA, provided that it terminates in the proper dinucleotide sequence.
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Moreau K, Charmetant J, Gallay K, Faure C, Verdier G, Ronfort C. Avian sarcoma and leukemia virus (ASLV) integration in vitro: mutation or deletion of integrase (IN) recognition sequences does not prevent but only reduces the efficiency and accuracy of DNA integration. Virology 2009; 392:94-102. [PMID: 19638332 DOI: 10.1016/j.virol.2009.06.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2009] [Revised: 05/21/2009] [Accepted: 06/18/2009] [Indexed: 11/15/2022]
Abstract
Integrase (IN) is the enzyme responsible for provirus integration of retroviruses into the host cell genome. We used an Avian Sarcoma and Leukemia Viruses (ASLV) integration assay to investigate the way in which IN integrates substrates mutated or devoid of one or both IN recognition sequences. We found that replacing U5 by non-viral sequences (U5del) or U3 by a mutated sequence (pseudoU3) resulted in two and three fold reduction of two-ended integration (integration of the two ends from a donor DNA) respectively, but had a slight effect on concerted integration (integration of both ends at the same site of target DNA). Further, IN was still able to integrate the viral ends of the double mutant (pseudoU3/U5del) in a two-ended and concerted integration reaction. However, efficiency and accuracy (i.e. fidelity of size duplication and of end cleavage) of integration were reduced.
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Affiliation(s)
- Karen Moreau
- Institut National de la Recherche Agronomique, UMR754, Lyon, F-69007, France
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9
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Kirshenboim N, Hayouka Z, Friedler A, Hizi A. Expression and characterization of a novel reverse transcriptase of the LTR retrotransposon Tf1. Virology 2007; 366:263-76. [PMID: 17524442 DOI: 10.1016/j.virol.2007.04.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2007] [Revised: 03/15/2007] [Accepted: 04/03/2007] [Indexed: 11/30/2022]
Abstract
The LTR retrotransposon of Schizosacharomyces pombe, Tf1, has several distinctive properties that can be related to the unique properties of its reverse transcriptase (RT). Consequently, we expressed, purified and studied the recombinant Tf1 RT. This monomeric protein possesses all activities typical to RTs: DNA and RNA-dependent DNA polymerase as well as an inherent ribonuclease H. The DNA polymerase activity shows preference to Mn(+)(2) or Mg(+)(2), depending on the substrate used, whereas the ribonuclease H strongly prefers Mn(+)(2). The most outstanding feature of Tf1 RT is its capacity to add non-templated nucleotides to the 3'-ends of the nascent DNA. This is mainly apparent in the presence of Mn(+)(2), as is the noticeable low fidelity of DNA synthesis. In all, Tf1 RT has a marked infidelity in synthesizing DNA at template ends, a phenomenon that can explain, as discussed herein, some of the features of Tf1 replication in the host cells.
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Affiliation(s)
- Noa Kirshenboim
- Department of Cell and Developmental Biology, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, 69978, Israel
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10
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Garfinkel DJ, Stefanisko KM, Nyswaner KM, Moore SP, Oh J, Hughes SH. Retrotransposon suicide: formation of Ty1 circles and autointegration via a central DNA flap. J Virol 2006; 80:11920-34. [PMID: 17005648 PMCID: PMC1676259 DOI: 10.1128/jvi.01483-06] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Despite their evolutionary distance, the Saccharomyces cerevisiae retrotransposon Ty1 and retroviruses use similar strategies for replication, integration, and interactions with their hosts. Here we examine the formation of circular Ty1 DNA, which is comparable to the dead-end circular products that arise during retroviral infection. Appreciable levels of circular Ty1 DNA are present with one-long terminal repeat (LTR) circles and deleted circles comprising major classes, while two-LTR circles are enriched when integration is defective. One-LTR circles persist when homologous recombination pathways are blocked by mutation, suggesting that they result from reverse transcription. Ty1 autointegration events readily occur, and many are coincident with and dependent upon DNA flap structures that result from DNA synthesis initiated at the central polypurine tract. These results suggest that Ty1-specific mechanisms minimize copy number and raise the possibility that special DNA structures are a targeting determinant.
