Abstract
Nonsense-mediated mRNA decay (NMD) is an RNA surveillance system that degrades mRNAs possessing premature translation termination codons (PTCs). Although NMD factors are well-conserved among eukaryotes, it is speculated that contexts of termination codons recognized as PTC are different depending on organisms.
We analyzed the contexts of positions of termination codons that are preferentially recognized as PTC in plants. The result indicated that PTC recognition in plants is dependent on distances between the termination codon and the 3' terminus of mRNA. In parallel, the termination codon positions in several species were comprehensively analyzed in silico. It was suggested that recognition motifs as PTCs in each organism would impose selective pressures on primary sequences of major mRNAs so that termination codons are not recognized by NMD. The positions of termination codon in natural mRNAs should reflect PTC recognition characteristics of each organism. Probably the NMD system influenced mRNA primary sequences through genome evolution.
