Genome-wide comparative analysis of Oryza sativa (japonica) and Arabidopsis thaliana 5'-UTR sequences for translational regulatory signals

Abstract

Untranslated regions of eukaryotic genes contain elements that in combination with proteins/RNAs modulate translation of individual messenger RNAs. Elements present in 5Ј-UTRs that influence translational efficiency include AUG sequence context, and presence of uAUGs/uORFs. To assess the level of 5Ј-UTR mediated translational regulation in rice, a genome-wide computational analysis of rice 5Ј-UTRs was carried out in comparison with 5Ј-UTRs of Arabidopsis. Rice 5Ј-UTRs were generally longer and more GC-rich than those of Arabidopsis. 30% of rice and 34% of Arabidopsis cDNAs contained upstream AUG triplets (uAUGs). For both organisms, a higher proportion of uAUG-less cDNAs possessed start codons which conformed to the consensus sequence context compared to uAUG-containing cDNAs. Although the GC composition of the start codon context varied between and within rice and Arabidopsis, the critical positions, ϩ4 and Ϫ3, were conserved. 24% of rice and 30% of Arabidopsis cDNAs possessed upstream open reading frames (uORFs). Combinatorial analyses of start-codon context, uAUG context and context of uAUGs of upstream open reading frames of individual genes indicate that about 30-34% of genes in rice and Arabidopsis are likely to be influenced at translational level by signals present in 5Ј-UTR as they possess uAUG/uORFs with sequence context conforming to the consensus sequence There was very little conservation of uAUG positions or uORFs between rice and Arabidopsis. However, there was conservation of uAUG positions between rice, wheat and barley.

A Role for Nonsense-Mediated mRNA Decay in Plants: Pathogen Responses Are Induced in Arabidopsis thaliana NMD Mutants

“…In common with most NMD target gene analyses in other systems [2] – [4] , there was no convincing enrichment of any of these features amongst the common NMD genes in Arabidopsis ( Table S6 ). For example, 34% of the 206 common NMD genes encode transcripts with an upstream open reading frame (uORF), in comparison to 30% of all Arabidopsis genes [69] . Limiting these analyses to the 23 non-pathogen responsive genes allows us to exclude the effects of activation of the SA-mediated defence response in up-regulating genes that are not directly targeted by NMD.…”

Analysis of five novel putative constitutive gene promoters in transgenic rice plants

“…The UTRs within transcripts often determine gene expression by influencing mRNA stability and translation efficiency. About 30% of the genes in rice and Arabidopsis are likely to be influenced at the translational level by signals present in their 5′-UTR as these motifs possess uAUG/uORFs with sequence similarities to regulatory consensus sequences ( Shashikanth et al , 2008 ). A potential mechanism for uORFs to affect translational efficiency is therefore to act as a decoy from the principal ORF, and thereby potentially to cause premature termination, the triggering of mRNA decay via NMD (Nonsense-Mediated mRNA Decay), or a delay in the attachment of the ribosomal complex and thus the initiation of translation at the correct AUG start codon ( Lawless et al , 2009 ).…”

Upstream Open Reading Frame Mediated Translation of WNK8 Is Required for ABA Response in Arabidopsis

“…Approximately 50% of protein-encoding genes possess one or more uORFs in humans [ 39 ]. In plants, 24–30% of the 5′-UTR of mRNAs contains uORFs; however, only a few uORFs have been identified and characterized [ 40 , 41 ]. Therefore, it is necessary to further explore uORFs in plants and investigate their translational control mechanisms, which could provide a deeper understanding of plant development and adaptations to changing environments.…”