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Affiliation(s)
- David J Garfinkel
- National Cancer Institute, P.O. Box B, Frederick, MD 21702-1201, USA.
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11
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Atwood-Moore A, Yan K, Judson RL, Levin HL. The self primer of the long terminal repeat retrotransposon Tf1 is not removed during reverse transcription. J Virol 2006; 80:8267-70. [PMID: 16873283 PMCID: PMC1563812 DOI: 10.1128/jvi.01915-05] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The long terminal repeat retrotransposon Tf1 of Schizosaccharomyces pombe uses a unique mechanism of self priming to initiate reverse transcription. Instead of using a tRNA, Tf1 primes minus-strand synthesis with an 11-nucleotide RNA removed from the 5' end of its own transcript. We tested whether the self primer of Tf1 was similar to tRNA primers in being removed from the cDNA by RNase H. Our analysis of Tf1 cDNA extracted from virus-like particles revealed the surprising observation that the dominant species of cDNA retained the self primer. This suggests that integration of the cDNA relies on mechanisms other than reverse transcription to remove the primer.
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Affiliation(s)
- Angela Atwood-Moore
- Section on Eukaryotic Transposable Elements, Laboratory of Gene Regulation and Development, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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12
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Shi X, Jarvis DL. A new rapid amplification of cDNA ends method for extremely guanine plus cytosine-rich genes. Anal Biochem 2006; 356:222-8. [PMID: 16875657 PMCID: PMC1618939 DOI: 10.1016/j.ab.2006.06.028] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2006] [Revised: 06/07/2006] [Accepted: 06/22/2006] [Indexed: 11/22/2022]
Abstract
Rapid amplification of cDNA ends (RACE) is widely used to determine the 5'- and 3'-terminal nucleotide sequences of genes. Many different RACE methods have been developed to meet various requirements, but none addresses the difficult problems that arise when trying to isolate the ends of extremely guanine plus cytosine (GC)-rich genes. In this study, we found that we were unable to isolate the correct 5' or 3' end of an insect gene, which appeared to include extremely GC-rich sequences, using current RACE methods. Thus, we developed a new RACE method that can be used for this purpose. This new method entails first-strand cDNA synthesis at 70 degrees C with Thermo-X reverse transcriptase in the presence of homoectoine, followed by a polymerase chain reaction with 98 degrees C denaturation steps and Phusion DNA polymerase in the presence of 1M betaine and 5% dimethyl sulfoxide (DMSO). The use of these conditions yielded 5'- and 3'-RACE products that were approximately 80% GC over 213 and 162bp, respectively, and included shorter internal regions of 82 to 89% GC.
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Affiliation(s)
- Xianzong Shi
- Department of Molecular Biology, University of Wyoming, 1000 E. University Avenue, Laramie, WY 82071 and
- Chesapeake-PERL, Inc., 8510A Corridor Rd, Savage, MD 20763
| | - Donald L. Jarvis
- Department of Molecular Biology, University of Wyoming, 1000 E. University Avenue, Laramie, WY 82071 and
- *Corresponding author: Phone: 307-766-4282, Fax: 307-766-5098,
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Atwood-Moore A, Ejebe K, Levin HL. Specific recognition and cleavage of the plus-strand primer by reverse transcriptase. J Virol 2006; 79:14863-75. [PMID: 16282486 PMCID: PMC1287563 DOI: 10.1128/jvi.79.23.14863-14875.2005] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Reverse transcriptases (RTs) of retroviruses and long terminal repeat (LTR)-retrotransposons possess DNA polymerase and RNase H activities. During reverse transcription these activities are necessary for the programmed sequence of events that include template switching and primer processing. Integrase then inserts the completed cDNA into the genome of the host cell. The RT of the LTR-retrotransposon Tf1 was subjected to random mutagenesis, and the resulting transposons were screened with genetic assays to test which mutations reduced reverse transcription and which inhibited integration. We identified a cluster of mutations in the RNase H domain of RT that were surprising because they blocked integration without reducing cDNA levels. The results of immunoblots demonstrated that these mutations did not reduce levels of RT or integrase. DNA blots showed that the mutations did not lower the amounts of full-length cDNA. The sequences of the 3' ends of the cDNA revealed that mutations within the cluster in RNase H specifically reduced the removal of the polypurine tract (PPT) primer from the ends of the cDNA. These results indicate that primer removal is not a necessary component of reverse transcription. The residues mutated in Tf1 RNase H are conserved in human immunodeficiency virus type 1 and make direct contact with DNA opposite the PPT. Thus, our results identify a conserved element in RT that contacts the PPT and is specifically required for PPT removal.
