Origin and Evolutionary Dynamics of the miR2119 and ADH1 Regulatory Module in Legumes

MiR398b Targets Superoxide Dismutase Genes in Soybean in Defense Against Heterodera glycines via Modulating Reactive Oxygen Species Homeostasis

MicroRNAs play crucial roles in plant defense responses. However, the underlying mechanism by which miR398b contributes to soybean responses to soybean cyst nematode (Heterodera glycines) remains elusive. In this study, by using Agrobacterium rhizogenes-mediated transformation of soybean hairy roots, we observed that miR398b and target genes GmCCS and GmCSD1b played vital functions in soybean-H. glycines interaction. The study revealed that the abundance of miR398b was downregulated by H. glycines infection, and overexpression of miR398b enhanced the susceptibility of soybean to H. glycines. Conversely, silencing of miR398b improved soybean resistance to H. glycines. Detection assays revealed that miR398b rapidly senses stress-induced reactive oxygen species, leading to the repression of target genes GmCCS and GmCSD1b and regulating the accumulation of plant defense genes against nematode infection. Moreover, exogenous synthetic ds-miR398b enhanced soybean sensitivity to H. glycines by modulating H2O2 and O2- levels. Functional analysis demonstrated that overexpression of GmCCS and GmCSD1b in soybean enhanced resistance to H. glycines. RNA interference-mediated repression of GmCCS and GmCSD1b in soybean increased susceptibility to H. glycines. RNA sequencing revealed that a majority of differentially expressed genes in overexpressed GmCCS were associated with oxidative stress. Overall, the results indicate that miR398b targets superoxide dismutase genes, which negatively regulate soybean resistance to H. glycines via modulating reactive oxygen species levels and defense signals.

Roles of non-coding RNAs in the hormonal and nutritional regulation in nodulation and nitrogen fixation

Symbiotic nitrogen fixation is an important component in the nitrogen cycle and is a potential solution for sustainable agriculture. It is the result of the interactions between the plant host, mostly restricted to legume species, and the rhizobial symbiont. From the first encounter between the host and the symbiont to eventual successful nitrogen fixation, there are delicate processes involved, such as nodule organogenesis, rhizobial infection thread progression, differentiation of the bacteroid, deregulation of the host defense systems, and reallocation of resources. All these processes are tightly regulated at different levels. Recent evidence revealed that non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), participate in these processes by controlling the transcription and translation of effector genes. In general, ncRNAs are functional transcripts without translation potential and are important gene regulators. MiRNAs, negative gene regulators, bind to the target mRNAs and repress protein production by causing the cleavage of mRNA and translational silencing. LncRNAs affect the formation of chromosomal loops, DNA methylation, histone modification, and alternative splicing to modulate gene expression. Both lncRNAs and circRNAs could serve as target mimics of miRNA to inhibit miRNA functions. In this review, we summarized and discussed the current understanding of the roles of ncRNAs in legume nodulation and nitrogen fixation in the root nodule, mainly focusing on their regulation of hormone signal transduction, the autoregulation of nodulation (AON) pathway and nutrient homeostasis in nodules. Unraveling the mediation of legume nodulation by ncRNAs will give us new insights into designing higher-performance leguminous crops for sustainable agriculture.

Deciphering the role of miRNA in reprogramming plant responses to drought stress

Drought is the most prevalent environmental stress that affects plants' growth, development, and crop productivity. However, plants have evolved adaptive mechanisms to respond to the harmful effects of drought. They reprogram their: transcriptome, proteome, and metabolome that alter their cellular and physiological processes and establish cellular homeostasis. One of the crucial regulatory processes that govern this reprogramming is post-transcriptional regulation by microRNAs (miRNAs). miRNAs are small non-coding RNAs, involved in the downregulation of the target mRNA via translation inhibition/mRNA degradation/miRNA-mediated mRNA decay/ribosome drop off/DNA methylation. Many drought-inducible miRNAs have been identified and characterized in plants. Their main targets are regulatory genes that influence growth, development, osmotic stress tolerance, antioxidant defense, phytohormone-mediated signaling, and delayed senescence during drought stress. Overexpression of drought-responsive miRNAs (Osa-miR535, miR160, miR408, Osa-miR393, Osa-miR319, and Gma-miR394) in certain plants has led to tolerance against drought stress indicating their vital role in stress mitigation. Similarly, knock down (miR166/miR398c) or deletion (miR169 and miR827) of miRNAs has also resulted in tolerance to drought stress. Likewise, engineered Arabidopsis plants with miR165, miR166 using short tandem target mimic strategy, exhibited drought tolerance. Since miRNAs regulate the expression of an array of drought-responsive genes, they can act as prospective targets for genetic manipulations to enhance drought tolerance in crops and achieve sustainable agriculture. Further investigations toward functional characterization of diverse miRNAs, and understanding stress-responses regulated by these miRNAs and their utilization in biotechnological applications is highly recommended.

