Failure to Relax Negative Supercoiling of DNA Is a Primary Cause of Mitotic Hyper-recombination in Topoisomerase-deficient Yeast Cells

Abstract

In the yeast Saccharomyces cerevisiae, DNA topoisomerases I and II can functionally substitute for each other in removing positive and negative DNA supercoils. Yeast ⌬top1 top2(ts) mutants grow slowly and present structural instability in the genome; over half of the rDNA repeats are excised in the form of extrachromosomal rings, and small circular minichromosomes strongly multimerize. Because these traits can be reverted by the extrachromosomal expression of either eukaryotic topoisomerase I or II, their origin is attributed to the persistence of unconstrained DNA supercoiling. Here, we examine whether the expression of the Escherichia coli topA gene, which encodes the bacterial topoisomerase I that removes only negative supercoils, compensates the phenotype of ⌬top1 top2(ts) yeast cells. We found that ⌬top1 top2(ts) mutants expressing E. coli topoisomerase I grow faster and do not manifest rDNA excision and minichromosome multimerization. Furthermore, the recombination frequency in repeated DNA sequences, which is increased by nearly two orders of magnitude in ⌬top1 top2(ts) mutants relative to the parental TOP؉ cells, is restored to normal levels when the bacterial topoisomerase is expressed. These results indicate that the suppression of mitotic hyper-recombination caused by eukaryotic topoisomerases I and II is effected mainly by the relaxation of negative rather than positive supercoils; they also highlight the potential of unconstrained negative supercoiling to promote homologous recombination.The budding yeast Saccharomyces cerevisiae has three structurally different DNA topoisomerases: topoisomerase I, a type IB enzyme encoded by TOP1; topoisomerase II, a type II enzyme encoded by TOP2; and topoisomerase III, a type IA enzyme encoded by TOP3 (For recent reviews see Refs. 1 and 2). Topoisomerase II is essential for cell viability because it is required to unlink intertwined pairs of replicated DNA domains at the time of mitosis (3). Another important role of topoisomerases is to prevent excessive supercoiling of DNA (4, 5). Yeast topoisomerase I efficiently relaxes the positive and negative DNA supercoils generated, respectively, in front of and behind the molecular ensembles that track along the double helix (6 -8). Because yeast null top1 mutants are viable (9, 10), the cellular roles of topoisomerase I must be fulfilled by yeast topoisomerase II, which is also efficient in the relaxation of positive and negative supercoils (Fig. 1). Conversely, the less abundant topoisomerase III does not have significant effects on the overall supercoiling of intracellular DNA (11).Genetic and biochemical studies have revealed that the DNA relaxation activity of yeast topoisomerases I and II has deep implications in genome stabilization (5, 12). Null top1 mutants have a high frequency of mitotic recombination in the rDNA cluster relative to TOPϩ cells (13). Single top2(ts) mutants, in which the weak topoisomerase II activity is abolished at 35°C, also show increased recombination in the rDNA (13) when grown at a perm...

Topoisomerase levels determine chemotherapy response in vitro and in vivo

“…2D and 4C). Studies in yeast suggest that an overall amount of topoisomerase activity may be required for cell viability because topoisomerase I/II double mutants exhibit more serious defects in DNA unwinding, chromatin structure, and cell cycle progression compared with either single mutant (33,34). If so, therapeutic poisoning of Top2A with simultaneous down-regulation of Top1 could cause cellular topoisomerase activity to fall below this crucial threshold, triggering cell death.…”

Topological constraints impair RNA polymerase II transcription and causes instability of plasmid-borne convergent genes

“…Stability of tandem rDNA repeats in yeast has been shown to be strongly dependent on DNA topoisomeases I and II, whereas this was not the case for direct repeats outside of the rDNA region (17). Hyper-recombination has been shown in plasmid-borne direct-repeats in double top1 top2 mutants (18). It has been proposed that this is mainly the result of the failure to relax the negative rather than the positive supercoiling of DNA (18).…”

“…Hyper-recombination has been shown in plasmid-borne direct-repeats in double top1 top2 mutants (18). It has been proposed that this is mainly the result of the failure to relax the negative rather than the positive supercoiling of DNA (18). Nevertheless, impairment of replication fork progression by obstacles or DNA lesions can lead to replication fork collapse that in turn could trigger recombination as a mechanism of replication restart (19).…”

Loss of Topoisomerase I leads to R-loop-mediated transcriptional blocks during ribosomal RNA synthesis

“…R-loops can also impede transcription elongation, as well as exposing the nontemplate strand to cleavage and recombination (for review, see Aguilera and GomezGonzalez 2008). Yeast top1D mutants show hyperrecombination of the rDNA array (Houseley et al 2007), while top1D top2-ts double mutants undergo major excisions of the rDNA repeats due to a failure to relax negative supercoils (Trigueros and Roca 2002).…”