Conserved upstream open reading frames in higher plants

Abstract

Background: Upstream open reading frames (uORFs) can down-regulate the translation of the main open reading frame (mORF) through two broad mechanisms: ribosomal stalling and reducing reinitiation efficiency. In distantly related plants, such as rice and Arabidopsis, it has been found that conserved uORFs are rare in these transcriptomes with approximately 100 loci. It is unclear how prevalent conserved uORFs are in closely related plants.

Results: We used a homology-based approach to identify conserved uORFs in five cereals (monocots) that could potentially regulate translation. Our approach used a modified reciprocal best hit method to identify putative orthologous sequences that were then analysed by a comparative R-nomics program called uORFSCAN to find conserved uORFs.

Conclusion: This research identified new genes that may be controlled at the level of translation by conserved uORFs. We report that conserved uORFs are rare (<150 loci contain them) in cereal transcriptomes, are generally short (less than 100 nt), highly conserved (50% median amino acid sequence similarity), position independent in their 5'-UTRs, and their start codon context and the usage of rare codons for translation does not appear to be important.

Figure 1

Tran_Figure1.eps. 'Overview of the uORFSCAN pipeline'. The pipeline consists of four steps: 1) Identifying putative orthologues using a modified reciprocal best hit (rbh) method, 2) Clustering of orthologues according to how many cereal species they are found in, 3) Using uORFSCAN program to find conserved uORFs using a comparative approach, and 4) manual curation of predicted conserved cereal and Arabidopsis uORFs.

Figure 2

Tran_Figure2.eps. 'The position of conserved uORFs within their 5'-UTRs'. It contains rice uORFs conserved in four other cereals and in Arabidopsis.

Figure 3

Tran_Figure3.eps. 'A frequency distribution of the length (nt) of rice uORFs conserved in four other cereals and in Arabidopsis.