Sequence diversity of yeast 2 microns RAF gene and its co-evolution with STB and REP1

Despite the extensive study of yeast 2 microns plasmid, the exact function of plasmid-encoded RAF gene is not clear. Variants of 2 microns plasmids from industrial Saccharomyces cerevisiae yeasts were isolated and characterized. Sequencing of RAF alleles revealed about 8% nucleotide and 10% amino acid diversities between 2 microns variants of closely related strains, RAF sequence variations were correlated with STB-REP1 sequence diversity. We also used restriction fragment length polymorphism linkage to screen a large number of yeast strains from different fermentation industries. The results clearly show a tight linkage of STB-REP1-RAF variations. Thus, our observations suggest that plasmid-borne cis- and trans-acting elements co-evolved to form an optimal molecular parasite and that RAF may play a role in active plasmid partitioning.