Evolution of Ty1 copy number control in yeast by horizontal transfer of agaggene

Abstract

Insertion of mobile DNA sequences typically has deleterious effects on host fitness, and thus diverse mechanisms have evolved to control mobile element proliferation across the tree of life. Mobility of the Ty1 retrotransposon in Saccharomyces yeasts is regulated by a novel form of copy number control (CNC) mediated by a self-encoded restriction factor derived from the Ty1 gag capsid gene that inhibits virus-like particle function. Here, we survey a panel of wild and human-associated strains of S. cerevisiae and S. paradoxus to investigate how genomic Ty1 content influences variation in Ty1 mobility. We observe high levels of mobility for a canonical Ty1 tester element in permissive strains that either lack full-length Ty1 elements or only contain full-length copies of the Ty1’ subfamily that have a divergent gag sequence. In contrast, low levels of canonical Ty1 mobility are observed in restrictive strains carrying full-length Ty1 elements containing canonical gag. Phylogenomic analysis of full-length Ty1 elements revealed that Ty1’ is the ancestral subfamily present in wild strains of S. cerevisiae, and that canonical Ty1 in S. cerevisiae is a derived subfamily that acquired gag from S. paradoxus by horizontal transfer and recombination. Our results provide evidence that variation in the ability of S. cerevisiae and S. paradoxus strains to repress canonical Ty1 transposition via CNC is encoded by the genomic content of different Ty1 subfamilies, and that self-encoded forms of transposon control can spread across species boundaries by horizontal transfer.

A natural variant of the essential host gene MMS21 restricts the parasitic 2-micron plasmid in Saccharomyces cerevisiae

“…Yeast species harbor a variety of SGEs including retrotransposable elements, RNA viruses and 2micron plasmids [13][14][15][16][17][18] . Yet, despite its long history as a popular model eukaryote, natural variation in cellular immunity factors against SGEs has been largely uncharacterized in S. cerevisiae and related species [19][20][21][22][23] . Here, we investigated whether S. cerevisiae strains harbor genetic variants that allow them to resist a highly successful SGE: 2micron plasmids.…”

“…Yeast species harbor a variety of SGEs including retrotransposable elements, RNA viruses and 2-micron (2μ) plasmids ( Rowley, 2017 ; Wickner, 1996 ; Kelly et al, 2012 ; Nakayashiki et al, 2005 ; Krastanova et al, 2005 ; Bleykasten-Grosshans and Neuvéglise, 2011 ). Yet, despite its long history as a popular model eukaryote, natural variation in cellular immunity factors against SGEs has been largely uncharacterized in S. cerevisiae and related species ( Rowley et al, 2016 ; Czaja et al, 2019 ; Scholes et al, 2001 ; Maxwell and Curcio, 2007 ; Rowley et al, 2018 ). Here, we investigated whether S. cerevisiae strains harbor genetic variants that allow them to resist a highly successful SGE: 2μ plasmids.…”