Coding of Non-coding RNA: Insights Into the Regulatory Functions of Pri-MicroRNA-Encoded Peptides in Plants

Abstract

Peptides composed of a short chain of amino acids can play significant roles in plant growth, development, and stress responses. Most of these functional peptides are derived by either processing precursor proteins or direct translation of small open reading frames present in the genome and sometimes located in the untranslated region sequence of a messenger RNA. Generally, canonical peptides serve as local signal molecules mediating short- or long-distance intercellular communication. Also, they are commonly used as ligands perceived by an associated receptor, triggering cellular signaling transduction. In recent years, increasing pieces of evidence from studies in both plants and animals have revealed that peptides are also encoded by RNAs currently defined as non-coding RNAs (ncRNAs), including long ncRNAs, circular RNAs, and primary microRNAs. Primary microRNAs (miRNAs) have been reported to encode regulatory peptides in Arabidopsis, grapevine, soybean, and Medicago, called miRNA-encoded peptides (miPEPs). Remarkably, overexpression or exogenous applications of miPEPs specifically increase the expression level of their corresponding miRNAs by enhancing the transcription of the MIRNA (MIR) genes. Here, we first outline the current knowledge regarding the coding of putative ncRNAs. Notably, we review in detail the limited studies available regarding the translation of miPEPs and their relevant regulatory mechanisms. Furthermore, we discuss the potential cellular and molecular mechanisms in which miPEPs might be involved in plants and raise problems that needed to be solved.

Small ORFs as New Regulators of Pri-miRNAs and miRNAs Expression in Human and Drosophila

“…Importantly, this study indicates that smORFs embedded in pri-miRNAs may exhibit dual functions: first they encode functional peptides (called miPEPs for miRNA-encoded peptides) and second, they may act as cis -regulatory elements involved in the regulation of pri-miRNA/miRNA expression. Whereas in plants, all miPEPs discovered so far have been found to upregulate their miRNA directly by enhancing the transcription of their associated pri-miRNA [ 67 ], this function is apparently not conserved for human and fly miPEPs [ 36 , 37 ]. Instead, in animals the regulation of pri-miRNA/miRNA expression may be carried out by the smORFs themselves, although the precise mechanism still requires further investigation.…”

Genome-Wide Identification and Characterization of Small Peptides in Maize

“…Primary miRNAs have been reported to encode regulatory peptides in Arabidopsis , grapevine ( Vitis vinifera ), soybean ( Glycine max ), and Medicago sp. ; these peptides are named miRNA-encoded peptides (miPEPs) (Ren et al, 2021 ). For example, miPEP171d1 plays a regulatory role in adventitious root formation and response to stress in plants (Ma et al, 2014 ; Gao et al, 2019 ; Chen et al, 2020 ).…”

Inter‐tissue and inter‐organ signaling in drought stress response and phenotyping of drought tolerance

“…Further analyses of the sORFs regulated by environmental stress will provide insights regarding the functions of various peptides in Arabidopsis. Moreover, some non‐coding RNA genes have been reported to encode peptides (Lauressergues et al, 2015 ; Ren et al, 2021 ). Therefore, the functions of these predicted peptide‐encoding genes have to be analyzed.…”