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Affiliation(s)
- Angela Atwood-Moore
- Section on Eukaryotic Transposable Elements, Laboratory of Gene Regulation and Development, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
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14
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Wilhelm FX, Wilhelm M, Gabriel A. Reverse transcriptase and integrase of the Saccharomyces cerevisiae Ty1 element. Cytogenet Genome Res 2005; 110:269-87. [PMID: 16093680 DOI: 10.1159/000084960] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2003] [Accepted: 02/02/2004] [Indexed: 11/19/2022] Open
Abstract
Integrase (IN) and reverse transcriptase (RT) play a central role in transposition of retroelements. The mechanism of integration by IN and the steps of the replication process mediated by RT are briefly described here. Recently, active recombinant forms of Ty1 IN and RT have been obtained. This has allowed a more detailed understanding of their biochemical and structural properties and has made possible combined in vitro and in vivo analyses of their functions. A focus of this review is to discuss some of the results obtained thus far with these two recombinant proteins and to propose future directions.
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Affiliation(s)
- F-X Wilhelm
- Institut de Biologie Moleculaire et Cellulaire, Strasbourg, France.
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15
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Hizi A, Levin HL. The integrase of the long terminal repeat-retrotransposon tf1 has a chromodomain that modulates integrase activities. J Biol Chem 2005; 280:39086-94. [PMID: 16188891 DOI: 10.1074/jbc.m506363200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Chromodomains in a variety of proteins mediate the formation of heterochromatin by interacting directly with histone H3, DNA, or RNA. A diverse family of long terminal repeat (LTR)-retrotransposons possesses chromodomains in their integrases (IN), suggesting that the chromodomains may control integration. The LTR-retrotransposon Tf1 of Schizosaccharomyces pombe is highly active and possesses a chromodomain in the COOH terminus of its IN. To test this chromodomain for a role in integration, recombinant INs with and without the chromodomain were assayed for activity in in vitro reactions. The full-length IN had integration activity with oligonucleotide substrates that modeled both the insertion reaction and a reverse reaction known as disintegration. The INs of retroviruses possess an additional activity termed 3' processing that must remove 2-3 nucleotides from the 3' ends of the viral cDNA before insertion can occur. These additional nucleotides are added during reverse transcription because of the position of the minus strand primer downstream of the LTR. The position of the primer for Tf1 suggests no nucleotides are added 3' of the LTR. It was therefore surprising that Tf1 IN was capable of 3' cleavage. The most unexpected result reported here was that the IN lacking the chromodomain had significantly higher activity and substantially reduced substrate specificity. These results reveal that both the activity and specificity of enzymes can be modulated by their chromodomains.
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Affiliation(s)
- Amnon Hizi
- Section on Eukaryotic Transposable Elements, Laboratory of Gene Regulation and Development, NICHD, National Institutes of Health, Bethesda, Maryland 20892, USA.
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16
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Coombes CE, Boeke JD. An evaluation of detection methods for large lariat RNAs. RNA (NEW YORK, N.Y.) 2005; 11:323-31. [PMID: 15661842 PMCID: PMC1370721 DOI: 10.1261/rna.7124405] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2004] [Accepted: 12/08/2004] [Indexed: 05/20/2023]
Abstract
Ty1 elements are long terminal repeat (LTR) retrotransposons that reside within the genome of Saccharomyces cerevisiae. It has been known for many years that the 2'-5' phosphodiesterase Dbr1p, which debranches intron lariats, is required for efficient Ty1 transposition. A recent report suggested the intriguing possibility that Ty1 RNA forms a lariat as a transposition intermediate. We set out to further investigate the nature of the proposed Ty1 lariat branchpoint. However, using a wide range of techniques we were unable to find any evidence for the proposed lariat structure. Furthermore, we demonstrate that some of the techniques used in the initial study describing the lariat are capable of incorrectly reporting a lariat structure. Thus, the role of the Dbr1 protein in Ty1 retrotransposition remains elusive.