A small RNA of miR2119b from soybean CMS line acts as a negative regulator of male fertility in transgenic Arabidopsis

The miR2119 is involved in the growth, development and abiotic stress response of some legumes, including Medicago truncatula, Phaseolus vulgaris and soybean (Glycine max (L.) Merr.). Our previous small RNA sequencing analysis showed that miR2119b was up-regulated in the flower buds of soybean cytoplasmic male sterile (CMS) line compared with its maintainer line, but the role and mechanism of miR2119b in the regulation of soybean male fertility are still unclear. In this study, the gma-miR2119b and its target gene alcohol dehydrogenase 1.3b (ADH1.3b) were characterized and found to be highly expressed in the flowers of soybean CMS line and its maintainer. Transgenic Arabidopsis plants overexpressing gma-miR2119b exhibit male fertility abnormalities, including pollen fertility and germination rate decreased. Enzyme activity detection found the ADH and catalase (CAT) enzyme activities in inflorescence of gma-miR2119b overexpressed plants were lower than those of wild-type. Bioinformatics and gene expression analysis showed that gma-miR2119b/GmADH1.3b module was responsive to high temperature (HT) stress during flowering. After HT stress, the gma-miR2119b overexpressed plants showed male sterility, including shorter filament, sterile pollen, indehiscent anther and non seed. Moreover, some key genes involved in HT response and reactive oxygen species (ROS) signal regulation pathway, including heat shock protein70, galactinol synthase 1 and CAT, showed down-regulated expression in transgenic plants under HT stress, suggesting that gma-miR2119b regulates male fertility via HT-ROS signaling pathway under HT stress. It was speculated that the gma-miR2119b acted as a negative regulator of male fertility in plants by regulating ADH1, HT-induced and ROS scavenging genes expression.

Non-Coding RNAs in Legumes: Their Emerging Roles in Regulating Biotic/Abiotic Stress Responses and Plant Growth and Development

Noncoding RNAs, including microRNAs (miRNAs), small interference RNAs (siRNAs), circular RNA (circRNA), and long noncoding RNAs (lncRNAs), control gene expression at the transcription, post-transcription, and translation levels. Apart from protein-coding genes, accumulating evidence supports ncRNAs playing a critical role in shaping plant growth and development and biotic and abiotic stress responses in various species, including legume crops. Noncoding RNAs (ncRNAs) interact with DNA, RNA, and proteins, modulating their target genes. However, the regulatory mechanisms controlling these cellular processes are not well understood. Here, we discuss the features of various ncRNAs, including their emerging role in contributing to biotic/abiotic stress response and plant growth and development, in addition to the molecular mechanisms involved, focusing on legume crops. Unravelling the underlying molecular mechanisms and functional implications of ncRNAs will enhance our understanding of the coordinated regulation of plant defences against various biotic and abiotic stresses and for key growth and development processes to better design various legume crops for global food security.

Research on Transboundary Regulation of Plant-Derived Exogenous MiRNA Based on Biological Big Data

In recent years, researchers have discovered plant miRNA (plant xenomiR) in mammalian samples, but it is unclear whether it exists stably and participates in regulation. In this paper, a cross-border regulation model of plant miRNAs based on biological big data is constructed to study the possible cross-border regulation of plant miRNAs. Firstly, a variety of human edible plants were selected, and based on the miRNA data detected in human experimental studies, screening was performed to obtain the plant xenomiR that may stably exist in the human body. Then, we use plant and animal target gene prediction methods to obtain the mRNAs of animals and plants that may be regulated, respectively. Finally, we use GO (Gene Ontology) and the Multiple Dimensional Scaling (MDS) algorithm to analyze the biological processes regulated by plants and animals. We obtain the relationship between different biological processes and explore the regulatory commonality and individuality of plant xenomiR in plants and humans. Studies have shown that the development and metabolic functions of the human body are affected by daily eating habits. Soybeans, corn, and rice can not only affect the daily development and metabolism of the human body but also regulate biological processes such as protein modification and mitosis. This conclusion explains the reasons for the different physiological functions of the human body. This research is an important meaning for the design of small RNA drugs in Chinese herbal medicine and the treatment of human nutritional diseases.