Evidence for cis- and trans-acting element coevolution of the 2-microns circle genome in Saccharomyces cerevisiae

We compared the DNA sequence of the yeast 2-microns plasmid cis-acting STB and transacting REP1 partition loci of laboratory haploid and industrial amphiploid strains. Several industrial strains had a unique STB sequence (type 1) sharing only 70% homology with laboratory STB (type 2). Type 1 plasmids had a REP1 protein with 6-10% amino acid substitutions when compared to REP1 of type 2 plasmids. All 2-microns variants that shared a similar STB consensus sequence exhibited a high degree of REP1 nucleotide and amino acid sequence conservation. These observations suggest molecular coevolution of trans-acting elements with cognate target DNA structure. Based on DNA sequencing and Southern hybridization analyses, we classified 2-microns variants into two main evolutionary lineages that differ at STB as well as REP1 loci. The role of molecular coevolution in yeast intra- and interspecies plasmid evolution was discussed.