Direct long read visualization reveals metabolic interplay between two antimalarial drug targets

Area of Science:

• Genomics
• Parasitology
• Drug Resistance

Background:

• Genome amplification is a key adaptive strategy for malaria parasites, often conferring drug resistance.
• Amplification of the dihydroorotate dehydrogenase (DHODH) gene is linked to antimalarial drug resistance.
• The GTP cyclohydrolase I (GCH1) amplicon's role in drug resistance was previously unexplored beyond antifolate resistance.

Approach:

• Utilized long-read sequencing and single-read visualization to analyze Plasmodium falciparum parasite lines.
• Quantified tandem GCH1 amplicon copy numbers in relation to DHODH gene copy number.
• Examined prior selection experiments to understand the co-evolutionary dynamics of GCH1 and DHODH amplifications.

Key Points:

• Parasites with increased DHODH copies exhibited significantly higher numbers of tandem GCH1 amplicons (up to 9) compared to parental lines (3).
• GCH1 amplicon expansions occurred in stepwise increments (2-unit increases).
• Successful DHODH amplification was contingent upon pre-existing GCH1 amplicons in parasite lines.

Conclusions:

• The GCH1 locus appears to confer a fitness advantage to malaria parasites exposed to DHODH inhibitors.
• This suggests a metabolic link between GCH1 and DHODH pathways, crucial for parasite survival under drug pressure.
• Understanding genomic variation and metabolic pathway interactions is vital for developing new antimalarials.