Checkpoint independence of most DNA replication origins in fission yeast

Background

In budding yeast, the replication checkpoint slows progress through S phase by inhibiting replication origin firing. In mammals, the replication checkpoint inhibits both origin firing and replication fork movement. To find out which strategy is employed in the fission yeast, Schizosaccharomyces pombe, we used microarrays to investigate the use of origins by wild-type and checkpoint-mutant strains in the presence of hydroxyurea (HU), which limits the pool of deoxyribonucleoside triphosphates (dNTPs) and activates the replication checkpoint. The checkpoint-mutant cells carried deletions either of rad3 (which encodes the fission yeast homologue of ATR) or cds1 (which encodes the fission yeast homologue of Chk2).

Results

Our microarray results proved to be largely consistent with those independently obtained and recently published by three other laboratories. However, we were able to reconcile differences between the previous studies regarding the extent to which fission yeast replication origins are affected by the replication checkpoint. We found (consistent with the three previous studies after appropriate interpretation) that, in surprising contrast to budding yeast, most fission yeast origins, including both early- and late-firing origins, are not significantly affected by checkpoint mutations during replication in the presence of HU. A few origins (~3%) behaved like those in budding yeast: they replicated earlier in the checkpoint mutants than in wild type. These were located primarily in the heterochromatic subtelomeric regions of chromosomes 1 and 2. Indeed, the subtelomeric regions defined by the strongest checkpoint restraint correspond precisely to previously mapped subtelomeric heterochromatin. This observation implies that subtelomeric heterochromatin in fission yeast differs from heterochromatin at centromeres, in the mating type region, and in ribosomal DNA, since these regions replicated at least as efficiently in wild-type cells as in checkpoint-mutant cells.

Conclusion

The fact that ~97% of fission yeast replication origins – both early and late – are not significantly affected by replication checkpoint mutations in HU-treated cells suggests that (i) most late-firing origins are restrained from firing in HU-treated cells by at least one checkpoint-independent mechanism, and (ii) checkpoint-dependent slowing of S phase in fission yeast when DNA is damaged may be accomplished primarily by the slowing of replication forks.     

A flavonoid, 5-hydroxy-3,7-dimethoxyflavone,from Kaempferia parviflora Wall. Ex. Baker as an inhibitor of Ca2+ signal-mediated cell-cycle regulation in yeast

Calcium (Ca²⁺) signal transduction pathways play important roles in the regulation of diverse biological processes in eukaryotes ranging from unicellular (e.g., yeasts) to complex multicellular (e.g., humans) organisms. Small-molecule inhibitors of Ca²⁺-signaling pathways in humans can be of great medical importance, as represented by the immunosuppressants FK506 and cyclosporine A. A high-throughput drug screening assay for inhibitors of Ca²⁺-signaling has been developed on the basis of the ability of test compounds to restore the severe growth defect of a Ca²⁺-sensitive zds1 null-mutant strain YNS17 of Saccharomyces cerevisiae in a medium containing a high concentration of calcium ions. A previous screening of Thai medicinal plants using this yeast-based assay indicated that the crude extract of Kaempferia parviflora Wall. Ex. Baker contains a potent inhibitory activity. The aim of this study was to isolate and characterize the pure compound(s) responsible for this inhibitory activity against Ca²⁺-mediated cell-cycle regulation in yeast. Dichloromethane and methanol extracts of K. parviflora rhizomes were subjected to bioassay-mediated chromatographic fractionation using this yeast [YNS17 (Δzds1) strain]-based assay to screen for and select positive fractions. From the dichloromethane extract, four known flavonoid compounds with significant inhibitory bioactivity were obtained: compounds 1 (5-hydroxy-3,7-dimethoxyflavone), 2 (5-hydroxy-7-methoxyflavone), 3 (5-hydroxy-3,7,4’-trimethoxyflavone) and 4 (5,7-dimethoxyflavone). The inhibitory activity of all four compounds was dose-dependent. Compound 1 exhibited the highest activity and with no observed cytotoxic activity against the yeast. The Ca²⁺ induced severe growth defect, abnormal budding morphology, and G2 cell-cycle delay of the Δzds1 yeast strain were all alleviated or abrogated by 200 μM compound 1. Therefore, we conclude that 5-hydroxy-3,7-dimethoxyflavone possesses a potent inhibitory activity against the Ca²⁺-mediated cell-cycle regulation.     

Enforcement of late replication origin firing by clusters of short G-rich DNA sequences

Previous studies in budding yeast suggested that the default firing time of most DNA replication origins is early in S phase and that origins can be forced to fire later by proximity to certain cis-acting sequences. However, these cis-acting sequences were not well defined. We have attempted to characterize cis-acting sequences that affect replication timing in the fission yeast. We identified a stretch of 200 bp that was sufficient to compel nearby origins to fire late. The 200-bp stretch was able to force an origin to fire late whether adjacent to the origin or approximately 800 bp away in opposite orientation. The stretch contains a cluster of three close matches to a G-rich, 10-bp late consensus sequence (LCS). The three LCS elements cooperate with each other and with other sequences within the 200-bp stretch to enforce late replication. Although only a few origins that fire in very late S phase have been identified in fission yeast, all of them are located close to a cluster of LCS elements.