The selfish yeast plasmid utilizes the condensin complex and condensed chromatin for faithful partitioning

Author summary The multi-copy 2-micron plasmid, a nearly ubiquitous resident in budding yeast nuclei, has almost the same stability as its host's chromosomes. The plasmid partitioning system, together with host-coded factors, apparently positions plasmid molecules at chromosome sites, enabling their chromosome-coupled segregation. Here, we demonstrate that plasmid association with chromosomes is not random. In vegetative yeast cells, telomeres and centromeres are among preferred plasmid localization sites, with an obvious bias favoring the former. Increased plasmid missegregation under forced non-disjunction of condensed chromosome loci such as telomeres and rDNA, or under induced missegregation of chromosome XII harboring the rDNA array, suggest a possible role for the condensin complex in plasmid segregation. This notion is supported by the interaction of the condensin component Brn1 with the plasmid partitioning proteins, its recruitment to the plasmid partitioning locus with the assistance of these proteins, and increased plasmid loss when Brn1 is inactivated. Our collective findings suggest that the plasmid targets condensed/heterochromatin-like chromosome regions for its chromosome association. The plasmid may thus minimize perturbations of genome functions, and optimize its evolutionary fitness without compromising that of the host. Analogous strategies may be utilized by selfish DNA elements in general, including the episomes of certain mammalian viruses. Equipartitioning by chromosome association and copy number correction by DNA amplification are at the heart of the evolutionary success of the selfish yeast 2-micron plasmid. The present analysis reveals frequent plasmid presence near telomeres (TELs) and centromeres (CENs) in mitotic cells, with a preference towards the former. Inactivation of Cdc14 causes plasmid missegregation, which is correlated to the non-disjunction of TELs (and of rDNA) under this condition. Induced missegregation of chromosome XII, one of the largest yeast chromosomes which harbors the rDNA array and is highly dependent on the condensin complex for proper disjunction, increases 2-micron plasmid missegregation. This is not the case when chromosome III, one of the smallest chromosomes, is forced to missegregate. Plasmid stability decreases when the condensin subunit Brn1 is inactivated. Brn1 is recruited to the plasmid partitioning locus (STB) with the assistance of the plasmid-coded partitioning proteins Rep1 and Rep2. Furthermore, in a dihybrid assay, Brn1 interacts with Rep1-Rep2. Taken together, these findings support a role for condensin and/or condensed chromatin in 2-micron plasmid propagation. They suggest that condensed chromosome loci are among favored sites utilized by the plasmid for its chromosome-associated segregation. By homing to condensed/quiescent chromosome locales, and not over-perturbing genome homeostasis, the plasmid may minimize fitness conflicts with its host. Analogous persistence strategies may be utilized by other extrachromosomal selfish genomes, for example, episomes of mammalian viruses that hitchhike on host chromosomes for their stable maintenance.

Automated summary

The study reveals that the 2-micron plasmid in yeast preferentially targets telomeres and centromeres on condensed chromosomes for its association and segregation. The presence of plasmids near these chromosome sites minimizes disruptions to genome function and enhances evolutionary fitness. The interaction between the plasmid and host factors, such as the condensin complex, plays a crucial role in ensuring proper plasmid segregation and stability.