1
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Janecki DM, Sen R, Szóstak N, Kajdasz A, Kordyś M, Plawgo K, Pandakov D, Philips A, Warkocki Z. LINE-1 mRNA 3' end dynamics shape its biology and retrotransposition potential. Nucleic Acids Res 2024; 52:3327-3345. [PMID: 38197223 PMCID: PMC11014359 DOI: 10.1093/nar/gkad1251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 12/16/2023] [Accepted: 12/20/2023] [Indexed: 01/11/2024] Open
Abstract
LINE-1 (L1) retrotransposons are mobile genetic elements that create new genomic insertions by a copy-paste mechanism involving L1 RNA/RNP intermediates. L1 encodes two ORFs, of which L1-ORF2p nicks genomic DNA and reverse transcribes L1 mRNA using the nicked DNA as a primer which base-pairs with poly(A) tail of L1 mRNA. To better understand the importance of non-templated L1 3' ends' dynamics and the interplay between L1 3' and 5' ends, we investigated the effects of genomic knock-outs and temporal knock-downs of XRN1, DCP2, and other factors. We hypothesized that in the absence of XRN1, the major 5'→3' exoribonuclease, there would be more L1 mRNA and retrotransposition. Conversely, we observed that loss of XRN1 decreased L1 retrotransposition. This occurred despite slight stabilization of L1 mRNA, but with decreased L1 RNP formation. Similarly, loss of DCP2, the catalytic subunit of the decapping complex, lowered retrotransposition despite increased steady-state levels of L1 proteins. In both XRN1 and DCP2 depletions we observed shortening of L1 3' poly(A) tails and their increased uridylation by TUT4/7. We explain the observed reduction of L1 retrotransposition by the changed qualities of non-templated L1 mRNA 3' ends demonstrating the important role of L1 3' end dynamics in L1 biology.
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Affiliation(s)
- Damian M Janecki
- Department of RNA Metabolism, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Raneet Sen
- Department of RNA Metabolism, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Natalia Szóstak
- Laboratory of Bioinformatics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Arkadiusz Kajdasz
- Department of RNA Metabolism, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Martyna Kordyś
- Department of RNA Metabolism, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Kinga Plawgo
- Department of RNA Metabolism, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Dmytro Pandakov
- Department of RNA Metabolism, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Anna Philips
- Laboratory of Bioinformatics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Zbigniew Warkocki
- Department of RNA Metabolism, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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2
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Zawadzka M, Andrzejewska-Romanowska A, Gumna J, Garfinkel DJ, Pachulska-Wieczorek K. Cell Compartment-Specific Folding of Ty1 Long Terminal Repeat Retrotransposon RNA Genome. Viruses 2022; 14:2007. [PMID: 36146813 PMCID: PMC9503155 DOI: 10.3390/v14092007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/01/2022] [Accepted: 09/08/2022] [Indexed: 11/16/2022] Open
Abstract
The structural transitions RNAs undergo during trafficking are not well understood. Here, we used the well-developed yeast Ty1 retrotransposon to provide the first structural model of genome (g) RNA in the nucleus from a retrovirus-like transposon. Through a detailed comparison of nuclear Ty1 gRNA structure with those established in the cytoplasm, virus-like particles (VLPs), and those synthesized in vitro, we detected Ty1 gRNA structural alterations that occur during retrotransposition. Full-length Ty1 gRNA serves as the mRNA for Gag and Gag-Pol proteins and as the genome that is reverse transcribed within VLPs. We show that about 60% of base pairs predicted for the nuclear Ty1 gRNA appear in the cytoplasm, and active translation does not account for such structural differences. Most of the shared base pairs are represented by short-range interactions, whereas the long-distance pairings seem unique for each compartment. Highly structured motifs tend to be preserved after nuclear export of Ty1 gRNA. In addition, our study highlights the important role of Ty1 Gag in mediating critical RNA-RNA interactions required for retrotransposition.
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Affiliation(s)
- Małgorzata Zawadzka
- Department of Structure and Function of Retrotransposons, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Angelika Andrzejewska-Romanowska
- Department of Structure and Function of Retrotransposons, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Julita Gumna
- Department of Structure and Function of Retrotransposons, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - David J. Garfinkel
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Katarzyna Pachulska-Wieczorek
- Department of Structure and Function of Retrotransposons, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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3
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Gumna J, Andrzejewska-Romanowska A, Garfinkel DJ, Pachulska-Wieczorek K. RNA Binding Properties of the Ty1 LTR-Retrotransposon Gag Protein. Int J Mol Sci 2021; 22:ijms22169103. [PMID: 34445809 PMCID: PMC8396678 DOI: 10.3390/ijms22169103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 08/21/2021] [Accepted: 08/22/2021] [Indexed: 11/16/2022] Open
Abstract
A universal feature of retroelement propagation is the formation of distinct nucleoprotein complexes mediated by the Gag capsid protein. The Ty1 retrotransposon Gag protein from Saccharomyces cerevisiae lacks sequence homology with retroviral Gag, but is functionally related. In addition to capsid assembly functions, Ty1 Gag promotes Ty1 RNA dimerization and cyclization and initiation of reverse transcription. Direct interactions between Gag and retrotransposon genomic RNA (gRNA) are needed for Ty1 replication, and mutations in the RNA-binding domain disrupt nucleation of retrosomes and assembly of functional virus-like particles (VLPs). Unlike retroviral Gag, the specificity of Ty1 Gag-RNA interactions remain poorly understood. Here we use microscale thermophoresis (MST) and electrophoretic mobility shift assays (EMSA) to analyze interactions of immature and mature Ty1 Gag with RNAs. The salt-dependent experiments showed that Ty1 Gag binds with high and similar affinity to different RNAs. However, we observed a preferential interaction between Ty1 Gag and Ty1 RNA containing a packaging signal (Psi) in RNA competition analyses. We also uncover a relationship between Ty1 RNA structure and Gag binding involving the pseudoknot present on Ty1 gRNA. In all likelihood, the differences in Gag binding affinity detected in vitro only partially explain selective Ty1 RNA packaging into VLPs in vivo.
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Affiliation(s)
- Julita Gumna
- Department of Structure and Function of Retrotransposons, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland; (J.G.); (A.A.-R.)
| | - Angelika Andrzejewska-Romanowska
- Department of Structure and Function of Retrotransposons, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland; (J.G.); (A.A.-R.)
| | - David J. Garfinkel
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA;
| | - Katarzyna Pachulska-Wieczorek
- Department of Structure and Function of Retrotransposons, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland; (J.G.); (A.A.-R.)
- Correspondence: ; Tel.: +48-61-852-85-03; Fax: +48-61-852-05-32
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4
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Andrzejewska A, Zawadzka M, Gumna J, Garfinkel DJ, Pachulska-Wieczorek K. In vivo structure of the Ty1 retrotransposon RNA genome. Nucleic Acids Res 2021; 49:2878-2893. [PMID: 33621339 PMCID: PMC7969010 DOI: 10.1093/nar/gkab090] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/28/2021] [Accepted: 02/02/2021] [Indexed: 12/25/2022] Open
Abstract
Long terminal repeat (LTR)-retrotransposons constitute a significant part of eukaryotic genomes and influence their function and evolution. Like other RNA viruses, LTR-retrotransposons efficiently utilize their RNA genome to interact with host cell machinery during replication. Here, we provide the first genome-wide RNA secondary structure model for a LTR-retrotransposon in living cells. Using SHAPE probing, we explore the secondary structure of the yeast Ty1 retrotransposon RNA genome in its native in vivo state and under defined in vitro conditions. Comparative analyses reveal the strong impact of the cellular environment on folding of Ty1 RNA. In vivo, Ty1 genome RNA is significantly less structured and more dynamic but retains specific well-structured regions harboring functional cis-acting sequences. Ribosomes participate in the unfolding and remodeling of Ty1 RNA, and inhibition of translation initiation stabilizes Ty1 RNA structure. Together, our findings support the dual role of Ty1 genomic RNA as a template for protein synthesis and reverse transcription. This study also contributes to understanding how a complex multifunctional RNA genome folds in vivo, and strengthens the need for studying RNA structure in its natural cellular context.
