Schizosaccharomyces pombe Retrotransposon Tf2 Mobilizes Primarily through Homologous cDNA Recombination

Abstract

The Tf2 retrotransposon, found in the fission yeast Schizosaccharomyces pombe, is nearly identical to its sister element, Tf1, in its reverse transcriptase-RNase H and integrase domains but is very divergent in the gag domain, the protease, the 5 untranslated region, and the U3 domain of the long terminal repeats. It has now been demonstrated that a neo-marked copy of Tf2 overexpressed from a heterologous promoter can mobilize into the S. pombe genome and produce true transposition events. However, the Tf2-neo mobilization frequency is 10-to 20-fold lower than that of Tf1-neo, and 70% of the Tf2-neo events are homologous recombination events generated independently of a functional Tf2 integrase. Thus, the Tf2 element is primarily dependent on homologous recombination with preexisting copies of Tf2 for its propagation. Finally, production of Tf2-neo proteins and cDNA was also analyzed; surprisingly, Tf2 was found to produce its reverse transcriptase as a single species in which it is fused to protease, unlike all other retroviruses and retrotransposons.Transposable elements constitute up to 50% of the eukaryotic genome (51, 53). Though they can act as positive forces in the evolution of an organism, both by providing part of the chromosomal architecture (30) and by providing a source of mutagens (1), they also represent a burden on the host cell genome and a potential threat to host cell viability, should they "jump" into an essential region of the genome or mediate a rearrangement thereof. Different transposable elements have developed different means to balance their survival with that of the host cell by controlling their spread within the genome. Most balancing mechanisms described thus far appear to involve control of either transposon expression or target site selection (9). These mechanisms often rely on host-specific factors, such as transcription factors (10, 27), splicing factors (47), and chromatin organization (58). Characterization of different transposable elements can therefore reveal both new mechanisms for control of element mobility and new hostelement interactions.Long terminal repeat (LTR)-type retrotransposons (hereafter referred to simply as retrotransposons) have been isolated from many different eukaryotic organisms, including fruit flies, maize, and the yeast Saccharomyces cerevisiae (6,23,(48)(49)(50). Retrotransposons resemble retroviruses in both genome structure and replication mechanism (9). Like retroviruses, they possess terminally redundant ends (LTRs), a primer binding site for the initiation of reverse transcription, and a polypurine tract that serves as the primer in second-strand synthesis of the cDNA copy of the element. A single mRNA encodes proteins homologous to the retroviral structural proteins capsid (CA) and, sometimes, nucleocapsid (NC) and to the retroviral enzymes protease (PR), reverse transcriptase-RNase H (RT), and integrase (IN). These proteins coassemble to form retrovirus-like particles in which reverse transcription of an RNA intermediate takes place. The res...

SREBP Controls Oxygen-Dependent Mobilization of Retrotransposons in Fission Yeast

“…A similar mechanism of cDNA mobilization has been observed for Ty elements in S. cerevisiae [36,37]. Mobilization of Tf2 by cDNA recombination to existing elements has been termed ''integration site recycling'' and may serve as a mechanism to protect the host cell genome while allowing Tf2 elements to evolve [23]. Collectively, these data demonstrate that Sre1 induces mobilization of Tf2 retrotransposons by homologous recombination in response to low oxygen.…”

“…Previous studies examined fission yeast Tf1 or Tf2 mobilization when these elements were highly overexpressed in the presence of oxygen from a heterologous promoter [23,32,33]. Interestingly unlike Tf1, the majority of Tf2 mobilization events (.70%) did not require the Tf2 integrase and thus occurred by cDNA recombination [23].…”

The diversity of retrotransposons in the yeast Cryptococcus neoformans

“…For instance, nearly all the retrotransposon families in both S. cerevisiae (Kim et al, 1998) and Sz. pombe (Levin and Boeke, 1992;Hoff et al, 1998) are still active, and there are no families represented just by solo LTRs, suggesting that elimination of nonfunctional elements is rapid in these species. In contrast, C. albicans has a large number of distinct families (Goodwin and Poulter, 2000).…”

Mapping genomic hotspots of DNA damage by a single-strand-DNA-compatible and strand-specific ChIP-seq method

“…5F). Tf2 mobilization is often mediated by integrase-independent recombination between its cDNA and pre-existing genomic copies of Tf2 (Hoff et al 1998;Sehgal et al 2007). We speculate that the binding of Rad52 to an immature form of Tf2 cDNA may contribute to this main mode of Tf2 transposition.…”