Characterization of plant microRNA-encoded peptides (miPEPs) reveals molecular mechanisms from the translation to activity and specificity

Abstract

MicroRNAs (miRNAs) are transcribed as long primary transcripts (pri-miRNAs) by RNA polymerase II. Plant pri-miRNAs encode regulatory peptides called miPEPs, which specifically enhance the transcription of the pri-miRNA from which they originate. However, paradoxically, whereas miPEPs have been identified in different plant species, they are poorly conserved, raising the question of the mechanisms underlying their specificity. To address this point, we identify and re-annotate multiple Arabidopsis thaliana pri-miRNAs in order to identify ORF encoding miPEPs. The study of several identified miPEPs in different species show that non-conserved miPEPs are only active in their plant of origin, whereas conserved ones are active in different species. Finally, we find that miPEP activity relies on the presence of its own miORF, explaining both the lack of selection pressure on miPEP sequence and the ability for non-conserved peptides to play a similar role, i.e., to activate the expression of their corresponding miRNA.

Roles of microRNAs in abiotic stress response and characteristics regulation of plant

“…For a long time, miRNAs are considered the class of non-coding small RNAs. However, recent studies have shown that primary miRNAs (pri-miRNAs) can encode for regulatory peptides, called miRNA-encoded peptides (miPEPs), which specifically enhance the levels of mature miRNAs by increasing the transcription of corresponding pri-miRNA (Lauressergues et al, 2022). So far, miPEPs have been reported in plant species and even in animals (Dozier and Plaza, 2022).…”

miRNA408 and its encoded peptide, miPEP408, regulate arsenic stress response in Arabidopsis

“…Several studies have shown that miRNA has an important regulatory role in biotic and abiotic stresses, such as nutrient deficiency conditions, which inhibit plant growth and development (Pagano et al, 2021; Basso et al, 2019; Fujii et al, 2005; Lin et al, 2013; Misra et al, 2010; Sharma et al, 2014). Research on miRNA-encoded peptides (miPEPs) began recently since a study revealed that a few pri-miRNAs have one or more open reading frames (ORFs), which regulate the associated miRNAs by enhancing their transcription (Lauressergues et al, 2015; Couzigou et al, 2015; Sharma et al, 2020; Lauressergues et al, 2022; Badola et al, 2022). Although the role of these miPEPs has been explored in various plants (Chen et al, 2020; Couzigou et al, 2016; Badola et al, 2022; Lauressergues et al, 2022) however, their mode of action under different stresses remains unexplored.…”

“…Research on miRNA-encoded peptides (miPEPs) began recently since a study revealed that a few pri-miRNAs have one or more open reading frames (ORFs), which regulate the associated miRNAs by enhancing their transcription (Lauressergues et al, 2015; Couzigou et al, 2015; Sharma et al, 2020; Lauressergues et al, 2022; Badola et al, 2022). Although the role of these miPEPs has been explored in various plants (Chen et al, 2020; Couzigou et al, 2016; Badola et al, 2022; Lauressergues et al, 2022) however, their mode of action under different stresses remains unexplored.…”

“…Several studies have shown that miRNA has an important regulatory role in biotic and abiotic stresses, such as nutrient deficiency conditions, which inhibit plant growth and development (Pagano et al, 2021;Fujii et al, 2005;Lin et al, 2013;Misra et al, 2010;Sharma et al, 2014). Research on miRNA-encoded peptides (miPEPs) began recently since a study revealed that a few pri-miRNAs have one or more open reading frames (ORFs), which regulate the associated miRNAs by enhancing their transcription (Lauressergues et al, 2015;Lauressergues et al, 2022;Badola et al, 2022).…”

“…Although the role of these miPEPs has been explored in various plants Badola et al, 2022;Lauressergues et al, 2022) however, their mode of action under different stresses remains unexplored.…”