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Affiliation(s)
- Angelika Andrzejewska
- Department of Structure and Function of Retrotransposons, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Małgorzata Zawadzka
- Department of Structure and Function of Retrotransposons, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Julita Gumna
- Department of Structure and Function of Retrotransposons, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - David J Garfinkel
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Katarzyna Pachulska-Wieczorek
- Department of Structure and Function of Retrotransposons, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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5
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Abstract
Host cell factors are integral to viral replication. Human immunodeficiency virus 1 (HIV-1), the retroviral agent of acquired immune deficiency syndrome, requires several host factors for reverse transcription of the viral genomic RNA (gRNA) into DNA shortly after viral entry. One of these host factors is the RNA lariat debranching enzyme (Dbr1), which cleaves the 2'-5' bond of branched and lariat RNAs. A recent study has revealed that Dbr1 cleaves HIV-1 gRNA lariats that form early after viral entry. Without Dbr1 activity, HIV-1 reverse transcription stalls, consistent with blockage of viral reverse transcriptase at gRNA branch points. These findings echo an earlier study with the long-terminal-repeat retrotransposon of Saccharomyces cerevisiae, Ty1, which is a retrovirus model. Currently, branching and debranching of viral gRNA are not widely recognized as features of HIV-1 replication, and the role of a gRNA lariat is not known. Future studies will determine whether these gRNA dynamics represent fundamental features of retroviral biology and whether they occur for other positive-sense RNA viruses.
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Affiliation(s)
- Thomas M Menees
- School of Biological and Chemical Sciences, University of Missouri-Kansas City, Kansas City, Missouri 64110, USA;
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6
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Romero-López C, Berzal-Herranz A. The Role of the RNA-RNA Interactome in the Hepatitis C Virus Life Cycle. Int J Mol Sci 2020; 21:ijms21041479. [PMID: 32098260 PMCID: PMC7073135 DOI: 10.3390/ijms21041479] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/18/2020] [Accepted: 02/19/2020] [Indexed: 02/05/2023] Open
Abstract
RNA virus genomes are multifunctional entities endowed with conserved structural elements that control translation, replication and encapsidation, among other processes. The preservation of these structural RNA elements constraints the genomic sequence variability. The hepatitis C virus (HCV) genome is a positive, single-stranded RNA molecule with numerous conserved structural elements that manage different steps during the infection cycle. Their function is ensured by the association of protein factors, but also by the establishment of complex, active, long-range RNA-RNA interaction networks-the so-called HCV RNA interactome. This review describes the RNA genome functions mediated via RNA-RNA contacts, and revisits some canonical ideas regarding the role of functional high-order structures during the HCV infective cycle. By outlining the roles of long-range RNA-RNA interactions from translation to virion budding, and the functional domains involved, this work provides an overview of the HCV genome as a dynamic device that manages the course of viral infection.
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7
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Gumna J, Purzycka KJ, Ahn HW, Garfinkel DJ, Pachulska-Wieczorek K. Retroviral-like determinants and functions required for dimerization of Ty1 retrotransposon RNA. RNA Biol 2019; 16:1749-1763. [PMID: 31469343 PMCID: PMC6844567 DOI: 10.1080/15476286.2019.1657370] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
During replication of long terminal repeat (LTR)-retrotransposons, their proteins and genome (g) RNA assemble into virus-like particles (VLPs) that are not infectious but functionally related to retroviral virions. Both virions and VLPs contain gRNA in a dimeric form, but contrary to retroviruses, little is known about how gRNA dimerization and packaging occurs in LTR-retrotransposons. The LTR-retrotransposon Ty1 from Saccharomyces cerevisiae is an informative model for studying LTR-retrotransposon and retrovirus replication. Using structural, mutational and functional analyses, we explored dimerization of Ty1 genomic RNA. We provide direct evidence that interactions of self-complementary PAL1 and PAL2 palindromic sequences localized within the 5′UTR are essential for Ty1 gRNA dimer formation. Mutations disrupting PAL1-PAL2 complementarity restricted RNA dimerization in vitro and Ty1 mobility in vivo. Although dimer formation and mobility of these mutants was inhibited, our work suggests that Ty1 RNA can dimerize via alternative contact points. In contrast to previous studies, we cannot confirm a role for PAL3, tRNAiMet as well as recently proposed initial kissing-loop interactions in dimer formation. Our data also supports the critical role of Ty1 Gag in RNA dimerization. Mature Ty1 Gag binds in the proximity of sequences involved in RNA dimerization and tRNAiMet annealing, but the 5′ pseudoknot in Ty1 RNA may constitute a preferred Gag-binding site. Taken together, these results expand our understanding of genome dimerization and packaging strategies utilized by LTR-retroelements.
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Affiliation(s)
- Julita Gumna
- Department of Structure and Function of Retrotransposons, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Katarzyna J Purzycka
- Department of Structure and Function of Retrotransposons, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Hyo Won Ahn
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - David J Garfinkel
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Katarzyna Pachulska-Wieczorek
- Department of Structure and Function of Retrotransposons, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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8
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Gamache ER, Doh JH, Ritz J, Laederach A, Bellaousov S, Mathews DH, Curcio MJ. Structure-Function Model for Kissing Loop Interactions That Initiate Dimerization of Ty1 RNA. Viruses 2017; 9:E93. [PMID: 28445416 PMCID: PMC5454406 DOI: 10.3390/v9050093] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 04/20/2017] [Accepted: 04/21/2017] [Indexed: 12/25/2022] Open
Abstract
The genomic RNA of the retrotransposon Ty1 is packaged as a dimer into virus-like particles. The 5' terminus of Ty1 RNA harbors cis-acting sequences required for translation initiation, packaging and initiation of reverse transcription (TIPIRT). To identify RNA motifs involved in dimerization and packaging, a structural model of the TIPIRT domain in vitro was developed from single-nucleotide resolution RNA structural data. In general agreement with previous models, the first 326 nucleotides of Ty1 RNA form a pseudoknot with a 7-bp stem (S1), a 1-nucleotide interhelical loop and an 8-bp stem (S2) that delineate two long, structured loops. Nucleotide substitutions that disrupt either pseudoknot stem greatly reduced helper-Ty1-mediated retrotransposition of a mini-Ty1, but only mutations in S2 destabilized mini-Ty1 RNA in cis and helper-Ty1 RNA in trans. Nested in different loops of the pseudoknot are two hairpins with complementary 7-nucleotide motifs at their apices. Nucleotide substitutions in either motif also reduced retrotransposition and destabilized mini- and helper-Ty1 RNA. Compensatory mutations that restore base-pairing in the S2 stem or between the hairpins rescued retrotransposition and RNA stability in cis and trans. These data inform a model whereby a Ty1 RNA kissing complex with two intermolecular kissing-loop interactions initiates dimerization and packaging.