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Affiliation(s)
- Candice E Coombes
- Department of Oncology, Johns Hopkins University School of Medicine, 339 Broadway Research Building, 733 North Broadway, Baltimore, MD 21205, USA
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Pandey M, Patel S, Gabriel A. Insights into the role of an active site aspartate in Ty1 reverse transcriptase polymerization. J Biol Chem 2004; 279:47840-8. [PMID: 15333632 DOI: 10.1074/jbc.m406019200] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Long terminal repeat-containing retrotransposons encode reverse transcriptases (RTs) that replicate their RNA into integratable, double-stranded DNA. A mutant version of the RT from Saccharomyces cerevisiae retrotransposon Ty1, in which one of the three active site aspartates has been changed to asparagine (D211N), is still capable of in vitro polymerization, although it is blocked for in vivo transposition. We generated recombinant WT and D211N Ty1 RTs to study RT function and determine specific roles for the Asp(211) residue. Presteady-state kinetic analysis of the two enzymes shows that the D211N mutation has minimal effect on nucleotide binding but reduces the k(pol) by approximately 230-fold. The mutation reduces binding affinity for both Mn(2+) and Mg(2+), indicating that the Asp(211) side chain helps create a tight metal binding pocket. Although both enzymes are highly processive and tend to remain bound to their initial substrate, each shows distinctive patterns of pausing, attributable to interactions between metal ions and the active site residue. These results provide insights to specific roles for the Asp(211) residue during polymerization and indicate unusual enzymatic properties that bear on the Ty1 replication pathway.
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Affiliation(s)
- Manjula Pandey
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854, USA
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18
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Abstract
Foamy viruses (FVs) or spumaviruses were described for the first time in the early 1950s in cell cultures derived from monkey kidneys. Later, FVs were isolated in several mammal species such as cats, cattle and horses. Highly prevalent in non-human primates they are not naturally present in humans, although several cases of simian-to-human transmissions have been described. Interestingly, the replication strategy of FVs differs in many aspects from that of other retroviruses, presenting features that are closely related to pararetroviruses, exemplified by the hepatitis B virus (HBV), but also characteristics that are closely related to yeast retrotransposons. These characteristics led to the creation of a distinct viral subfamily by the International Committee on Virus Taxonomy in 2002; the Spumaretrovirinae.
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Affiliation(s)
- Olivier Delelis
- CNRS UPR9051, Hôpital Saint-Louis, Centre Hayem, 1 Avenue Claude Vellefaux, 75475 Paris Cedex 10, Paris, France
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19
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Juretzek T, Holm T, Gärtner K, Kanzler S, Lindemann D, Herchenröder O, Picard-Maureau M, Rammling M, Heinkelein M, Rethwilm A. Foamy virus integration. J Virol 2004; 78:2472-7. [PMID: 14963145 PMCID: PMC369232 DOI: 10.1128/jvi.78.5.2472-2477.2004] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
It had been suggested that during integration of spumaretroviruses (foamy viruses) the right (U5) end of the cDNA is processed, while the left (U3) remains uncleaved. We confirmed this hypothesis by sequencing two-long terminal repeat (LTR) circle junctions of unintegrated DNA. Based on an infectious foamy virus molecular clone, a set of constructs harboring mutations at the 5' end of the U3 region in the 3' LTR was analyzed for particle export, reverse transcription, and replication. Following transient transfection some mutants were severely impaired in generating infectious virus, while others replicated almost like the wild type. The replication competence of the mutants was unrelated to the cleavability of the newly created U3 end. This became obvious with two mutants both belonging to the high-titer type. One mutant containing a dinucleotide artificially transferred from the right to the left end was trimmed upon integration, while another one with an unrelated dinucleotide in that place was not. The latter construct in particular showed that the canonical TG motif at the beginning of the provirus is not essential for foamy virus integration.
