RecQ helicases in the malaria parasite Plasmodium falciparum affect genome stability, gene expression patterns and DNA replication dynamics.

Abstract

The malaria parasite Plasmodium falciparum has evolved an unusual genome structure. The 33 majority of the genome is relatively stable, with mutation rates similar to most eukaryotic 34 species. However, some regions are very unstable with high recombination rates, driving the 35 generation of new immune evasion-associated var genes. The molecular factors controlling 36 the inconsistent stability of this genome are not known. Here we studied the roles of the two 37 putative RecQ helicases in P. falciparum, PfBLM and PfWRN. When PfWRN was knocked 38 down, recombination rates increased four-fold, generating chromosomal abnormalities, a 39 high rate of chimeric var genes and many microindels, particularly in known ‘fragile sites’. 40 This is the first identification of a gene involved in suppressing recombination and 41 maintaining genome stability in Plasmodium. By contrast, no change in mutation rate 42 appeared when the second RecQ helicase, PfBLM, was mutated. At the transcriptional 43 level, however, both helicases evidently modulate the transcription of large cohorts of genes, 44 with several hundred genes – including a large proportion of vars – showing deregulated 45 expression in each RecQ mutant. Aberrant processing of stalled replication forks is a 46 possible mechanism underlying elevated mutation rates and this was assessed by 47 measuring DNA replication dynamics in the RecQ mutant lines. Replication forks moved 48 slowly and stalled at elevated rates in both mutants, confirming that RecQ helicases are 49 required for efficient DNA replication. Overall, this work identifies the Plasmodium RecQ 50 helicases as major players in DNA replication, antigenic diversification and genome stability 51 in the most lethal human malaria parasite, with important implications for genome evolution 52 in this pathogen.