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Affiliation(s)
- Eric R Gamache
- Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA.
| | - Jung H Doh
- Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA.
| | - Justin Ritz
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA.
| | - Alain Laederach
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA.
| | - Stanislav Bellaousov
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, NY 14642, USA.
| | - David H Mathews
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, NY 14642, USA.
| | - M Joan Curcio
- Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA.
- Department of Biomedical Sciences, University at Albany-SUNY, Albany, NY 12201, USA.
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9
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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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10
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Nishida Y, Pachulska-Wieczorek K, Błaszczyk L, Saha A, Gumna J, Garfinkel DJ, Purzycka KJ. Ty1 retrovirus-like element Gag contains overlapping restriction factor and nucleic acid chaperone functions. Nucleic Acids Res 2015; 43:7414-31. [PMID: 26160887 PMCID: PMC4551931 DOI: 10.1093/nar/gkv695] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 06/26/2015] [Indexed: 12/13/2022] Open
Abstract
Ty1 Gag comprises the capsid of virus-like particles and provides nucleic acid chaperone (NAC) functions during retrotransposition in budding yeast. A subgenomic Ty1 mRNA encodes a truncated Gag protein (p22) that is cleaved by Ty1 protease to form p18. p22/p18 strongly inhibits transposition and can be considered an element-encoded restriction factor. Here, we show that only p22 and its short derivatives restrict Ty1 mobility whereas other regions of GAG inhibit mobility weakly if at all. Mutational analyses suggest that p22/p18 is synthesized from either of two closely spaced AUG codons. Interestingly, AUG1p18 and AUG2p18 proteins display different properties, even though both contain a region crucial for RNA binding and NAC activity. AUG1p18 shows highly reduced NAC activity but specific binding to Ty1 RNA, whereas AUG2p18 shows the converse behavior. p22/p18 affects RNA encapsidation and a mutant derivative defective for RNA binding inhibits the RNA chaperone activity of the C-terminal region (CTR) of Gag-p45. Moreover, affinity pulldowns show that p18 and the CTR interact. These results support the idea that one aspect of Ty1 restriction involves inhibition of Gag-p45 NAC functions by p22/p18-Gag interactions.
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Affiliation(s)
- Yuri Nishida
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Katarzyna Pachulska-Wieczorek
- Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Leszek Błaszczyk
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
| | - Agniva Saha
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Julita Gumna
- Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - David J Garfinkel
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Katarzyna J Purzycka
- Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
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11
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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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12
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Purzycka KJ, Garfinkel DJ, Boeke JD, Le Grice SFJ. Influence of RNA structural elements on Ty1 retrotransposition. Mob Genet Elements 2014; 3:e25060. [PMID: 23914314 PMCID: PMC3681743 DOI: 10.4161/mge.25060] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 05/16/2013] [Indexed: 11/25/2022] Open
Abstract
The long-terminal repeat (LTR)-retrotransposon Ty1 is a mobile genetic element that replicates through an RNA intermediate. Retroelement genomic transcripts contain internal structures fundamental to gene expression and propagation. In addition, long non-coding antisense RNAs overlap the 5′-terminal region of the genomic RNA and confer post-translational copy number control. Although LTR- retrotransposons are functionally related to retroviruses, little is known about the structural determinants required for genomic RNA packaging or reverse transcription. This commentary summarizes two recent papers that provide the first snapshot of genomic RNA structures from the retrotransposon Ty1 involved in transposition. We combined structural approaches with functional and genetic assays to determine if antisense RNAs anneal with the genomic RNA. Analysis of various steps in the Ty1 life cycle showed that a novel RNA pseudoknot contributes to retrotransposon function. Comparing different RNA states provides additional information about regions potentially involved in Ty1 RNA dimerization or packaging.
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Affiliation(s)
- Katarzyna J Purzycka
- RNA Structure and Function Laboratory; Institute of Bioorganic Chemistry; Polish Academy of Sciences; Poznań, Poland ; HIV Drug Resistance Program; National Cancer Institute; Frederick, MD USA
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13
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Monot C, Kuciak M, Viollet S, Mir AA, Gabus C, Darlix JL, Cristofari G. The specificity and flexibility of l1 reverse transcription priming at imperfect T-tracts. PLoS Genet 2013; 9:e1003499. [PMID: 23675310 PMCID: PMC3649969 DOI: 10.1371/journal.pgen.1003499] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 03/22/2013] [Indexed: 01/18/2023] Open
Abstract
L1 retrotransposons have a prominent role in reshaping mammalian genomes. To replicate, the L1 ribonucleoprotein particle (RNP) first uses its endonuclease (EN) to nick the genomic DNA. The newly generated DNA end is subsequently used as a primer to initiate reverse transcription within the L1 RNA poly(A) tail, a process known as target-primed reverse transcription (TPRT). Prior studies demonstrated that most L1 insertions occur into sequences related to the L1 EN consensus sequence (degenerate 5′-TTTT/A-3′ sites) and frequently preceded by imperfect T-tracts. However, it is currently unclear whether—and to which degree—the liberated 3′-hydroxyl extremity on the genomic DNA needs to be accessible and complementary to the poly(A) tail of the L1 RNA for efficient priming of reverse transcription. Here, we employed a direct assay for the initiation of L1 reverse transcription to define the molecular rules that guide this process. First, efficient priming is detected with as few as 4 matching nucleotides at the primer 3′ end. Second, L1 RNP can tolerate terminal mismatches if they are compensated within the 10 last bases of the primer by an increased number of matching nucleotides. All terminal mismatches are not equally detrimental to DNA extension, a C being extended at higher levels than an A or a G. Third, efficient priming in the context of duplex DNA requires a 3′ overhang. This suggests the possible existence of additional DNA processing steps, which generate a single-stranded 3′ end to allow L1 reverse transcription. Based on these data we propose that the specificity of L1 reverse transcription initiation contributes, together with the specificity of the initial EN cleavage, to the distribution of new L1 insertions within the human genome. Jumping genes are DNA sequences present in the genome of most living organisms. They contribute to genome dynamics and occasionally result in hereditary genetic diseases or cancer. L1 elements are the only autonomously active jumping genes in the human genome. They replicate through an RNA–mediated copy-and-paste mechanism by cleaving the host genome and then using this new DNA end as a primer to reverse transcribe its own RNA, generating a new L1 DNA copy. The molecular determinants that influence L1 target site choice are not fully understood. Here we present a quantitative assay to measure the influence of DNA target site sequence and structure on the reverse transcription step. By testing more than 65 potential DNA primers, we observe that not all sites are equally extended by the L1 machinery, and we define the rules guiding this process. In particular, we highlight the importance of partial sequence complementarity between the target site and the L1 RNA extremity, but also the high level of flexibility of this process, since detrimental terminal mismatches can be compensated by an increasing number of interacting nucleotides. We propose that this mechanism contributes to the distribution of new L1 insertions within the human genome.