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Affiliation(s)
- Thomas Juretzek
- Institut für Virologie, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
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20
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Abstract
Ty elements of Saccharomyces cerevisiae are long terminal repeat (LTR) retroelements related to retroviruses. Normal levels of Ty1 transposition require Dbr1p, a cellular enzyme that cleaves 2'-5' RNA bonds. We show that Ty1 RNAs lacking identifiable 5' ends accumulate in virus-like particles (VLPs) in dbr1 mutants. Debranching this RNA in vitro with Dbr1p creates an uncapped version of the normal Ty1 RNA 5' end. We show that the 5' nucleotide (nt) of Ty1 RNA forms a 2'-5' bond with a nt near the 3' end of the same RNA, creating a lariat. The properties of the lariat suggest it forms by a novel mechanism and that branching and debranching may play roles in Ty1 reverse transcription at the minus-strand transfer step.
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Affiliation(s)
- Zhi Cheng
- School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO 64110, USA
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21
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Bibillo A, Eickbush TH. End-to-end template jumping by the reverse transcriptase encoded by the R2 retrotransposon. J Biol Chem 2004; 279:14945-53. [PMID: 14752111 DOI: 10.1074/jbc.m310450200] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The reverse transcriptase encoded by the non-long terminal repeat retrotransposon R2 has been shown to be able to jump from the 5'-end of one RNA template (the donor) to the 3'-end of a second RNA template (the acceptor) in the absence of preexisting sequence identity between the two templates. These jumps between RNA templates have similarity to the end-to-end template jumps described for the RNA-directed RNA polymerases encoded by certain RNA viruses. Here we describe for the first time the mechanism by which such end-to-end template jumps can occur. Most template jumps by the R2 reverse transcriptase are brought about by the enzyme's ability to add nontemplated (overhanging) nucleotides to the cDNA when it reaches the end of the donor RNA. The enzyme then anneals these overhanging nucleotides to sequences at the 3'-end of the acceptor RNA. The annealing is most efficient if it involves the terminal nucleotide(s) of the acceptor RNA but can occur to sites at least 5 nucleotides from the 3'-end. These end-to-end jumps are similar to steps proposed to be part of the integration reaction of non-long terminal repeat retrotransposons and can explain chimeric integration products derived from multiple RNA templates.
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Affiliation(s)
- Arkadiusz Bibillo
- Department of Biology, University of Rochester, Rochester, New York 14627, USA.
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22
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Abstract
The replication strategy of foamy viruses diverges in many aspects from what is commonly accepted as the rules of retroviral replication. Although many questions on the details of the replication pathway are still unanswered, it appears that foamy viruses have adopted a strategy which functionally bridges the retroviral and the hepadnaviral replication pathways. A number of experimental findings in favour of the view that foamy viruses are reverse transcribing DNA viruses which integrate into the host cell genome are discussed.
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Affiliation(s)
- A Rethwilm
- Institut für Virologie, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Fetscherstr. 74, Dresden, 01307 Germany.
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23
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Abstract
Retrotransposons have proliferated extensively in eukaryotic lineages; the genomes of many animals and plants comprise 50% or more retrotransposon sequences by weight. There are several persuasive arguments that the enzymatic lynchpin of retrotransposon replication, reverse transcriptase (RT), is an ancient enzyme. Moreover, the direct progenitors of retrotransposons are thought to be mobile self-splicing introns that actively propagate themselves via reverse transcription, the group II introns, also known as retrointrons. Retrointrons are represented in modern genomes in very modest numbers, and thus far, only in certain eubacterial and organellar genomes. Archaeal genomes are nearly devoid of RT in any form. In this study, I propose a model to explain this unusual distribution, and rationalize it with the proposed ancient origin of the RT gene. A cap and tail hypothesis is proposed. By this hypothesis, the specialized terminal structures of eukaryotic mRNA provide the ideal molecular environment for the lengthening, evolution, and subsequent massive expansion of highly mobile retrotransposons, leading directly to the retrotransposon-cluttered structure that typifies modern metazoan genomes and the eventual emergence of retroviruses.
