uORFlight: a vehicle towards uORF-mediated translational regulation mechanisms in eukaryotes

Abstract

1 Upstream open reading frames (uORFs) are prevalent in eukaryotic mRNAs. They 2 act as a translational control element for precisely tuning the expression of the 3 downstream major open reading frame (mORF) with essential cellular functionalities. 4 uORF variation has been clearly associated with several human diseases. In contrast, 5 natural uORF variants in plants have not ever been identified or linked with any 6 phenotypic changes. The paucity of such evidence encouraged us to generate this 7 database-uORFlight (http://uorflight.whu.edu.cn). It facilitates the exploration of uORF 8 variation among different splicing models of Arabidopsis and rice genes. Most 9 importantly, users can evaluate uORF frequency among different accessions at the 10 population scale and find out the causal single nucleotide polymorphism (SNP) or 11 insertion/deletion (INDEL) which can be associated with phenotypic variation through 12 database mining or simple experiments. Such information will help to make hypotheses 13 of uORF function in plant development or adaption to changing environments on the 14 basis of the cognate mORF function. This database also curates plant uORF relevant 15 literature into distinct groups. To be broadly interesting, our database expands uORF 16 annotation into more species of fungi (Botrytis cinerea), plant (Brassica napus, Glycine 17 max, Gossypium raimondii, Medicago truncatula, Solanum lycopersicum, Solanum 18 tuberosum, Triticum aestivum and Zea mays), metazoan (Caenorhabditis elegans and 19 Drosophila melanogaster) and vertebrate (Homo sapiens, Mus musculus and Danio 20 rerio). Therefore, uORFlight will light up the runway toward how uORF genetic 21 variation determines phenotypic diversity and advance our understanding of 22 translational control mechanisms. 23 24 mediated by the cooperative action between different mRNA elements and trans-acting 1 factors (1). Upstream open reading frames (uORFs) are among the mRNA elements that 2 can confer precise control of protein translation. 3 A uORF initiation codon resides upstream of the coherent mORF, and will be first 4 encountered by 43S scanning ribosome (including 40S ribosomal subunit and eIF2 5 ternary complex). Sequentially, 60S subunit joins in and reconstitutes 80S ribosome for 6 uORF translation elongation, after which the 40S and 60S are disjointed and 40S may 7 remain associated with mRNA. Therefore, usually uORF translation is prioritized over 8 mORF, leading to hindered translation of the mORF. Only in situations where the 9 remaining 40S ribosomes regain fresh eIF2 ternary complex and other unknown 10 reinitiation factors, or when uORF initiation codon is bypassed by the scanning 11 ribosome, the downstream mORF has the chance to be translated (Figure 1a). The 12 former situation is termed as reinitiation and the latter as leaky scanning, two 13 mechanisms that have been accepted as an explanation of limited mORF expression 14 under normal growth and developmental conditions (2-4). Most importantly, a uORF 15 can confer selective mORF ...