Saccharomyces cerevisiae RNA lariat debranching enzyme, Dbr1p, is required for completion of reverse transcription by the retrovirus-like element Ty1 and cleaves branched Ty1 RNAs

2021 ◽  
Vol 296 (2) ◽  
pp. 409-422
Author(s):  
Thomas M. Menees
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Reverse Transcription ◽  
Debranching Enzyme

scholarly journals Multiple molecular determinants for retrotransposition in a primer tRNA.

1995 ◽  
Vol 15 (1) ◽  
pp. 217-226 ◽  
Author(s):  
J B Keeney ◽  
K B Chapman ◽  
V Lauermann ◽  
D F Voytas ◽  
S U Aström ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Reverse Transcription ◽  
Primer Binding Site ◽  
Specific Interactions ◽  
Acceptor Stem ◽  
Transcription Process ◽  
Molecular Determinants ◽  
Genetic Assay ◽  
Strong Stop ◽  
Interspecies Hybrid

Retroviruses and long terminal repeat-containing retroelements use host-encoded tRNAs as primers for the synthesis of minus strong-stop DNA, the first intermediate in reverse transcription of the retroelement RNA. Usually, one or more specific tRNAs, including the primer, are selected and packaged within the virion. The reverse transcriptase (RT) interacts with the primer tRNA and initiates DNA synthesis. The structural and sequence features of primer tRNAs important for these specific interactions are poorly understood. We have developed a genetic assay in which mutants of tRNA(iMet), the primer for the Ty1 retrotransposon of Saccharomyces cerevisiae, can be tested for the ability to serve as primers in the reverse transcription process. This system allows any tRNA mutant to be tested, regardless of its ability to function in the initiation of protein synthesis. We find that mutations in the T psi C loop and the acceptor stem regions of the tRNA(iMet) affect transposition most severely. Conversely, mutations in the anticodon region have only minimal effects on transposition. Further study of the acceptor stem and other mutants demonstrates that complementarity to the element primer binding site is a necessary but not sufficient requirement for effective tRNA priming. Finally, we have used interspecies hybrid initiator tRNA molecules to implicate nucleotides in the D arm as additional recognition determinants. Ty3 and Ty1, two very distantly related retrotransposons, require similar molecular determinants in this primer tRNA for transposition.

scholarly journals Ty1 Mobilizes Subtelomeric Y′ Elements in Telomerase-Negative Saccharomyces cerevisiae Survivors

2004 ◽  
Vol 24 (22) ◽  
pp. 9887-9898 ◽  
Author(s):  
Patrick H. Maxwell ◽  
Candice Coombes ◽  
Alison E. Kenny ◽  
Joseph F. Lawler ◽  
Jef D. Boeke ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Transcription Factor ◽  
Cell Division ◽  
Long Terminal Repeat ◽  
Reverse Transcription ◽  
Telomere Maintenance ◽  
Nonpermissive Temperature ◽  
Telomeric Dna ◽  
Copy Numbers ◽  
Ty1 Retrotransposition

ABSTRACT When telomerase is inactivated in Saccharomyces cerevisiae, telomeric DNA shortens with every cell division, and cells stop dividing after ∼100 generations. Survivors that form in these senescent populations and resume growing have variably amplified arrays of subtelomeric Y′ elements. We marked a chromosomal Y′ element with the his3AI retrotransposition indicator gene and found that Y′HIS3 cDNA was incorporated into the genome at ∼10- to 1,000-fold-higher frequencies in survivors compared to telomerase-positive strains. Y′HIS3 cDNA mobility was significantly reduced if assayed at 30°C, a nonpermissive temperature for Ty1 retrotransposition, or in the absence of Tec1p, a transcription factor for Ty1. Microarray analysis revealed that Y′ RNA is preferentially associated with Ty1 virus-like particles (VLPs). Genomic copies of Y′HIS3 cDNA typically have downstream oligo(A) tracts, followed by a complete Ty1 long terminal repeat and TYA1 or TYB1 sequences. These data are consistent with the use of Ty1 cDNA to prime reverse transcription of polyadenylated Y′ RNA within Ty1 VLPs. Unmarked Y′-oligo(A)-Ty1 cDNA was also detected in survivors, reaching copy numbers of ∼10−2 per genome. We propose that Y′-oligo(A)-Ty1 cDNA recombines with Y′ elements at eroding telomeres in survivors and may play a role in telomere maintenance in the absence of telomerase.

