Comprehensive genome-wide identification of angiosperm upstream ORFs with peptide sequences conserved in various taxonomic ranges using a novel pipeline, ESUCA

• Published in: BMC genomics Vol. 21; no. 1; p. 260
• Main Authors: Takahashi, Hiro, Hayashi, Noriya, Hiragori, Yuta, Sasaki, Shun, Motomura, Taichiro, Yamashita, Yui, Naito, Satoshi, Takahashi, Anna, Fuse, Kazuyuki, Satou, Kenji, Endo, Toshinori, Kojima, Shoko, Onouchi, Hitoshi
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 30-03-2020; BioMed Central; BMC
• Subjects: 5' Untranslated Regions; Algorithms; Amino acids; Arabidopsis - genetics; Arabidopsis thaliana; Bioinformatics; Comparative analysis; Computational Biology - methods; Conserved sequence; Flowers & plants; Gene expression; Gene Expression Regulation, Plant - genetics; Genomes; Genomics; Magnoliopsida - genetics; Nascent peptide; Open reading frames; Open Reading Frames - genetics; Peptides; Phylogeny; Pipelines; Proteins; Regulatory sequences; Species; Taxonomy; Transcription; Translation; Translational regulation; Upstream; Upstream ORF; Translational regulation; Upstream ORF; Bioinformatics; Nascent peptide
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-020-6662-5

Upstream open reading frames (uORFs) in the 5'-untranslated regions (5'-UTRs) of certain eukaryotic mRNAs encode evolutionarily conserved functional peptides, such as cis-acting regulatory peptides that control translation of downstream main ORFs (mORFs). For genome-wide searches for uORFs with conserved peptide sequences (CPuORFs), comparative genomic studies have been conducted, in which uORF sequences were compared between selected species. To increase chances of identifying CPuORFs, we previously developed an approach in which uORF sequences were compared using BLAST between Arabidopsis and any other plant species with available transcript sequence databases. If this approach is applied to multiple plant species belonging to phylogenetically distant clades, it is expected to further comprehensively identify CPuORFs conserved in various plant lineages, including those conserved among relatively small taxonomic groups.
To efficiently compare uORF sequences among many species and efficiently identify CPuORFs conserved in various taxonomic lineages, we developed a novel pipeline, ESUCA. We applied ESUCA to the genomes of five angiosperm species, which belong to phylogenetically distant clades, and selected CPuORFs conserved among at least three different orders. Through these analyses, we identified 89 novel CPuORF families. As expected, ESUCA analysis of each of the five angiosperm genomes identified many CPuORFs that were not identified from ESUCA analyses of the other four species. However, unexpectedly, these CPuORFs include those conserved across wide taxonomic ranges, indicating that the approach used here is useful not only for comprehensive identification of narrowly conserved CPuORFs but also for that of widely conserved CPuORFs. Examination of the effects of 11 selected CPuORFs on mORF translation revealed that CPuORFs conserved only in relatively narrow taxonomic ranges can have sequence-dependent regulatory effects, suggesting that most of the identified CPuORFs are conserved because of functional constraints of their encoded peptides.
This study demonstrates that ESUCA is capable of efficiently identifying CPuORFs likely to be conserved because of the functional importance of their encoded peptides. Furthermore, our data show that the approach in which uORF sequences from multiple species are compared with those of many other species, using ESUCA, is highly effective in comprehensively identifying CPuORFs conserved in various taxonomic ranges.