Variation in upstream open reading frames contributes to allelic diversity in maize protein abundance

Authors: GAGE, JOSEPH - North Carolina State University; MALI, SUJINA - Washington University; MCLOUGHLIN, FIONN - Washington University; KHAIPHO-BURCH, MERRITT - Cornell University; MONIER, BRANDON - Cornell University; BAILEY-SERRES, JULIA - University Of California, Riverside; VIERSTRA, RICHARD - Washington University; Buckler, Edward - Ed

Submitted to: Proceedings of the National Academy of Sciences (PNAS)
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/22/2022
Publication Date: 3/29/2022
Citation: Gage, J.L., Mali, S., McLoughlin, F., Khaipho-Burch, M., Monier, B., Bailey-Serres, J., Vierstra, R.D., Buckler IV, E.S. 2022. Variation in upstream open reading frames contributes to allelic diversity in maize protein abundance. Proceedings of the National Academy of Sciences (PNAS). 119(14). Article e2112516119. https://doi.org/10.1073/pnas.2112516119.
DOI: https://doi.org/10.1073/pnas.2112516119

Interpretive Summary: We know that genetic differences between individuals can cause apparent physical differences. In many cases, those physical differences are caused by different levels of gene expression. What is still unclear, however, are the mechanisms by which genetic differences cause differing levels of gene expression across the genome. One specific mechanism of regulating gene expression (called “upstream open reading frames”; “uORFs”) has been discovered in limited cases and highly controlled experiments, but we do not know the extent to which it influences differences between natural populations of crop plants. We show that genetic variation can alter the function of uORFs and cause changes in gene expression. We also show that genetic variation which alters uORF function is important for physical differences between individuals. This work allows us to identify a small set of genetic variation that has large effects on gene expression and physical differences between individuals. We can consider about 5,000x less genetic variation when searching for causes of different gene expression between individuals. Because there is so much genetic variation between individuals, reducing the search space dramatically is helpful for building targeted models that predict plant performance, and may also be of use for identifying targets for gene editing or genome engineering.

Technical Abstract: The 5' untranslated region (UTR) sequence of eukaryotic mRNAs may contain upstream open reading frames (uORFs), which can regulate translation of the main ORF (mORF). The current model of translational regulation by uORFs posits that when a ribosome scans a mRNA and encounters an uORF, translation of that uORF can prevent ribosomes from reaching the mORF and cause decreased mORF translation. In this study, we first observed that rare variants in the 5' UTR dysregulate maize (Zea mays L.) protein abundance. Upon further investigation, we found that rare variants near the start codon of uORFs can repress or derepress mORF translation, causing allelic changes in protein abundance. This finding holds for common variants as well, and common variants that modify uORF start codons also contribute disproportionately to metabolic and whole-plant phenotypes, suggesting that translational regulation by uORFs serves an adaptive function. These results provide evidence for the mechanisms by which natural sequence variation modulates gene expression, and ultimately, phenotype.