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Affiliation(s)
- Jef D Boeke
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.
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24
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Golinelli MP, Hughes SH. Nontemplated base addition by HIV-1 RT can induce nonspecific strand transfer in vitro. Virology 2002; 294:122-34. [PMID: 11886271 DOI: 10.1006/viro.2001.1322] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
After minus-strand strong-stop DNA (-sssDNA) synthesis, the RNA template is degraded by the RNase H activity of reverse transcriptase (RT), generating a single-stranded DNA. The genomes of some retroviruses contain sequences that could lead to self-priming of their minus signsssDNA. Self-priming was prevented by annealing a DNA oligonucleotide to the 3' end of model DNAs that corresponded to the 3' ends of the -sssDNAs (-R ssDNA) from human immunodeficiency virus type 1 (HIV-1), type 2 (HIV-2), and human T-cell leukemia virus type 1 (HTLV-1) but nonspecific strand transfer to ssDNA molecules in solution was induced in vitro (Golinelli and Hughes, 2001). This nonspecific strand transfer involved the addition of a nontemplated base to the 3' end of -R ssDNAs that was part of a blunt-ended duplex. In the case of HIV-2 -R ssDNA, A and C were added more efficiently than G and T. Strand transfer to ssDNA in solution occurred only if the nontemplated base could form a basepair with the last base at the 3' end of the ssDNA. If there was a mismatch, strand transfer did not occur. There was no detectable strand transfer to internal sites in the target ssDNA except to the second position from the 3' end of the DNA acceptor when the sequences at the 3' ends of the two DNAs allowed the formation of two basepairs. The nontemplated base addition and the one-basepair strand transfer were both affected by the salt concentration in the reaction, the nature of the reverse transcriptase (HIV-1 versus Moloney murine leukemia virus), and the sequence at the 3' end of -R ssDNA. NC reduced the efficiency of nonspecific strand transfer in vitro, suggesting that NC may have a role in reducing nonspecific strand transfer in vivo.
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Affiliation(s)
- Marie-Pierre Golinelli
- HIV Drug Resistance Program, National Cancer Institute, NCI-Frederick, Frederick, MD 21702-1201, USA
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25
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Lawler JF, Merkulov GV, Boeke JD. A nucleocapsid functionality contained within the amino terminus of the Ty1 protease that is distinct and separable from proteolytic activity. J Virol 2002; 76:346-54. [PMID: 11739699 PMCID: PMC135695 DOI: 10.1128/jvi.76.1.346-354.2002] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ty1 is the most successful of the five endogenous yeast retrotransposons. The life cycle of Ty1 dictates that a number of nucleocapsid (NC)-facilitated events occur although the protein(s) responsible for these events has not been identified. The positioning of the NC peptide is conserved at the carboxy terminus of the Gag protein among most long terminal repeat (LTR)-containing retroelements. An analogous region of Ty1 that simultaneously encodes part of Gag, protease (PR), and the C-terminal p4 peptide was mutagenized. Some of these mutations result in smaller-than-normal virus-like particles (VLPs). The mutants were also found to impair an NC-like functionality contained within the amino terminus of the protease that is distinct and separable from its proteolytic activity. Remarkably, these mutants have distinct defects in reverse transcription.