Characterization of products of TY1-mediated reverse transcription in Saccharomyces cerevisiae

1991 ◽  
Vol 226-226 (1-2) ◽  
pp. 145-153 ◽  
Author(s):  
Frank Müller ◽  
Wernher Laufer ◽  
Uwe Pott ◽  
Michael Ciriacy
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Reverse Transcription

Posttranslational Inhibition of Ty1 Retrotransposition by Nucleotide Excision Repair/Transcription Factor TFIIH Subunits Ssl2p and Rad3p

Genetics ◽  
1998 ◽  
Vol 148 (4) ◽  
pp. 1743-1761
Author(s):  
Bum-Soo Lee ◽  
Conrad P Lichtenstein ◽  
Brenda Faiola ◽  
Lori A Rinckel ◽  
William Wysock ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Transcription Factor ◽  
Nucleotide Excision Repair ◽  
Reverse Transcription ◽  
Excision Repair ◽  
Dna Helicase ◽  
Site Preferences ◽  
Nucleotide Excision ◽  
Ty1 Retrotransposition ◽  
High Level

Abstract rtt4-1 (regulator of Ty transposition) is a cellular mutation that permits a high level of spontaneous Ty1 retrotransposition in Saccharomyces cerevisiae. The RTT4 gene is allelic with SSL2 (RAD25), which encodes a DNA helicase present in basal transcription (TFIIH) and nucleotide excision repair (NER) complexes. The ssl2-rtt (rtt4-1) mutation stimulates Ty1 retrotransposition, but does not alter Ty1 target site preferences, or increase cDNA or mitotic recombination. In addition to ssl2-rtt, the ssl2-dead and SSL2-1 mutations stimulate Ty1 transposition without altering the level of Ty1 RNA or proteins. However, the level of Ty1 cDNA markedly increases in the ssl2 mutants. Like SSL2, certain mutations in another NER/TFIIH DNA helicase encoded by RAD3 stimulate Ty1 transposition. Although Ssl2p and Rad3p are required for NER, inhibition of Ty1 transposition is independent of Ssl2p and Rad3p NER functions. Our work suggests that NER/TFIIH subunits antagonize Ty1 transposition posttranslationally by inhibiting reverse transcription or destabilizing Ty1 cDNA.

scholarly journals An anomalous Ty1 structure attributed to an error in reverse transcription

1986 ◽  
Vol 6 (4) ◽  
pp. 1334-1338
Author(s):  
B Errede ◽  
M Company ◽  
R Swanstrom
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Nucleotide Sequence ◽  
Reverse Transcription ◽  
Inverted Repeat ◽  
Repeat Structure

We have determined the nucleotide sequence of both delta elements of a Ty1 transposon inserted near the CYC7 gene in the Saccharomyces cerevisiae CYC7-H2 mutant. The upstream delta element in this Ty1 has an unusual inverted repeat structure that may have been formed by an error during reverse transcription.

Involvement of cDNA in homologous recombination between Ty elements in Saccharomyces cerevisiae

1992 ◽  
Vol 12 (4) ◽  
pp. 1613-1620
Author(s):  
C Melamed ◽  
Y Nevo ◽  
M Kupiec
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Homologous Recombination ◽  
Reverse Transcriptase ◽  
Gene Conversion ◽  
Reverse Transcription ◽  
Repeated Sequences ◽  
Homologous Gene ◽  
Ty Elements ◽  
Low Level ◽  
Ty Element

Strains carrying a marked Ty element (TyUra) in the LYS2 locus were transformed with plasmids bearing a differently marked Ty1 element (Ty1Neo) under the control of the GAL promoter. When these strains were grown in glucose, a low level of gene conversion events involving TyUra was detected. Upon growth on galactose an increase in the rate of gene conversion was seen. This homologous recombination is not the consequence of increased levels of transposition. When an intron-containing fragment was inserted into Ty1Neo, some of the convertants had the intron removed, implying an RNA intermediate. Mutations that affect reverse transcriptase or reverse transcription of Ty1Neo greatly reduce the induction of recombination in galactose. Thus, Ty cDNA is involved in homologous gene conversion with chromosomal copies of Ty elements. Our results have implications about the way families of repeated sequences retain homogeneity throughout evolution.

RNA Lariat Debranching Enzyme as a Retroviral and Long-Terminal-Repeat Retrotransposon Host Factor

2020 ◽  
Vol 7 (1) ◽  
pp. 189-202
Author(s):  
Thomas M. Menees
Keyword(s):  
Long Terminal Repeat ◽  
Viral Entry ◽  
Reverse Transcription ◽  
Immune Deficiency Syndrome ◽  
Terminal Repeat ◽  
Host Factors ◽  
Branch Points ◽  
Debranching Enzyme ◽  
Long Terminal Repeat Retrotransposon ◽  
Hiv 1

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.

scholarly journals An anomalous Ty1 structure attributed to an error in reverse transcription.

1986 ◽  
Vol 6 (4) ◽  
pp. 1334-1338 ◽  
Author(s):  
B Errede ◽  
M Company ◽  
R Swanstrom
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Nucleotide Sequence ◽  
Reverse Transcription ◽  
Inverted Repeat ◽  
Repeat Structure

We have determined the nucleotide sequence of both delta elements of a Ty1 transposon inserted near the CYC7 gene in the Saccharomyces cerevisiae CYC7-H2 mutant. The upstream delta element in this Ty1 has an unusual inverted repeat structure that may have been formed by an error during reverse transcription.

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