DNA replication dynamics are associated with genome composition in Plasmodium species

Abstract

Plasmodium species have variable genome compositions: many have an A/T-content of at least 80% while others are similar in composition to human cells. Here, we made a direct comparison of DNA replication dynamics in two Plasmodium species whose genomes differ by ~20% A/T-content. This yielded fundamental insights into how DNA composition may affect replication. The highly A/T-biased genome of P. falciparum showed unusual replication dynamics that were not observed in the more balanced P. knowlesi - which had dynamics more like those of human cell lines. We observed that replication forks moved 50% slower in P. falciparum than in P. knowlesi. In P. falciparum, replication forks slowed down over the course of S-phase whereas in P. knowlesi, fork speed increased as in human cells. Furthermore, in both P. knowlesi and human cells, replication forks were strikingly slowed by sequences of particularly high A/T-bias, but in P. falciparum, although replication forks were inherently slow, they were not particularly slow in such biased sequences. Thus, the replisome of P. falciparum may have evolved alongside its extremely biased genome, making it unusually robust to sequence bias. Since several antimalarial drugs act to stall DNA replication, this study may have implications for the effectiveness of, and development of, antimalarial therapies.