miR858a-encoded peptide, miPEP858a, interacts with miR858a promoter and requires C-terminus for the associated functions

Abstract

MicroRNAs (miRNAs) play a crucial role in regulating gene expression as processed products of primary miRNAs (pri-miRNAs). Recent studies suggest that certain pri-miRNAs encode miRNA-encoded Peptides (miPEPs), influencing miRNA function. Despite this emerging insight, molecular mechanisms and the specific domain or essential amino acid residues required for the functionality of these miPEPs have yet to be explored. Here, we report that the pri-miR858a-encoded peptide, miPEP858a, interacts with the promoter region of the MIR858 gene and its C-terminal region consisting of 14 amino acid residues is indispensable for its functionality. DNA-protein interaction through Yeast-one-hybrid and ChIP-qPCR analysis revealed that miPEP858 interacts with specific region in the MIR858 promoter. An exogenous application of a truncated peptide, the C-terminal region, resulted in enhanced expression and related phenotypic effects, similar to complete miPEP858. Furthermore, C-terminal region of miPEP858a complemented mutant plants lacking miPEP858, highlighting their regulatory role in miR858a expression and associated target genes, impacting flavonoid biosynthesis and plant development. These findings suggest that full-length miPEP858a may not be essential for its functionality. Identifying functional domains of other peptides offers promise, potentially reducing synthesis costs for application in crop plants and avoiding laborious biotechnological approaches to enhance agronomic traits.