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Affiliation(s)
- Joseph F Lawler
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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26
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Boutabout M, Wilhelm M, Wilhelm FX. DNA synthesis fidelity by the reverse transcriptase of the yeast retrotransposon Ty1. Nucleic Acids Res 2001; 29:2217-22. [PMID: 11376139 PMCID: PMC55714 DOI: 10.1093/nar/29.11.2217] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The fidelity of the yeast retrotransposon Ty1 reverse transcriptase (RT) was determined by an assay based on gel electrophoresis. Steady-state kinetics analyses of deoxyribonucleotide (dNTP) incorporation at a defined primer-template site indicate that Ty1 RT misincorporates dNTP at a frequency of 0.45 x 10(-5) for the A(t):A mispair in which dATP is misincorporated opposite a template A to 6.27 x 10(-5) for the C(t):A mispair. The G(t):G and T(t):T mispairs are formed with very low efficiency. The fidelity parameters of Ty1 RT do not depend on whether RNA or DNA are copied. Relative to lentiviral RTs (HIV-1, HIV-2 or EIAV) Ty1 RT is approximately 10-fold less error prone. Our data also show that the Ty1 RT is able to recapitulate two error-generating mechanisms: extension of mismatches and non-templated addition of nucleotides at the end of a blunt-end primer-template.
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Affiliation(s)
- M Boutabout
- Unité Propre de Recherche 9002 du Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, 15 rue R. Descartes, 67084 Strasbourg, France
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27
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Kiechle M, Friedl AA, Manivasakam P, Eckardt-Schupp F, Schiestl RH. DNA integration by Ty integrase in yku70 mutant Saccharomyces cerevisiae cells. Mol Cell Biol 2000; 20:8836-44. [PMID: 11073984 PMCID: PMC86530 DOI: 10.1128/mcb.20.23.8836-8844.2000] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the present work we examined nonhomologous integration of plasmid DNA in a yku70 mutant. Ten of 14 plasmids integrated as composite elements, including Ty sequences probably originating from erroneous strand-switching and/or priming events. Three additional plasmids integrated via Ty integrase without cointegrating Ty sequences, as inferred from 5-bp target site duplication and integration site preferences. Ty integrase-mediated integration of non-Ty DNA has never been observed in wild-type cells, although purified integrase is capable of using non-Ty DNA as a substrate in vitro. Hence our data implicate yKu70 as the cellular function preventing integrase from accepting non-Ty DNA as a substrate.
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Affiliation(s)
- M Kiechle
- Institute of Radiobiology, GSF Research Center, D-85764 Neuherberg, Germany
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28
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Bacharach E, Gonsky J, Lim D, Goff SP. Deletion of a short, untranslated region adjacent to the polypurine tract in Moloney murine leukemia virus leads to formation of aberrant 5' plus-strand DNA ends in vivo. J Virol 2000; 74:4755-64. [PMID: 10775614 PMCID: PMC111998 DOI: 10.1128/jvi.74.10.4755-4764.2000] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Experiments were performed to determine the function of a 28-nucleotide untranslated sequence lying between the envelope gene and the polypurine tract (PPT) sequence in the Moloney murine leukemia virus (Mo-MuLV) genome. A mutant virus carrying a deletion of this sequence (Mo-MuLVDelta28) replicated more slowly than wild-type (wt) virus and reverted by recombination with endogenous sequences during growth in NIH 3T3 cells. We show that this deletion did not affect the level of viral protein expression or genomic RNA packaging. Mo-MuLVDelta28 served as a helper virus as efficiently as the wt virus; in contrast, a retroviral vector harboring this mutation exhibited reduced transduction efficiency, indicating that the mutation acts not in trans but in cis. Analysis of acutely infected cells revealed that reduced levels of viral DNA were generated by reverse transcription of the Mo-MuLVDelta28 RNA as compared to the wt RNA. Analysis of DNA circle junctions revealed that plus-strand DNA of Mo-MuLVDelta28 but not wt virus often retained the PPT and additional upstream sequences. These structures suggest that aberrant 5' ends of plus-strand DNA were generated by a failure to remove the PPT RNA primer and/or by mispriming at sites upstream of the PPT. These data demonstrate that the major role of the sequences immediately upstream of the PPT is specifying efficient and accurate plus-strand DNA synthesis.
