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Novel pipeline identifies new upstream ORFs and non-AUG initiating main ORFs with conserved amino acid sequences in the 5 ' leader of mRNAs in Arabidopsis thaliana
Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands; Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Utrecht, The Netherlands .ORCID iD: 0000-0002-5605-7984
2019 (English)In: RNA: A publication of the RNA Society, ISSN 1355-8382, E-ISSN 1469-9001, Vol. 25, no 3, p. 292-304Article in journal (Refereed) Published
Abstract [en]

Eukaryotic mRNAs contain a 5' leader sequence preceding the main open reading frame (mORF) and, depending on the species, 20%-50% of eukaryotic mRNAs harbor an upstream ORF (uORF) in the 5' leader. An unknown fraction of these uORFs encode sequence conserved peptides (conserved peptide uORFs, CPuORFs). Experimentally validated CPuORFs demonstrated to regulate the translation of downstream mORFs often do so in a metabolite concentration-dependent manner. Previous research has shown that most CPuORFs possess a start codon context suboptimal for translation initiation, which turns out to be favorable for translational regulation. The suboptimal initiation context may even include non-AUG start codons, which makes CPuORFs hard to predict. For this reason, we developed a novel pipeline to identify CPuORFs unbiased of start codon using well-annotated sequence data from 31 eudicot plant species and rice. Our new pipeline was able to identify 29 novel Arabidopsis thaliana (Arabidopsis) CPuORFs, conserved across a wide variety of eudicot species of which 15 do not initiate with an AUG start codon. In addition to CPuORFs, the pipeline was able to find 14 conserved coding regions directly upstream and in frame with the mORF, which likely initiate translation on a non-AUG start codon. Altogether, our pipeline identified highly conserved coding regions in the 5' leaders of Arabidopsis transcripts, including in genes with proven functional importance such as LHY, a key regulator of the circadian clock, and the RAPTOR1 subunit of the target of rapamycin (TOR) kinase.

Place, publisher, year, edition, pages
Cold Spring Harbor Laboratory Press (CSHL), 2019. Vol. 25, no 3, p. 292-304
Keywords [en]
5 '-UTR, translation, translational initiation, translational stalling, uORF
National Category
Biochemistry and Molecular Biology Bioinformatics and Systems Biology
Identifiers
URN: urn:nbn:se:umu:diva-157198DOI: 10.1261/rna.067983.118ISI: 000459007300003PubMedID: 30567971OAI: oai:DiVA.org:umu-157198DiVA, id: diva2:1303291
Projects
Bio4EnergyAvailable from: 2019-04-09 Created: 2019-04-09 Last updated: 2019-08-30Bibliographically approved

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Hanson, Johannes

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