Extended Interactions Between the Primer tRNAiMet and Genomic RNA of the Yeast Ty1 Retrotransposon

Friant, Sylvie; Heyman, T.; Wilhelm, M.L.; Wilhelm, F.X.

doi:10.1093/nar/24.3.441

Cited by 58 publications

(83 citation statements)

References 27 publications

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“…Each of these complementary segments is essential for efficient initiation of Ty3 reverse transcription. In the yeast retrotransposon Ty1, the 3Ј end, TΨC-and D-arms of primer tRNA i Met make contact with three PBS sequences all located near the 5Ј end of the genomic RNA (Friant et al, 1996(Friant et al, , 1998, providing an interesting parallel with the bipartite PBS structure described herein for Ty3. Furthermore, mutations in Ty1 RNA that impair interactions with the TΨC and D-arms of tRNA i Met severely attenuate transposition in vivo (Friant et al, 1996(Friant et al, , 1998.…”

Section: Discussionmentioning

confidence: 86%

“…In the yeast retrotransposon Ty1, the 3Ј end, TΨC-and D-arms of primer tRNA i Met make contact with three PBS sequences all located near the 5Ј end of the genomic RNA (Friant et al, 1996(Friant et al, , 1998, providing an interesting parallel with the bipartite PBS structure described herein for Ty3. Furthermore, mutations in Ty1 RNA that impair interactions with the TΨC and D-arms of tRNA i Met severely attenuate transposition in vivo (Friant et al, 1996(Friant et al, , 1998. This situation in Ty3, and to a lesser extent in Ty1, is different from that prevailing in retroviruses where a canonical 5Ј 18 nucleotide PBS is commonly the major binding site of primer tRNA as well as the start site for reverse transcription (Coffin, 1985; Met (Keeney et al, 1995) to Ty3 3Ј RNA (lanes 1-6) and 5Ј-3Ј RNA (lanes 7-12).…”

Section: Discussionmentioning

confidence: 86%

“…Met to the PBS (data not shown; Friant et al, 1996). Dimerization of tRNA i Met probably occurs by interaction between the 5Ј ends since this domain contains a 12 nucleotide palindrome (position 2-13, GCGCCGUGGCGC) (Keeney et al, 1995), and a DNA oligonucleotide complementary to the palindrome or a deletion of the 15 5Ј nucleotides completely inhibits Ty3 RNA and tRNA i Met dimerization by NC protein (data not shown; see also Figure 5).…”

Section: Discussionmentioning

confidence: 91%

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The yeast Ty3 retrotransposon contains a 5'-3' bipartite primer-binding site and encodes nucleocapsid protein NCp9 functionally homologous to HIV-1 NCp7

et al. 1998

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Retroviruses, including HIV-1 and the distantly related yeast retroelement Ty3, all encode a nucleoprotein required for virion structure and replication. During an in vitro comparison of HIV-1 and Ty3 nucleoprotein function in RNA dimerization and cDNA synthesis, we discovered a bipartite primer-binding site (PBS) for Ty3 composed of sequences located at opposite ends of the genome. Ty3 cDNA synthesis requires the 3Ј PBS for primer tRNA i Met annealing to the genomic RNA, and the 5Ј PBS, in cis or in trans, as the reverse transcription start site. Ty3 RNA alone is unable to dimerize, but formation of dimeric tRNA i Met bound to the PBS was found to direct dimerization of Ty3 RNAtRNA i Met . Interestingly, HIV-1 nucleocapsid protein NCp7 and Ty3 NCp9 were interchangeable using HIV-1 and Ty3 RNA template-primer systems. Our findings impact on the understanding of non-canonical reverse transcription as well as on the use of Ty3 systems to screen for anti-NCp7 drugs.

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Section: Discussionmentioning

confidence: 86%

Section: Discussionmentioning

confidence: 86%

Section: Discussionmentioning

confidence: 91%

See 1 more Smart Citation

The yeast Ty3 retrotransposon contains a 5'-3' bipartite primer-binding site and encodes nucleocapsid protein NCp9 functionally homologous to HIV-1 NCp7

et al. 1998

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“…The PBS is part of a conserved 59-TGGTATCAGAGCC-39 sequence, which serves to complement the 39 sequence of tRNA (Met) and to activate the transcription of mRNA (Akama and Tanifuji 1989). The polypurine tract site with the conserved AGGGGGAG motif (Friant et al 1996) is speculated to prime the synthesis of second-strand DNA. Between the two sites, a large single ORF was identified.…”

