Uracil moieties in Plasmodium falciparum genomic DNA

Abstract

Plasmodium falciparum parasites undergo multiple genome duplication events during their development. Within the intraerythrocytic stages, parasites encounter an oxidative environment and DNA synthesis necessarily proceeds under these circumstances. In addition to these conditions, the extreme AT bias of the P. falciparum genome poses further constraints for DNA synthesis. Taken together, these circumstances may allow appearance of damaged bases in the Plasmodium DNA . Here, we focus on uracil that may arise in DNA either via oxidative deamination or thymine‐replacing incorporation. We determine the level of uracil at the ring, trophozoite, and schizont intraerythrocytic stages and evaluate the base‐excision repair potential of P. falciparum to deal with uracil‐ DNA repair. We find approximately 7–10 uracil per million bases in the different parasite stages. This level is considerably higher than found in other wild‐type organisms from bacteria to mammalian species. Based on a systematic assessment of P. falciparum genome and transcriptome databases, we conclude that uracil‐ DNA repair relies on one single uracil‐ DNA glycosylase and proceeds through the long‐patch base‐excision repair route. Although potentially efficient, the repair route still leaves considerable level of uracils in parasite DNA , which may contribute to mutation rates in P. falciparum .

Rapid and quantitative antimalarial drug efficacy testing via the magneto-optical detection of hemozoin

“…In fact, our analysis shows that 25 ± 15% and 65 ± 15% of the total hemozoin is produced during the ring and the trophozoite stage, respectively, while less than 10% of hemozoin production is observed during the schizont stage. In summary, the hemozoin production characteristics determined by the RMOD method are in accordance with the primary functions of the different developmental stages and the previously proposed hemozoin production characteristics 21 – 26 . After the schizonts rupture, the hemozoin is released and the merozoites start a new cycle by invading new red blood cells.…”

“…Based on the synchronization window of 8 ± 4 h, characteristic to the cultures at the beginning of the assay, and the numerous washing steps applied before assay initiation, we presume that most of the hemozoin detected at assay initiation was produced by the parasites of the actual intraerythrocytic cycle. A steep increase in hemozoin concentration is observable starting from ~ 6-12 h of parasite age and lasting until ~ 34 h. The corresponding parasite stages, i.e., the mid-late ring and the first half of the trophozoite stages can be classified as the G1 phase of the cell cycle of P. falciparum, suggesting an increased rate of metabolic processes taking place during this time [18][19][20] . After ~ 34 h, the late trophozoite stage is the period of DNA replication, aka.…”

“…the S phase. It is followed by the schizont stage, when the packaging of genetic material occurs to create new merozoites and, thus, low hemoglobin metabolism is expected [18][19][20] . In fact, our analysis shows that 25 ± 15% and 65 ± 15% of the total hemozoin is produced during the ring and the trophozoite stage, respectively, while less than 10% of hemozoin production is observed during the schizont stage.…”

Genome-wide alterations of uracil distribution patterns in human DNA upon chemotherapeutic treatments

“…Densitometry was done using ImageJ (Fiji) software (National Institutes of Health, US). Analysis of the data and the calculation of the number of deoxyuridine nucleotides in the unknown genomic DNA was described before ( Molnár et al, 2018 ; Róna et al, 2016 ). Briefly, the number of uracil/million bases in the unknown samples were determined by interpolating their normalized intensities to the calibration curve of the standard.…”

Genome-wide alterations of uracil distribution patterns in human DNA upon chemotherapeutic treatments

“…Densitometry was done using ImageJ (Fiji) software (National Institutes of Health, US). Analysis of the data and the calculation of the number of deoxyuridine nucleotides in the unknown genomic DNA was described before (Molnár, Marton, Izrael, Pálinkás, & Vértessy, 2018; Róna et al, 2016). Briefly, the number of uracil/million bases in the unknown samples were determined by interpolating their normalized intensities to the calibration curve of the standard.…”