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Affiliation(s)
- Clément Monot
- INSERM, U1081, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- CNRS, UMR 7284, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- University of Nice-Sophia-Antipolis, Faculty of Medicine, Nice, France
| | - Monika Kuciak
- INSERM, U1081, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- CNRS, UMR 7284, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- University of Nice-Sophia-Antipolis, Faculty of Medicine, Nice, France
| | - Sébastien Viollet
- INSERM, U1081, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- CNRS, UMR 7284, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- University of Nice-Sophia-Antipolis, Faculty of Medicine, Nice, France
| | - Ashfaq Ali Mir
- INSERM, U1081, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- CNRS, UMR 7284, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- University of Nice-Sophia-Antipolis, Faculty of Medicine, Nice, France
| | - Caroline Gabus
- Ecole Normale Supérieure de Lyon, Human Virology Department, INSERM U758, Lyon, France
| | - Jean-Luc Darlix
- Ecole Normale Supérieure de Lyon, Human Virology Department, INSERM U758, Lyon, France
| | - Gaël Cristofari
- INSERM, U1081, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- CNRS, UMR 7284, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- University of Nice-Sophia-Antipolis, Faculty of Medicine, Nice, France
- * E-mail:
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14
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Huang Q, Purzycka KJ, Lusvarghi S, Li D, LeGrice SF, Boeke JD. Retrotransposon Ty1 RNA contains a 5'-terminal long-range pseudoknot required for efficient reverse transcription. RNA (NEW YORK, N.Y.) 2013; 19:320-32. [PMID: 23329695 PMCID: PMC3677243 DOI: 10.1261/rna.035535.112] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Accepted: 11/26/2012] [Indexed: 05/04/2023]
Abstract
Ty1 retrotransposon RNA has the potential to fold into a variety of distinct structures, mutation of which affects retrotransposition frequencies. We show here that one potential functional structure is located at the 5' end of the genome and can assume a pseudoknot conformation. Chemoenzymatic probing of wild-type and mutant mini-Ty1 RNAs supports the existence of such a structure, while molecular genetic analyses show that mutations disrupting pseudoknot formation interfere with retrotransposition, indicating that it provides a critical biological function. These defects are enhanced at higher temperatures. When these mutants are combined with compensatory changes, retrotransposition is restored, consistent with pseudoknot architecture. Analyses of mutants suggest a defect in Ty1 reverse transcription. Collectively, our data allow modeling of a three-dimensional structure for this novel critical cis-acting signal of the Ty1 genome.
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Affiliation(s)
- Qing Huang
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- The High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Katarzyna J. Purzycka
- National Cancer Institute, Frederick, Maryland 21702, USA
- Laboratory of Structural Chemistry of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznań, Poland
| | | | - Donghui Li
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- The High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | | | - Jef D. Boeke
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- The High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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15
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Purzycka KJ, Legiewicz M, Matsuda E, Eizentstat LD, Lusvarghi S, Saha A, Le Grice SFJ, Garfinkel DJ. Exploring Ty1 retrotransposon RNA structure within virus-like particles. Nucleic Acids Res 2012; 41:463-73. [PMID: 23093595 PMCID: PMC3592414 DOI: 10.1093/nar/gks983] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Ty1, a long terminal repeat retrotransposon of Saccharomyces, is structurally and functionally related to retroviruses. However, a differentiating aspect between these retroelements is the diversity of the replication strategies used by long terminal repeat retrotransposons. To understand the structural organization of cis-acting elements present on Ty1 genomic RNA from the GAG region that control reverse transcription, we applied chemoenzymatic probing to RNA/tRNA complexes assembled in vitro and to the RNA in virus-like particles. By comparing different RNA states, our analyses provide a comprehensive structure of the primer-binding site, a novel pseudoknot adjacent to the primer-binding sites, three regions containing palindromic sequences that may be involved in RNA dimerization or packaging and candidate protein interaction sites. In addition, we determined the impact of a novel form of transposon control based on Ty1 antisense transcripts that associate with virus-like particles. Our results support the idea that antisense RNAs inhibit retrotransposition by targeting Ty1 protein function rather than annealing with the RNA genome.
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Affiliation(s)
- Katarzyna J Purzycka
- RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
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16
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Wainberg MA, Cohen EA. Jean-Luc Darlix: Renaissance scientist and retrovirologist par excellence. Retrovirology 2011; 8:59. [PMID: 21767377 PMCID: PMC3152887 DOI: 10.1186/1742-4690-8-59] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Accepted: 07/18/2011] [Indexed: 11/10/2022] Open
Abstract
Jean-Luc Darlix was recently recognized with the first Retrovirology Lifetime Achievement Award on the occasion of his "retirement" symposium in Lyon.
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17
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Novel transcript truncating function of Rap1p revealed by synthetic codon-optimized Ty1 retrotransposon. Genetics 2011; 190:523-35. [PMID: 22135353 DOI: 10.1534/genetics.111.136648] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Extensive mutagenesis via massive recoding of retrotransposon Ty1 produced a synthetic codon-optimized retrotransposon (CO-Ty1). CO-Ty1 is defective for retrotransposition, suggesting a sequence capable of down-regulating retrotransposition. We mapped this sequence to a critical ~20-bp region within CO-Ty1 reverse transcriptase (RT) and confirmed that it reduced Ty1 transposition, protein, and RNA levels. Repression was not Ty1 specific; when introduced immediately downstream of the green fluorescent protein (GFP) stop codon, GFP expression was similarly reduced. Rap1p mediated this down-regulation, as shown by mutagenesis and chromatin immunoprecipitation. A regular threefold drop is observed in different contexts, suggesting utility for synthetic circuits. A large reduction of RNAP II occupancy on the CO-Ty1 construct was observed 3' to the identified Rap1p site and a novel 3' truncated RNA species was observed. We propose a novel mechanism of transcriptional regulation by Rap1p whereby it serves as a transcriptional roadblock when bound to transcription unit sequences.
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18
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Piekna-Przybylska D, Bambara RA. Requirements for efficient minus strand strong-stop DNA transfer in human immunodeficiency virus 1. RNA Biol 2011; 8:230-6. [PMID: 21444998 DOI: 10.4161/rna.8.2.14802] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
After HIV-1 enters a human cell, its RNA genome is converted into double stranded DNA during the multistep process of reverse transcription. First (minus) strand DNA synthesis is initiated near the 5' end of the viral RNA, where only a short fragment of the genome is copied. In order to continue DNA synthesis the virus employs a complicated mechanism, which enables transferring of the growing minus strand DNA to a remote position at the genomic 3' end. This is called minus strand DNA transfer. The transfer enables regeneration of long terminal repeat sequences, which are crucial for viral genomic DNA integration into the host chromosome. Numerous factors have been identified that stimulate minus strand DNA transfer. In this review we focus on describing protein-RNA and RNA-RNA interactions, as well as RNA structural features, known to facilitate this step in reverse transcription.
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Affiliation(s)
- Dorota Piekna-Przybylska
- Department of Biochemistry and Biophysics, and the Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
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19
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Abstract
Long terminal repeat (LTR) retrotransposons are not only the ancient predecessors of retroviruses, but they constitute significant fractions of the genomes of many eukaryotic species. Studies of their structure and function are motivated by opportunities to gain insight into common functions of retroviruses and retrotransposons, diverse mechanisms of intracellular genomic mobility, and host factors that diminish or enhance retrotransposition. This review focuses on the nucleocapsid (NC) protein of a Saccharomyces cerevisiae LTR retrotransposon, the metavirus, Ty3. Retrovirus NC promotes genomic (g)RNA dimerization and packaging, tRNA primer annealing, reverse transcription strand transfers, and host protein interactions with gRNA. Studies of Ty3 NC have revealed key roles for Ty3 NC in formation of retroelement assembly sites (retrosomes), and in chaperoning primer tRNA to both dimerize and circularize Ty3 gRNA. We speculate that Ty3 NC, together with P-body and stress-granule proteins, plays a role in transitioning Ty3 RNA from translation template to gRNA, and that interactions between the acidic spacer domain of Ty3 Gag3 and the adjacent basic NC domain control condensation of the virus-like particle.