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Affiliation(s)
- E Bacharach
- Department of Biochemistry and Molecular Biophysics, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA
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29
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Jaaskelainen M, Mykkanen AH, Arna T, Vicient CM, Suoniemi A, Kalendar R, Savilahti H, Schulman AH. Retrotransposon BARE-1: expression of encoded proteins and formation of virus-like particles in barley cells. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 1999; 20:413-422. [PMID: 10607294 DOI: 10.1046/j.1365-313x.1999.00616.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Retrotransposons are ubiquitous and major components of plant genomes, and are characteristically retroviral-like in their genomic structure and in the major proteins encoded. Nevertheless, few have been directly demonstrated to be transcribed or reverse transcribed. The BARE-1 retrotransposon family of barley (Hordeum vulgare) is highly prevalent, actively transcribed, and contains well conserved functional regions. Insertion sites for BARE-1 are highly polymorphic in the barley genome. Here we show that BARE-1 is translated and the capsid protein (GAG) and integrase (IN) components of the predicted polyprotein are processed into polypeptides of expected size. Some of the GAG sediments as virus-like particles together with IN and with BARE-1 cDNA. Reverse transcriptase activity is also present in gradient fractions containing BARE-1 translation products. Virus-like particles have also been visualized in fractions containing BARE-1 components. Thus BARE-1 components necessary for carrying out the life cycle of an active retrotransposon appear to be present in vivo, and to assemble. This would suggest that post-translational mechanisms may be at work to prevent rapid genome inflation through unrestricted integration.
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30
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Abstract
Chromosomal double-strand breaks (DSBs) can be repaired by either homology-dependent or homology-independent pathways. Using a novel intron-based genetic assay to identify rare homology-independent DNA rearrangements associated with repair of a chromosomal DSB in S. cerevisiae, we observed that approximately 20% of rearrangements involved endogenous DNA insertions at the break site. We have analyzed 37 inserts and find they fall into two distinct classes: Ty1 cDNA intermediates varying in length from 140 bp to 3.4 kb and short mitochondrial DNA fragments ranging in size from 33 bp to 219 bp. Several inserts consist of multiple noncontiguous mitochondrial DNA segments. These results demonstrate an ongoing mechanism for genome evolution through acquisition of organellar and mobile DNAs at DSB sites.
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MESH Headings
- Base Sequence
- Cell Nucleus/drug effects
- Cell Nucleus/enzymology
- Cell Nucleus/genetics
- Chromosome Breakage/genetics
- Chromosomes, Fungal/drug effects
- Chromosomes, Fungal/genetics
- DNA Repair/drug effects
- DNA Repair/genetics
- DNA, Fungal/genetics
- DNA, Mitochondrial/genetics
- Deoxyribonucleases, Type II Site-Specific/metabolism
- Enzyme Induction/drug effects
- Evolution, Molecular
- Galactose/pharmacology
- Genes, Fungal/genetics
- Introns/genetics
- Molecular Weight
- Mutation/genetics
- Recombination, Genetic/drug effects
- Recombination, Genetic/genetics
- Retroelements/genetics
- Saccharomyces cerevisiae/cytology
- Saccharomyces cerevisiae/drug effects
- Saccharomyces cerevisiae/enzymology
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae Proteins
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- X Yu
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854, USA
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31
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Abstract
Ty1, the genetically tractable retrotransposable element found in the yeast Saccharomyces cerevisiae, closely resembles vertebrate retroviruses both in structure and in mechanism of replication. By direct sequence analysis, we examined the rate and spectrum of new mutations appearing during a single cycle of Ty1 replication. The rate of new mutations was comparable to those seen for replicating retroviruses. All observed changes were base substitutions, and their location suggested that template ends may be hot spots for generating these mutations. To test this, we developed methods to examine, at the nucleotide level, the end structure of the expected Ty1 replication intermediates. Our results demonstrate that Ty1 reverse transcriptase can add terminal non-templated bases in vivo during each step in replication. Furthermore, Ty1 RNAse H creates multiple template ends by imprecisely cleaving RNA. This expands the range of sites of subsequent non-templated base addition. Finally, on reaching template ends, Ty1 reverse transcriptase can strand transfer to inappropriate templates. Taken together, these mutagenic mechanisms may influence the evolution of particular regions of the Ty1 genome and serve as a mechanism to regulate the overall level of Ty1 transposition in its host cell.
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Affiliation(s)
- A Gabriel
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08855, USA.
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