Section: Resultsmentioning

confidence: 99%

A New Family of Ty1-copia-Like Retrotransposons Originated in the Tomato Genome by a Recent Horizontal Transfer Event

et al. 2009

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Rider is a novel and recently active Ty1-copia-like retrotransposon isolated from the T3238fer mutant of tomato. Structurally, it is delimited by a duplication of target sites and contains two long terminal direct repeats and an internal open reading frame, which encodes a Ty1-copia-type polyprotein with characteristic protein domains required for retrotransposition. The family of Rider elements has an intermediate copy number and is scattered in the chromosomes of tomato. Rider family members in the tomato genome share high sequence similarity, but different structural groups were identified (full-size elements, deletion derivatives, and solo LTRs). Southern blot analysis in Solanaceae species showed that Rider was a Lycopersicon-specific element. Sequence analysis revealed that among other plants, two Arabidopsis elements (named as Rider-like 1 and Rider-like 2) are most similar to Rider in both the coding and noncoding regions. RT-PCR analysis indicates that Rider is constitutively expressed in tomato plants. The phylogeny-based parsimony analysis and the sequence substitution analyses of these data suggest that these Rider-like elements originated from a recent introgression of Rider into the tomato genome by horizontal transfer 1-6 million years ago. Considering its transcriptional activity and the recent insertion of the element into at least two genes, Rider is a recently active retrotransposon in the tomato genome.

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“…1). Extended tRNA-vRNA interactions were also identified in avian retroviruses (14,15) and in yeast retrotransposon Ty1 (16) and proposed in HIV-2 (17).…”

mentioning

confidence: 89%

Dynamics of the HIV-1 Reverse Transcription Complex during Initiation of DNA Synthesis

Lanchy

Isel

Keith

et al. 2000

Journal of Biological Chemistry

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Initiation of human immunodeficiency virus-1 (HIV-1) reverse transcription requires formation of a complex containing the viral RNA (vRNA), tRNA 3 Lys and reverse transcriptase (RT). The vRNA and the primer tRNA 3 Lys form several intermolecular interactions in addition to annealing of the primer 3 end to the primer binding site (PBS). These interactions are crucial for the efficiency and the specificity of the initiation of reverse transcription. However, as they are located upstream of the PBS, they must unwind as DNA synthesis proceeds. Here, the dynamics of the complex during initiation of reverse transcription was followed by enzymatic probing. Our data revealed reciprocal effects of the tertiary structure of the vRNA⅐tRNA 3 Lys complex and reverse transcriptase (RT) at a distance from the polymerization site. The structure of the initiation complex allowed RT to interact with the template strand up to 20 nucleotides upstream from the polymerization site. Conversely, nucleotide addition by RT modified the tertiary structure of the complex at 10 -14 nucleotides from the catalytic site. The viral sequences became exposed at the surface of the complex as they dissociated from the tRNA following primer extension. However, the counterpart tRNA sequences became buried inside the complex. Surprisingly, they became exposed when mutations prevented the intermolecular interactions in the initial complex, indicating that the fate of the tRNA depended on the tertiary structure of the initial complex.Reverse transcription is a key step in the retroviral replication cycle (1, 2), during which the virus-encoded reverse transcriptase (RT), 1 which possesses RNA-and DNA-dependent DNA polymerase and RNase H activities (3), converts the genomic RNA into double-stranded DNA. In retroviruses, initiation of reverse transcription requires annealing of the 18 3Ј-terminal nucleotides of a cellular tRNA to the primer binding site (PBS), located near the 5Ј end of the RNA genome (4 -6).In human immunodeficiency virus type 1(HIV-1), a strong selective pressure maintains tRNA 3 Lys as primer. Mutating the PBS to match the 3Ј end of other tRNAs dramatically reduces viral replication, and rapid reversion to the wild-type PBS is observed (7-9). A similar situation also prevails in avian leukosis viruses (10). In vitro, HIV-1 RT is able to discriminate against non-self-tRNA primers (7, 11). Interestingly, the specificity of the initiation of HIV-1 reverse transcription correlates with virus-specific interactions between the primer tRNA 3 Lys and the viral RNA (vRNA). Chemical and enzymatic probing revealed intricate intermolecular interactions between the anticodon loop and stem, part of the variable loop of tRNA 3Lys , and sequences upstream of the PBS (12, 13) (Fig. 1). Extended tRNA-vRNA interactions were also identified in avian retroviruses (14, 15) and in yeast retrotransposon Ty1 (16) and proposed in HIV-2 (17).In HIV-1, the best-characterized specific intermolecular interaction involves the anticodon loop of tRNA 3Lys and an A-rich...

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Extended Interactions Between the Primer tRNAiMet and Genomic RNA of the Yeast Ty1 Retrotransposon

Cited by 58 publications

References 27 publications

The yeast Ty3 retrotransposon contains a 5'-3' bipartite primer-binding site and encodes nucleocapsid protein NCp9 functionally homologous to HIV-1 NCp7

The yeast Ty3 retrotransposon contains a 5'-3' bipartite primer-binding site and encodes nucleocapsid protein NCp9 functionally homologous to HIV-1 NCp7

A New Family of Ty1-copia-Like Retrotransposons Originated in the Tomato Genome by a Recent Horizontal Transfer Event

Dynamics of the HIV-1 Reverse Transcription Complex during Initiation of DNA Synthesis

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