Frequent GU wobble pairings reduce translation efficiency in Plasmodium falciparum

Sherwin Chan,Mats Wahlgren,Jun-Hong Ch’Ng,Jessada Thutkawkorapin

doi:10.1038/s41598-017-00801-9

Sherwin Chan, Mats Wahlgren + Show 2 more

Open Access

https://doi.org/10.1038/s41598-017-00801-9

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Abstract

Plasmodium falciparum genome has 81% A+T content. This nucleotide bias leads to extreme codon usage bias and culminates in frequent insertion of asparagine homorepeats in the proteome. Using recodonized GFP sequences, we show that codons decoded via G:U wobble pairing are suboptimal codons that are negatively associated to protein translation efficiency. Despite this, one third of all codons in the genome are GU wobble codons, suggesting that codon usage in P. falciparum has not been driven to maximize translation efficiency, but may have evolved as translational regulatory mechanism. Particularly, asparagine homorepeats are generally encoded by locally clustered GU wobble AAT codons, we demonstrated that this GU wobble-rich codon context is the determining factor that causes reduction of protein level. Moreover, insertion of clustered AAT codons also causes destabilization of the transcripts. Interestingly, more frequent asparagine homorepeats insertion is seen in single-exon genes, suggesting transcripts of these genes may have been programmed for rapid mRNA decay to compensate for the inefficiency of mRNA surveillance regulation on intronless genes. To our knowledge, this is the first study that addresses P. falciparum codon usage in vitro and provides new insights on translational regulation and genome evolution of this parasite.

Highlights

Degeneracy of the universal genetic code dictates that the 20 amino acids are decoded by 61 triplet codons
When GU wobble AAT codons were inserted in tandem that is reminiscent of asparagine homorepeats, the insertion caused destabilization of the transcripts
In this study we determine that GU wobble pairings are suboptimal for translation in P. falciparum

Summary

Introduction

Degeneracy of the universal genetic code dictates that the 20 amino acids are decoded by 61 triplet codons. Amino acid repeats usually increase the propensity for protein aggregation, so the expansion of asparagine homorepeats is intriguing Both codon usage bias and asparagine homorepeats had been the subject of previous studies[14,15,16,17,18,19,20,21]. Earlier studies on codon usage in P. falciparum were mainly conducted in silico, such as the computing of genome-wide ‘Relative synonymous codon usage’ values as well as describing codon optimality using ‘effective number of codons’ values between highly and lowly expressed genes[15,16,17, 21] To complement these in silico studies, we used GFP reporter assays to investigate the in vitro effect of different codon usages on translation elongation in Plasmodium falciparum. We discuss the possible driving forces for the pervasive use of GU wobble codons in the genome and their potential to reframe our understanding of gene regulation in the parasite

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