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Affiliation(s)
- Suzanne B Sandmeyer
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA USA.
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20
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Beerens N, Kjems J. Circularization of the HIV-1 genome facilitates strand transfer during reverse transcription. RNA (NEW YORK, N.Y.) 2010; 16:1226-35. [PMID: 20430859 PMCID: PMC2874174 DOI: 10.1261/rna.2039610] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2009] [Accepted: 02/23/2010] [Indexed: 05/18/2023]
Abstract
Two obligatory DNA strand transfers take place during reverse transcription of a retroviral RNA genome. The first strand transfer involves a jump from the 5' to the 3' terminal repeat (R) region positioned at each end of the viral genome. The process depends on base pairing between the cDNA synthesized from the 5' R region and the 3' R RNA. The tertiary conformation of the viral RNA genome may facilitate strand transfer by juxtaposing the 5' R and 3' R sequences that are 9 kb apart in the linear sequence. In this study, RNA sequences involved in an interaction between the 5' and 3' ends of the HIV-1 genome were mapped by mutational analysis. This interaction appears to be mediated mainly by a sequence in the extreme 3' end of the viral genome and in the gag open reading frame. Mutation of 3' R sequences was found to inhibit the 5'-3' interaction, which could be restored by a complementary mutation in the 5' gag region. Furthermore, we find that circularization of the HIV-1 genome does not affect the initiation of reverse transcription, but stimulates the first strand transfer during reverse transcription in vitro, underscoring the functional importance of the interaction.
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Affiliation(s)
- Nancy Beerens
- Department of Molecular Biology, Aarhus University, DK-8000 Aarhus C, Denmark
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21
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Posttranslational interference of Ty1 retrotransposition by antisense RNAs. Proc Natl Acad Sci U S A 2009; 106:15657-62. [PMID: 19721006 DOI: 10.1073/pnas.0908305106] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Transposable elements impact genome function by altering gene expression and causing chromosome rearrangements. As a result, organisms have evolved mechanisms, such as RNA-interference, to minimize the level of transposition. However, organisms without the conserved RNAi pathways, like Saccharomyces cerevisiae, must use other mechanisms to prevent transposon movement. Here, we provide evidence that antisense (AS) RNAs from the retrovirus-like element Ty1 inhibit retrotransposition posttranslationally in Saccharomyces. Multiple Ty1AS transcripts overlap Ty1 sequences necessary for copy number control (CNC) and inhibit transposition in trans. Altering Ty1 copy number or deleting sequences in the CNC region that are required for reverse transcription affect Ty1AS RNA level and Ty1 movement. Ty1AS RNAs are enriched in virus-like particles, and are associated with a dramatic decrease in the level of integrase, less reverse transcriptase, and an inability to synthesize Ty1 cDNA. Thus, Ty1AS RNAs are part of an intrinsic mechanism that limits retrotransposition by reducing the level of proteins required for replication and integration.
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22
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Nassal M. Hepatitis B viruses: reverse transcription a different way. Virus Res 2008; 134:235-49. [PMID: 18339439 DOI: 10.1016/j.virusres.2007.12.024] [Citation(s) in RCA: 280] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2007] [Revised: 11/28/2007] [Accepted: 12/05/2007] [Indexed: 02/07/2023]
Abstract
Hepatitis B virus (HBV), the causative agent of B-type hepatitis in humans, is the type member of the Hepadnaviridae, hepatotropic DNA viruses that replicate via reverse transcription. Beyond long-established differences to retroviruses in gene expression and overall replication strategy newer work has uncovered additional distinctions in the mechanism of reverse transcription per se. These include protein-priming by the unique extra terminal protein domain of the reverse transcriptase (RT) utilizing an RNA hairpin for de novo initiation of first strand DNA synthesis, and the strict dependence of this process on cellular chaperones. Recent in vitro reconstitution systems enabled first biochemical insights into this multifactorial reaction, complemented by high resolution structural information on the RNA, though not yet the protein, level. Genetic approaches have revealed long-distance interactions in the nucleic acid templates as an important factor enabling the puzzling template switches required to produce the relaxed circular (RC) DNA found in infectious virions. Finally, the failure of even potent HBV RT inhibitors to eliminate nuclear covalently closed circular (ccc) DNA, the functional equivalent of integrated proviral DNA, has spurred a renewed interest in the mechanism of cccDNA generation. These new developments are in the focus of this review.
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Affiliation(s)
- Michael Nassal
- University Hospital Freiburg, Internal Medicine 2/Molecular Biology, Hugstetter Str. 55, D-79106 Freiburg, Germany.
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23
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Nucleocapsid protein function in early infection processes. Virus Res 2008; 134:39-63. [PMID: 18279991 DOI: 10.1016/j.virusres.2007.12.006] [Citation(s) in RCA: 124] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2007] [Revised: 12/13/2007] [Accepted: 12/13/2007] [Indexed: 01/15/2023]
Abstract
The role of nucleocapsid protein (NC) in the early steps of retroviral replication appears largely that of a facilitator for reverse transcription and integration. Using a wide variety of cell-free assay systems, the properties of mature NC proteins (e.g. HIV-1 p7(NC) or MLV p10(NC)) as nucleic acid chaperones have been extensively investigated. The effect of NC on tRNA annealing, reverse transcription initiation, minus-strand-transfer, processivity of reverse transcription, plus-strand-transfer, strand-displacement synthesis, 3' processing of viral DNA by integrase, and integrase-mediated strand-transfer has been determined by a large number of laboratories. Interestingly, these reactions can all be accomplished to varying degrees in the absence of NC; some are facilitated by both viral and non-viral proteins and peptides that may or may not be involved in vivo. What is one to conclude from the observation that NC is not strictly required for these necessary reactions to occur? NC likely enhances the efficiency of each of these steps, thereby vastly improving the productivity of infection. In other words, one of the major roles of NC is to enhance the effectiveness of early infection, thereby increasing the probability of productive replication and ultimately of retrovirus survival.
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24
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Shin MK, Kim JH, Ryu DK, Ryu WS. Circularization of an RNA template via long-range base pairing is critical for hepadnaviral reverse transcription. Virology 2007; 371:362-73. [PMID: 17988705 DOI: 10.1016/j.virol.2007.09.042] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2007] [Revised: 09/15/2007] [Accepted: 09/27/2007] [Indexed: 11/19/2022]
Abstract
Although an overall genetic strategy for hepadnaviral reverse transcription has been established, the mechanism that underlies the minus-strand transfer is still poorly defined. We and others independently identified a novel cis-acting element, termed beta or varphi, respectively, that is critical for the minus-strand DNA synthesis of hepatitis B virus. A 5'-3', long-range interaction of the RNA template was proposed that involves the 5' epsilon sequence (encapsidation signal) and the 3' beta/varphi sequence. We subjected the hypothesized base pairing to genetic analysis. The data indicated that mutations abrogating the hypothesized base pairing markedly impaired minus-strand DNA synthesis, while compensatory mutations that restored the base pairing rescued the minus-strand DNA synthesis. These results demonstrated the critical role of the 5'-3', long-range interaction in minus-strand DNA synthesis. We speculate that such a long-range interaction may precisely juxtapose a donor to an acceptor during minus-strand transfer.
