Both neighboring codon adjacent nucleotides and codon optimality influence mRNA decay rates.

Area of Science:

• Molecular Biology
• Genetics
• Plant Science

Background:

• Codon optimality-mediated decay (COMD) is a key eukaryotic mRNA decay pathway.
• Conservation of COMD in plants remained unconfirmed.
• Understanding COMD in plants is crucial for gene expression regulation.

Purpose of the Study:

• To investigate the conservation of COMD in Arabidopsis thaliana.
• To identify sequence features influencing cotranslational mRNA decay rates in plants.
• To develop a model predicting mRNA decay based on codon frequencies.

Main Methods:

• Comparative analysis of codon usage bias and mRNA half-lives in Arabidopsis.
• Development of a codon-decay rate model.
• Computational identification of sequence features impacting decay.
• Analysis of published datasets from wheat and fission yeast.

Main Results:

• A codon-decay rate model explained 21% of decay rate variance in Arabidopsis.
• Codon optimality was not reading-frame dependent in Arabidopsis.
• Adjacent nucleotides of neighboring codons significantly influence mRNA decay rates.
• This influence is conserved in wheat and fission yeast.

Conclusions:

• Plants utilize a COMD pathway similar to yeast and humans.
• mRNA decay rates are influenced by codon sequence and adjacent nucleotides, independent of tRNA levels.
• This suggests selection for synonymous codons decoded via wobble base pairing.