Forces acting on codon bias in malaria parasites

Area of Science:

• Genomics
• Molecular Biology
• Parasitology

Background:

• Malaria parasites, particularly Plasmodium falciparum, possess highly AT-biased genomes.
• Codon bias, the non-uniform usage of synonymous codons, is a significant genomic feature in many organisms.

Purpose of the Study:

• To investigate the composition of synonymous codons and stop codons in the core genomes of malaria parasites.
• To understand the influence of local DNA context and gene expression levels on codon bias across different Plasmodium species.

Main Methods:

• Analysis of synonymous coding sites and stop codons in the genomes of Plasmodium falciparum, Plasmodium vivax, and Plasmodium berghei.
• Examination of DNA dinucleotide composition (CpG, CpC) and codon usage bias (A3:G3, T3:C3 ratios) in relation to gene expression levels.

Main Results:

• Local DNA context, including CpG suppression and CpC enhancement, impacts codon bias similarly across P. falciparum, P. vivax, and P. berghei.
• Intense gene expression in P. falciparum and P. berghei correlates with increased A3:G3 bias and reduced T3:C3 bias at 2-fold synonymous sites.
• Highly expressed genes in these species show a strong bias towards TAA stop codons and an increase in the TAAA tetranucleotide.

Conclusions:

• Expression-linked codon usage patterns suggest adaptation to tRNA pools and avoidance of translation-slowing interactions.
• The observed AT-richness and codon bias in Plasmodium may represent a fitness adaptation.
• Distinct lifecycle and population dynamics might explain the lower codon bias observed in Plasmodium vivax.