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Affiliation(s)
- Myeong-Kyun Shin
- Department of Biochemistry, Yonsei University, 134 Shinchondong, Seodaemungu, Seoul, 120-749, South Korea
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25
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Pratico ED, Silverman SK. Ty1 reverse transcriptase does not read through the proposed 2',5'-branched retrotransposition intermediate in vitro. RNA (NEW YORK, N.Y.) 2007; 13:1528-36. [PMID: 17652136 PMCID: PMC1950764 DOI: 10.1261/rna.629607] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
2',5'-branched RNA was recently proposed as a key Ty1 retrotransposition intermediate, for which cleavage by lariat debranching enzyme (Dbr1p) enables reverse transcription to continue synthesizing the complete Ty1 cDNA. Because dbr1 cells can produce substantial Ty1 cDNA despite lacking Dbr1p, the obligatory intermediacy of branched RNA would require that Ty1 reverse transcriptase (RT) can read through the proposed branch site with considerable efficiency. Here we have used deoxyribozyme-synthesized 2',5'-branched RNA corresponding exactly to the proposed Ty1 branch site for a direct test of this read-through ability. Using an in vitro assay that incorporates all components known to be required for Ty1 cDNA synthesis (including the TyA chaperone protein), Ty1 RT can elongate up to the branch site. Strand transfer from the 2'-arm to the 3'-arm of the branch is observed when the Ty1 RT is RNase H+ (i.e., wild-type) but not when the Ty1 RT is RNase H-. When elongating from either the 2'-arm or the 3'-arm, Ty1 RT reads through the branch site with <or=0.3% efficiency. This is at least 60-fold lower than would be necessary to explain in vivo Ty1 cDNA synthesis in dbr1 cells, because others have reported 18% cDNA synthesis relative to wild-type cells. Our finding that Ty1 RT cannot efficiently read through the proposed Ty1 branch site is inconsistent with the hypothesis that branched RNA is an obligatory Ty1 retrotransposition intermediate. This suggests that Dbr1p acts as other than a 2',5'-phosphodiesterase during Ty1 retrotransposition.
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Affiliation(s)
- Elizabeth D Pratico
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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26
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Abstract
Genomic RNA circularization has been proposed for several RNA viruses. In this study, we examined if the 5′ and 3′ ends of the 9-kb HIV-1 RNA genome can interact. In vitro assays demonstrated a specific interaction between transcripts encompassing the 5′ and 3′ terminal 1 kb, suggesting that the HIV-1 RNA genome can circularize. Truncation of the transcripts indicated that the 5′–3′ interaction is formed by 600–700 nt in the gag open reading frame and the terminal 123 nt of the genomic RNA. Detailed RNA structure probing indicates that sequences flanking the 3′ TAR hairpin interact with complementary sequences in the gag gene. Phylogenetic analysis indicates that all HIV-1 subtypes can form the 5′/3′ interaction despite considerable sequence divergence, suggesting an important role of RNA circularization in the HIV-1 replication cycle.
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Affiliation(s)
| | | | | | - Ben Berkhout
- *To whom correspondence should be addressed.+31 205 664 822+31 206 916 531
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27
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Lewellyn EB, Loeb DD. Base pairing between cis-acting sequences contributes to template switching during plus-strand DNA synthesis in human hepatitis B virus. J Virol 2007; 81:6207-15. [PMID: 17409141 PMCID: PMC1900078 DOI: 10.1128/jvi.00210-07] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2007] [Accepted: 03/26/2007] [Indexed: 11/20/2022] Open
Abstract
Hepadnaviruses utilize two template switches (primer translocation and circularization) during synthesis of plus-strand DNA to generate a relaxed-circular (RC) DNA genome. In duck hepatitis B virus (DHBV) three cis-acting sequences, 3E, M, and 5E, contribute to both template switches through base pairing, 3E with the 3' portion of M and 5E with the 5' portion of M. Human hepatitis B virus (HBV) also contains multiple cis-acting sequences that contribute to the accumulation of RC DNA, but the mechanisms through which these sequences contribute were previously unknown. Three of the HBV cis-acting sequences (h3E, hM, and h5E) occupy positions equivalent to those of the DHBV 3E, M, and 5E. We present evidence that h3E and hM contribute to the synthesis of RC DNA through base pairing during both primer translocation and circularization. Mutations that disrupt predicted base pairing inhibit both template switches while mutations that restore the predicted base pairing restore function. Therefore, the h3E-hM base pairing appears to be a conserved requirement for template switching during plus-strand DNA synthesis of HBV and DHBV. Also, we show that base pairing is not sufficient to explain the mechanism of h3E and hM, as mutating sequences adjacent to the base pairing regions inhibited both template switches. Finally, we did not identify predicted base pairing between h5E and the hM region, indicating a possible difference between HBV and DHBV. The significance of these similarities and differences between HBV and DHBV will be discussed.
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Affiliation(s)
- Eric B Lewellyn
- McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, 1400 University Ave., Madison, WI 53706, USA
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28
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Gabus C, Ivanyi-Nagy R, Depollier J, Bucheton A, Pelisson A, Darlix JL. Characterization of a nucleocapsid-like region and of two distinct primer tRNALys,2 binding sites in the endogenous retrovirus Gypsy. Nucleic Acids Res 2006; 34:5764-77. [PMID: 17040893 PMCID: PMC1635307 DOI: 10.1093/nar/gkl722] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Mobile LTR-retroelements comprising retroviruses and LTR-retrotransposons form a large part of eukaryotic genomes. Their mode of replication and abundance favour the notion that they are major actors in eukaryote evolution. The Gypsy retroelement can spread in the germ line of the fruit fly Drosophila melanogaster via both env-independent and env-dependent processes. Thus, Gypsy is both an active retrotransposon and an infectious retrovirus resembling the gammaretrovirus MuLV. However, unlike gammaretroviruses, the Gypsy Gag structural precursor is not processed into Matrix, Capsid and Nucleocapsid (NC) proteins. In contrast, it has features in common with Gag of the ancient yeast TY1 retroelement. These characteristics of Gypsy make it a very interesting model to study replication of a retroelement at the frontier between ancient retrotransposons and retroviruses. We investigated Gypsy replication using an in vitro model system and transfection of insect cells. Results show that an unstructured domain of Gypsy Gag has all the properties of a retroviral NC. This NC-like peptide forms ribonucleoparticle-like complexes upon binding Gypsy RNA and directs the annealing of primer tRNALys,2 to two distinct primer binding sites (PBS) at the genome 5′ and 3′ ends. Only the 5′ PBS is indispensable for cDNA synthesis in vitro and in Drosophila cells.
