What Do We Know about Barley miRNAs?

Abstract

Plant miRNAs are powerful regulators of gene expression at the post-transcriptional level, which was repeatedly proved in several model plant species. miRNAs are considered to be key regulators of many developmental, homeostatic, and immune processes in plants. However, our understanding of plant miRNAs is still limited, despite the fact that an increasing number of studies have appeared. This systematic review aims to summarize our current knowledge about miRNAs in spring barley (Hordeum vulgare), which is an important agronomical crop worldwide and serves as a common monocot model for studying abiotic stress responses as well. This can help us to understand the connection between plant miRNAs and (not only) abiotic stresses in general. In the end, some future perspectives and open questions are summarized.

Keywords: barley; environmental stress; gene expression; miRNAs; plants; regulation.

Figure 1

Schematic representation of the miRNAs biogenesis. Genes encoding miRNAs are transcribed by RNA polymerase II and modified on their ends (m⁷G cap and polyA tail) and thus the primary microRNA (pri-miRNA) arise. Then, the typical stem-loop structure is formed by complementary base pairing and cleaved at the dicing bodies (consisting of several proteins including DCL1, HYL1, SE, TIGH, and DDL) resulting in miRNA duplex formation which can be later 2′-O-methylated (ensured by the HEN1 protein). Guide miRNA is incorporated into the RISC consisting of several proteins, and transported into the cytoplasm, where mRNA target recognition and cleavage can take place while the passenger miRNA is released away. Proteins from the Argonaute family (AGOs) can modify the stability of the miRNAs and also affect the interaction with target mRNAs. This figure was created using BioRender (https://biorender.com/; accessed on 20 June 2022).

Figure 2

miRNAs play important roles also in the developmental processes. In spring barley (Hordeum vulgare), specific miRNAs were linked with the targets involved in the regulation of flowering, root development, seed germination, and also with stomata development. Inhibition is indicated by the red ┴ mark, while positive effect by the green arrow. This figure was created using BioRender (https://biorender.com/; accessed on 20 June 2022).

Figure 3

miRNAs form a complex regulatory network in barley (Hordeum vulgare). Environmental cues, both abiotic (i.e., spectral quality and intensity of the incident light, growth temperature, drought, high salinity, heavy metals exposure, etc.) and biotic (for example pathogens) can affect the expression of miRNAs and thus also their target genes. This figure was created using BioRender (https://biorender.com/; accessed on 20 June 2022).

Figure 4

Biological processes and Molecular functions of miRNA targets in barley. In the upper half of the image, the most abundant GOs of all conserved miRNA targets in barley are shown. In the lower half of the image, the most abundant GOs of degradome-supported miRNA targets are depicted. Blue bar plots stand for biological processes, whereas the orange ones correspond to molecular functions.

Figure 5

Barley pri-miR5049c structure together with miR5049 putative mRNA targets. pri-miRNA structure was computed via RNAfold web server [149] and visualized in the form of a Forna diagram [150]. Nucleotides in blue circles correspond to the mature 21nt-long miRNA region. Grey lines depict inhibition of specific mRNA targets (if the line is full and the description is in red, mRNA cleavage was predicted, according to TarDB: “Cleavage is predicted if miRNA 5′ positions 9–11 have the perfect match”). Chromosome numbers correspond to the location of genes encoding particular mRNAs, Un stands for Unplaced locus.

Figure 6

Future goals in miRNAs research in barley, divided into dry-lab and wet-lab categories, and possible future applications.