Analysis of a Ty1‐less variant of Saccharomyces paradoxus: the gain and loss of Ty1 elements

Abstract

Because Ty elements transpose through an RNA intermediate, element accumulation through retrotransposition must be regulated or offset by element loss to avoid uncontrolled genome expansion. Here we examine the fate of Ty sequences in Saccharomyces strain 337, a strain that is reported to lack Ty1 and Ty2 elements, but contains remnant solo long terminal repeats (LTRs). Although strain 337 was initially classified as Saccharomyces cerevisiae, our work indicates that this strain is more closely related to S. paradoxus. Several degenerate Ty1 and Ty2 LTRs were mapped to the same insertion sites as full-length Ty1 and Ty2 elements in S. cerevisiae, suggesting that this strain lost Ty elements by LTR-LTR recombination. Southern analysis indicates that strain 337 also lacks Ty4 and Ty5 elements. We estimated the rates of element gain and loss in this strain by introducing a single transpositioncompetent Ty1 element. The results indicate that Ty1 retrotransposition occurs at a much higher rate than elimination, suggesting that copy-number-dependent cofactors or environmental conditions contribute to the loss of Ty elements in this genome.

Extension of Saccharomyces paradoxus Chronological Lifespan by Retrotransposons in Certain Media Conditions Is Associated with Changes in Reactive Oxygen Species

“…We used a plasmid to introduce copies of a Ty1 retrotransposon into the genome of a Ty-less lab strain of S. paradoxus (Garfinkel et al 2003;Moore et al 2004) to address the impact of retrotransposons on yeast chronological lifespan. Conditions to induce Ty1 mobility were varied to obtain strains with different Ty1 copy numbers, and the approximate Ty1 copy number in clonal populations was determined through quantitative PCR.…”

“…LTR retrotransposons are also referred to as extrachromosomally primed (EP) retrotransposons, since they code for a protein that forms a cytoplasmic virus-like particle in which the retrotransposon RNA is packaged and reverse transcribed by an element-encoded reverse transcriptase prior to integration into a genomic site (Beauregard et al 2008). S. paradoxus is a very closely related species to S. cerevisiae, and a strain of S. paradoxus has been reported to completely lack sequences from the coding regions of Ty retrotransposons (Moore et al 2004). This is an exceptional system, since the multicopy nature of retrotransposons typically prevents the generation of populations of a species that do not have retrotransposons.…”

Single-Nucleotide-Specific Targeting of the Tf1 Retrotransposon Promoted by the DNA-Binding Protein Sap1 of Schizosaccharomyces pombe

“…These data indicate that Sap1 contributes to the efficiency and position of Tf1 integration. KEYWORDS Sap1; Tf1; integration; transposition; Schizosaccharomyces pombe R ETROTRANSPOSONS are pervasive among eukaryotes and, in many cases, account for a substantial portion of the host genome (Moore et al 2004;Scheifele et al 2009;Levin and Moran 2011). The ability of these elements to selectively integrate into specific target sequences has been paramount to their success because the employment of specific targeting mechanisms has allowed these retrotransposons to propagate within host genomes without disrupting genes and compromising the host's survival (Levin and Moran 2011).…”

Posttranslational interference of Ty1 retrotransposition by antisense RNAs

“…We have used a Ty1-less strain of Saccharomyces paradoxus (14) to study a Ty1 copy number control (CNC) system that acts posttranscriptionally and may inhibit reverse transcription (15). CNC requires Ty1 sequences, but occurs when a multicopy pGTy1 element is repressed or contains a minimal segment of mostly GAG sequence.…”