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Affiliation(s)
| | | | - Julien Depollier
- Institut de Génétique Humaine141, rue de la Cardonille, 34396 MONTPELLIER Cedex 5, France
| | - Alain Bucheton
- Institut de Génétique Humaine141, rue de la Cardonille, 34396 MONTPELLIER Cedex 5, France
| | - Alain Pelisson
- Institut de Génétique Humaine141, rue de la Cardonille, 34396 MONTPELLIER Cedex 5, France
| | - Jean-Luc Darlix
- To whom correspondence should be addressed. Tel: +33 4 72 72 81 69; Fax: +33 4 72 72 87 77;
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29
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Abraham TM, Loeb DD. Base pairing between the 5' half of epsilon and a cis-acting sequence, phi, makes a contribution to the synthesis of minus-strand DNA for human hepatitis B virus. J Virol 2006; 80:4380-7. [PMID: 16611897 PMCID: PMC1471998 DOI: 10.1128/jvi.80.9.4380-4387.2006] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2005] [Accepted: 02/09/2006] [Indexed: 01/17/2023] Open
Abstract
Synthesis of minus-strand DNA of human hepatitis B virus (HBV) can be divided into three phases: initiation of DNA synthesis, the template switch, and elongation of minus-strand DNA. Although much is known about minus-strand DNA synthesis, the mechanism(s) by which this occurs has not been completely elucidated. Through a deletion analysis, we have identified a cis-acting element involved in minus-strand DNA synthesis that lies within a 27-nucleotide region between DR2 and the 3' copy of DR1. A subset of this region (termed Phi) has been hypothesized to base pair with the 5' half of epsilon (H. Tang and A. McLachlan, Virology, 303:199-210, 2002). To test the proposed model, we used a genetic approach in which multiple sets of variants that disrupted and then restored putative base pairing between the 5' half of epsilon and phi were analyzed. Primer extension analysis, using two primers simultaneously, was performed to measure encapsidated pregenomic RNA (pgRNA) and minus-strand DNA synthesized in cell culture. The efficiency of minus-strand DNA synthesis was defined as the amount of minus-strand DNA synthesized per encapsidation event. Our results indicate that base pairing between phi and the 5' half of epsilon contributes to efficient minus-strand DNA synthesis. Additional results are consistent with the idea that the primary sequence of phi and/or epsilon also contributes to function. How base pairing between phi and epsilon contributes to minus-strand DNA synthesis is not known, but a simple speculation is that phi base pairs with the 5' half of epsilon to juxtapose the donor and acceptor sites to facilitate the first-strand template switch.
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Affiliation(s)
- Teresa M Abraham
- McArdle Laboratory for Cancer Research, University of Wisconsin Medical School, 1400 University Ave., Madison, Wisconsin 53706, USA
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30
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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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Lesage P, Todeschini AL. Happy together: the life and times of Ty retrotransposons and their hosts. Cytogenet Genome Res 2005; 110:70-90. [PMID: 16093660 DOI: 10.1159/000084940] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2003] [Accepted: 03/18/2004] [Indexed: 11/19/2022] Open
Abstract
The aim of this review is to describe the level of intimacy between Ty retrotransposons (Ty1-Ty5) and their host the yeast Saccharomyces cerevisiae. The effects of Ty location in the genome and of host proteins on the expression and mobility of Ty elements are highlighted. After a brief overview of Ty diversity and evolution, we describe the factors that dictate Ty target-site preference and the impact of targeting on Ty and adjacent gene expression. Studies on Ty3 and Ty5 have been especially informative in unraveling the role of host factors (Pol III machinery and silencing proteins, respectively) and integrase in controlling the specificity of integration. In contrast, not much is known regarding Ty1, Ty2 and Ty4, except that their insertion depends on the transcriptional competence of the adjacent Pol III gene and might be influenced by some chromatin components. This review also brings together recent findings on the regulation of Ty1 retrotransposition. A large number of host proteins (over 30) involved in a wide range of cellular processes controls either directly or indirectly Ty1 mobility, primarily at post-transcriptional steps. We focus on several genes for which more detailed analyses have permitted the elaboration of regulatory models. In addition, this review describes new data revealing that repression of Ty1 mobility also involves two forms of copy number control that act at both the trancriptional and post-transcriptional levels. Since S. cerevisiae lacks the conserved pathways for copy number control via transcriptional and post-transcriptional gene silencing found in other eukaryotes, Ty1 copy number control must be via another mechanism whose features are outlined. Ty1 response to stress also implicates activation at both transcriptional and postranscriptional steps of Ty1. Finally, we provide several insights in the role of Ty elements in chromosome evolution and yeast adaptation and discuss the factors that might limit Ty ectopic recombination.
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Affiliation(s)
- P Lesage
- Institut de Biologie Physico-Chimique, CNRS UPR 9073, Paris, France.
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Böhmdorfer G, Hofacker IL, Garber K, Jelenic S, Nizhynska V, Hirochika H, Stadler PF, Bachmair A. Unorthodox mRNA start site to extend the highly structured leader of retrotransposon Tto1 mRNA increases transposition rate. RNA (NEW YORK, N.Y.) 2005; 11:1181-91. [PMID: 16043504 PMCID: PMC1370802 DOI: 10.1261/rna.2640105] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Retroelement RNAs serve as templates for both translation and reverse transcription into extrachromosomal DNA. DNA copies may be inserted into the host genome to multiply element sequences. This transpositional activity of retroelements is usually restricted to specific conditions, particularly to conditions that impose stress on the host organism. In this work, we examined how the mRNA initiation point, and features of primary and secondary structure, of tobacco retrotransposon Tto1 RNA influence its transpositional activity. We found that the most abundant Tto1 RNA is not a substrate for reverse transcription. It is poorly translated, and its 5'-end does not contain a region of redundancy with the most prominent 3'-end. In contrast, expression of an mRNA with the 5'-end extended by 28 nucleotides allows translation and gives rise to transposition events in the heterologous host, Arabidopsis thaliana. In addition, the presence of extended hairpins and of two short open reading frames in the 5'-leader sequence of Tto1 mRNA suggests that translation does not involve ribosome scanning from the mRNA 5'-end to the translation initiation site.
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Affiliation(s)
- Gudrun Böhmdorfer
- Max Planck Institute for Plant Breeding Research, Carlvon-Linné-Weg 10, D-50829 Cologne, Germany
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Pratico ED, Wang Y, Silverman SK. A deoxyribozyme that synthesizes 2',5'-branched RNA with any branch-site nucleotide. Nucleic Acids Res 2005; 33:3503-12. [PMID: 15967808 PMCID: PMC1153712 DOI: 10.1093/nar/gki656] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2005] [Revised: 05/26/2005] [Accepted: 05/26/2005] [Indexed: 11/14/2022] Open
Abstract
RNA molecules with internal 2',5'-branches are intermediates in RNA splicing, and branched RNAs have recently been proposed as retrotransposition intermediates. A broadly applicable in vitro synthetic route to branched RNA that does not require self-splicing introns or spliceosomes would substantially improve our ability to study biochemical processes that involve branched RNA. We recently described 7S11, a deoxyribozyme that was identified by in vitro selection and has general RNA branch-forming ability. However, an important restriction for 7S11 is that the branch-site RNA nucleotide must be a purine (A or G), because a pyrimidine (U or C) is not tolerated. Here, we describe the compact 6CE8 deoxyribozyme (selected using a 20 nt random region) that synthesizes 2',5'-branched RNA with any nucleotide at the branch site. The Mn2+-dependent branch-forming ligation reaction is between an internal branch-site 2'-hydroxyl nucleophile on one RNA substrate with a 5'-triphosphate on another RNA substrate. The preference for the branch-site nucleotide is U > C congruent with A > G, although all four nucleotides are tolerated with useful ligation rates. Nearly all other nucleotides elsewhere in both RNA substrates allow ligation activity, except that the sequence requirement for the RNA strand with the 5'-triphosphate is 5'-pppGA, with 5'-pppGAR (R = purine) preferred. These characteristics permit 6CE8 to prepare branched RNAs of immediate practical interest, such as the proposed branched intermediate of Ty1 retrotransposition. Because this branched RNA has two strands with identical sequence that emerge from the branch site, we developed strategies to control which of the two strands bind with the deoxyribozyme during the branch-forming reaction. The ability to synthesize the proposed branched RNA of Ty1 retrotransposition will allow us to explore this important biochemical pathway in greater detail.
