Conserved upstream open reading frames in higher plants.
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.


CONCLUSIONS
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.
Tran
Michael K
MK
Australian Centre for Plant Functional Genomics PMB 1 Glen Osmond SA 5064, Australia. michael.tran@acpfg.com.au
Schultz
Carolyn J
CJ
Baumann
Ute
U
D020121:5' Untranslated Regions / Q000235:genetics; D003062:Codon / Q000235:genetics / Q000378:metabolism; D017124:Conserved Sequence / Q000235:genetics*; D020224:Expressed Sequence Tags; D016366:Open Reading Frames / Q000235:genetics*; D010944:Plants / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics; D017421:Sequence Analysis
D020121:5' Untranslated Regions; D003062:Codon; D018749:RNA, Plant