MicroRNA528 and Its Regulatory Roles in Monocotyledonous Plants

Abstract

MicroRNA528 (miR528) is a microRNA found only in monocotyledonous (monocot) plants. It has been widely reported that miR528 is involved in the regulation of plant growth and development, such as flowering, architecture, and seed and embryogenic development, in addition to playing a crucial role in response to various biotic and abiotic stresses, such as plant pathogens, salt stress, heat/cold stress, water stress, arsenic stress, oxidative stress, heavy-metal stress, and nutrient stress. Given that it is specific to monocot plants, to which the major staple food crops such as rice and wheat belong, a review of studies investigating its diverse functional roles and underlying mechanisms is presented. This review focuses on the processes in which miR528 and its targets are involved and examines their regulatory relationships with significant participation in plant development and stress responses. It is anticipated that more biological functions and evolutionary effects of miRNA targets will be elucidated with the increase in knowledge of miRNA evolution and examination of target mRNAs.

Keywords: MicroRNAs; miR528; plant development; post-transcriptional gene regulation; stress.

Figure 1

The sequence alignment and phylogenetic analysis of miR528. (A) Alignment of mature miR528 sequences. miR528 derived from 17 monocot plant species, including Asparagus officinalis L. (aof), Brachypodium distachyon (L.) P.Beauv. (bdi), Musa acuminata Colla (mac), Oryza glaberrima Steud. (ogl), Oryza nivara S.D.Sharma and Shastry (oni), Oryza rufipogon Griff. (Oru), Oryza sativa L. (osa), Panicum hallii Vasey (pha), Panicum virgatum L. (pvi), Phalaenopsis aphrodite Rchb.f. (pap), Phoenix dactylifera L. (pda), Saccharum hybrid cultivar (scu), Setaria italica (L.) P. Beauvois (sit), Sorghum bicolor (L.) Moench (sbi), Spirodela polyrhiza (L.) Schleid. (spo), Triticum aestivum L. (tae), and Zea mays L. (zma). The black-shaded blocks indicate highly conserved residues. (B) The phylogenetic tree reconstructed with precursors of miR528. We aligned the miR528 precursor sequences of all the 17 monocot plant species using Molecular Evolutionary Genetics Analysis (MEGA) version 6.06 software [31] with MUltiple Sequence Comparison by Log-Expectation (MUSCLE) and reconstructed the phylogenetic tree using the maximum likelihood (ML) method using the general time reversible (GTR) substitution model with the default set of gamma distribution among-site rate variation. To compare the similarities and differences of the ML phylogenetic tree, we also reconstructed the phylogenetic tree with the maximum parsimony (MP) method using MEGA (Supplementary Figure S1). The phylogenetic tree of the 17 monocot plants used in the study was gathered from Monocots Plant Annotated Genomes Database (PLAZA) 4.5 (https://bioinformatics.psb.ugent.be/plaza/, accessed on 6 December 2024) [32]. The 17 monocot plants belong to five orders of the Liliopsida. The five orders are as follows: Alismatales, Asparagales, Principes, Zingiberales, and Poales. Poaceae is a large and nearly ubiquitous family of monocotyledonous flowering plants known as grasses, containing two sister lineages (or clades): the Panicoideae, Arundinoideae, Chloridoideae, Micrairoideae, Aristidoideae, and Danthonioideae (PACMAD) clade and the Bambusoideae, Oryzoideae, and Pooideae (BOP) clade. The name of the PACMAD clade comes from the first initials of the six included subfamilies, i.e., Panicoideae, Arundinoideae, Chloridoideae, Micrairoideae, Aristidoideae, and Danthonioideae [33]. The BOP clade contains three subfamilies from whose initials its name derives: bamboos (Bambusoideae); Oryzoideae, including rice; and Pooideae, including important cereal crops such as wheat [34].

Figure 2

The target genes of miR528. (A) The sequence logos of miR528 target sites. Toolkit for Biologists integrating various biological data handling tools (TBtools) was used to draw the sequence logos (https://github.com/CJ-Chen/TBtools/, accessed on 25 December 2024) [38]. The sequence logos of miR528 target sites are conserved in rice, corn, wheat, millet, and switchgrass. These conserved target genes encode three types proteins, including plastocyanin-like domain-containing proteins, F-box domain- and (or) leucine-rich repeat (LRR)-containing proteins, and the copper/zinc superoxide dismutase. osa-miR528, zma-miR528, tae-miR528, sit-miR528, and pvi-miR528 represent the sequence logos of all the predicted miR528 target sites in rice, corn, wheat, millet, and switchgrass, respectively. (B–D) The conserved target genes of miR528. The target genes of miR528 were predicted by searching the transcripts for complementary sequences using the psRNATarget server with a more stringent cut-off threshold: maximum expectation (E) = 3.0 (https://www.zhaolab.org/psRNATarget/, accessed on 26 December 2024) [36]. Degradome sequencing data were downloaded from the PmiREN database. The upper parts of B-D present the alignments of miR528 with its target sequences, and the lower parts are the frequency of the 5′ end of the degradome tags within the full-length target transcripts. The solid lines indicate matched RNA base pairs. One dot shows G-U mismatch, and two dots represent other types of mismatch. (B) LOC_Os07g38290 and GRMZM2G107562, encoding a plastocyanin-like domain-containing protein, are the targets of miR528 in rice and maize, respectively; (C) LOC_Os06g06050 and GRMZM2G040278, encoding F-box domain- and (or) LRR-containing proteins, are the targets of miR528 in rice and maize, respectively; (D) LOC_Os08g44770 and GRMZM2G106928, encoding a copper/zinc superoxide dismutase, are the targets of miR528 in rice and maize, respectively. (E–H) Examples of non-conserved target genes of miR528 predicted in different monocot species, including genes involved in flowering regulation, glycosylation, alkaloid biosynthesis, and transcriptional regulation. The black line represents intron, the rectangle filled yellow represents exon, and miRNA complementary sites (red) are shown. The RNA sequences of each complementary site from 5′ to 3′ and the miR528 sequence from 3′ to 5′ are shown in the expanded regions.