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Affiliation(s)
- Elizabeth D. Pratico
- Department of Biochemistry, University of Illinois at Urbana-Champaign600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Yangming Wang
- Department of Biochemistry, University of Illinois at Urbana-Champaign600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Scott K. Silverman
- To whom correspondence should be addressed. Tel: +1 217 244 4489; Fax: +1 217 244 8024;
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Miller JT, Khvorova A, Scaringe SA, Le Grice SFJ. Synthetic tRNALys,3 as the replication primer for the HIV-1HXB2 and HIV-1Mal genomes. Nucleic Acids Res 2004; 32:4687-95. [PMID: 15342789 PMCID: PMC516074 DOI: 10.1093/nar/gkh813] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In order to determine the contribution of modified bases on the efficiency with which tRNA(Lys,3) is used in vitro as the HIV-1 replication primer, the properties of synthetic derivatives prepared by three independent methods were compared to the natural, i.e. fully modified, tRNA. When prepared directly by in vitro run-off transcription, we show here that the predominant tRNA species is 77 nt, representing a non-templated addition of a single nucleotide. As a consequence, this aberrant tRNA inefficiently primes (-) strand strong stop DNA synthesis from the primer binding site (PBS) on the HIV-1 viral RNA genome to which it must hybridize. In contrast, correctly sized tRNA(Lys,3) can be prepared by (i) total chemical synthesis and ligation of 'half' tRNAs, (ii) transcription of a cassette whose DNA template contained strategically placed 2'-O-Methyl-containing ribonucleotides and (iii) processing from a larger precursor by means of targeted cleavage with Escherichia coli RNase H. When each of these 76 nt tRNAs was supplemented into a (-) strand strong stop DNA synthesis reaction utilizing the HXB2 strain of HIV-1, the amount of product obtained was comparable to that from the fully modified counterpart. Parallel assays monitoring early events in (-) strand strong stop DNA synthesis using either the HXB2 or Mal strain of HIV-1 RNA as the template indicated little difference in the pattern or total product amount when primed with either natural or synthetic tRNA(Lys,3). In addition, nuclease mapping of PBS-bound tRNA suggests inter-molecular base pairing between bases of the tRNA anticodon domain and the U-rich U5-IR loop of the viral 5' leader region is less stable on the HIV-1(HXB2) genome than the HIV-1(Mal) isolate.
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Affiliation(s)
- Jennifer T Miller
- Reverse Transcriptase Biochemistry Section, HIV Drug Resistance Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA
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Cristofari G, Ivanyi-Nagy R, Gabus C, Boulant S, Lavergne JP, Penin F, Darlix JL. The hepatitis C virus Core protein is a potent nucleic acid chaperone that directs dimerization of the viral (+) strand RNA in vitro. Nucleic Acids Res 2004; 32:2623-31. [PMID: 15141033 PMCID: PMC419467 DOI: 10.1093/nar/gkh579] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The hepatitis C virus (HCV) is an important human pathogen causing chronic hepatitis, liver cirrhosis and hepatocellular carcinoma. HCV is an enveloped virus with a positive-sense, single-stranded RNA genome encoding a single polyprotein that is processed to generate viral proteins. Several hundred molecules of the structural Core protein are thought to coat the genome in the viral particle, as do nucleocapsid (NC) protein molecules in Retroviruses, another class of enveloped viruses containing a positive-sense RNA genome. Retroviral NC proteins also possess nucleic acid chaperone properties that play critical roles in the structural remodelling of the genome during retrovirus replication. This analogy between HCV Core and retroviral NC proteins prompted us to investigate the putative nucleic acid chaperoning properties of the HCV Core protein. Here we report that Core protein chaperones the annealing of complementary DNA and RNA sequences and the formation of the most stable duplex by strand exchange. These results show that the HCV Core is a nucleic acid chaperone similar to retroviral NC proteins. We also find that the Core protein directs dimerization of HCV (+) RNA 3' untranslated region which is promoted by a conserved palindromic sequence possibly involved at several stages of virus replication.
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Affiliation(s)
- Gaël Cristofari
- LaboRetro, INSERM #412, ENS, 46, allée d'Italie, 69364 Lyon Cedex 07, France
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Gabus C, Mazroui R, Tremblay S, Khandjian EW, Darlix JL. The fragile X mental retardation protein has nucleic acid chaperone properties. Nucleic Acids Res 2004; 32:2129-37. [PMID: 15096575 PMCID: PMC407820 DOI: 10.1093/nar/gkh535] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The fragile X syndrome is the most common cause of inherited mental retardation resulting from the absence of the fragile X mental retardation protein (FMRP). FMRP contains two K-homology (KH) domains and one RGG box that are landmarks characteristic of RNA-binding proteins. In agreement with this, FMRP associates with messenger ribonucleoparticles (mRNPs) within actively translating ribosomes, and is thought to regulate translation of target mRNAs, including its own transcript. To investigate whether FMRP might chaperone nucleic acid folding and hybridization, we analysed the annealing and strand exchange activities of DNA oligonucleotides and the enhancement of ribozyme-directed RNA substrate cleavage by FMRP and deleted variants relative to canonical nucleic acid chaperones, such as the cellular YB-1/p50 protein and the retroviral nucleocapsid protein HIV-1 NCp7. FMRP was found to possess all the properties of a potent nucleic acid chaperone, requiring the KH motifs and RGG box for optimal activity. These findings suggest that FMRP may regulate translation by acting on RNA-RNA interactions and thus on the structural status of mRNAs.
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Affiliation(s)
- Caroline Gabus
- LaboRetro, Unité INSERM de Virologie Humaine (412), ENS, 46 allée d'Italie, 69364 Lyon cedex 07, France
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Affiliation(s)
- Philip S Perlman
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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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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Marr SF, Telesnitsky A. Mismatch extension during strong stop strand transfer and minimal homology requirements for replicative template switching during Moloney murine leukemia virus replication. J Mol Biol 2003; 330:657-74. [PMID: 12850138 PMCID: PMC7173232 DOI: 10.1016/s0022-2836(03)00597-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Reverse transcription requires two replicative template switches, called minus and plus strand strong stop transfer, and can include additional, recombinogenic switches. Donor and acceptor template homology facilitates both replicative and recombinogenic transfers, but homology-independent determinants may also contribute. Here, improved murine leukemia virus-based assays were established and the effects of varying extents of mismatches and complementarity between primer and acceptor template regions were assessed. Template switch accuracy was addressed by examining provirus structures, and efficiency was measured using a competitive titer assay. The results demonstrated that limited mismatch extension occurred readily during both minus and plus strand transfer. A strong bias for correct targeting to the U3/R junction and against use of alternate regions of homology was observed during minus strand transfer. Transfer to the U3/R junction was as accurate with five bases of complementarity as it was with an intact R, and as few as 3nt targeted transfer to a limited extent. In contrast, 12 base recombinogenic acceptors were utilized poorly and no accurate switch was observed when recombination acceptors retained only five bases of complementarity. These findings confirm that murine leukemia virus replicative and recombinogenic template switches differ in homology requirements, and support the notion that factors other than primer-template complementarity may contribute to strong stop acceptor template recognition.
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