MicroRNA 399 as a potential integrator of photo-response, phosphate homeostasis, and sucrose signaling under long day condition

Role of plant microRNAs and their corresponding pathways in fluctuating light conditions

In recent years, it has been established that microRNAs (miRNAs) are critical for various plant physiological regulations in numerous species. Next-generation sequencing technologies have aided to our understandings related to the critical role of miRNAs during environmental stress conditions and plant development. Light influences not just miRNA accumulation but also their biological activities via regulating miRNA gene transcription, biosynthesis, and RNA-induced silencing complex (RISC) activity. Light-regulated routes, processes, and activities can all be affected by miRNAs. Here, we will explore how light affects miRNA gene expression and how conserved and novel miRNAs exhibit altered expression across different plant species in response to variable light quality. Here, we will mainly discuss recent advances in understanding how miRNAs are involved in photomorphogenesis, and photoperiod-dependent plant biological processes such as cell proliferation, metabolism, chlorophyll pigment synthesis and axillary bud growth. The review concludes by presenting future prospects via hoping that light-responsive miRNAs can be exploited in a better way to engineer economically important crops to ensure future food security.

Regulatory role of microRNAs (miRNAs) in the recent development of abiotic stress tolerance of plants

MicroRNAs (miRNAs) are a distinct groups of single-stranded non-coding, tiny regulatory RNAs approximately 20-24 nucleotides in length. miRNAs negatively influence gene expression at the post-transcriptional level and have evolved considerably in the development of abiotic stress tolerance in a number of model plants and economically important crop species. The present review aims to deliver the information on miRNA-mediated regulation of the expression of major genes or Transcription Factors (TFs), as well as genetic and regulatory pathways. Also, the information on adaptive mechanisms involved in plant abiotic stress responses, prediction, and validation of targets, computational tools, and databases available for plant miRNAs, specifically focus on their exploration for engineering abiotic stress tolerance in plants. The regulatory function of miRNAs in plant growth, development, and abiotic stresses consider in this review, which uses high-throughput sequencing (HTS) technologies to generate large-scale libraries of small RNAs (sRNAs) for conventional screening of known and novel abiotic stress-responsive miRNAs adds complexity to regulatory networks in plants. The discoveries of miRNA-mediated tolerance to multiple abiotic stresses, including salinity, drought, cold, heat stress, nutritional deficiency, UV-radiation, oxidative stress, hypoxia, and heavy metal toxicity, are highlighted and discussed in this review.

miR775 integrates light, sucrose and auxin associated pathways to regulate root growth in Arabidopsis thaliana

MicroRNAs (miRNAs), a class of single-stranded non-coding RNA of 20-24 nucleotides, regulate gene expression by target gene transcript cleavage or translation inhibition. The phytohormone auxin is a crucial regulator of almost every process involved in plant growth and development. Several studies have demonstrated the involvement of miRNA(s) in the regulation of the auxin signaling pathway and plant development. However, very few studies have identified the auxin-mediated regulation of miRNA(s). In this study, we reveal the detailed mechanism of auxin-mediated regulation of the cell wall-related miR775- Galactosyl transferase (GalT) module, which plays an important role in root growth in Arabidopsis thaliana. We also showed two interdependent mechanisms by which miR775 regulates root growth: miR775-GalT and light-mediated sucrose-dependent pathways. Treatment of GUS reporter lines with Indole Acetic Acid (IAA), sucrose, and light apparently enhanced the abundance of miR775 in root tissue. miR775 overexpressing (miR775OX) lines showed changes in root architecture, including increased primary root growth and root hair, by targeting GalT. miR775OX lines also showed tolerance toward low Pi. These results provide new insights into the auxin regulation of cell wall-related miR775 and suggest its significant role in plant root growth and development by modifying the cell wall.

Photocontrol of Axillary Bud Outgrowth by MicroRNAs: Current State-of-the-Art and Novel Perspectives Gained From the Rosebush Model

Shoot branching is highly dependent on environmental factors. While many species show some light dependence for branching, the rosebush shows a strict requirement for light to allow branching, making this species an excellent model to further understand how light impinges on branching. Here, in the first part, we provide a review of the current understanding of how light may modulate the complex regulatory network of endogenous factors like hormones (SL, IAA, CK, GA, and ABA), nutrients (sugar and nitrogen), and ROS to control branching. We review the regulatory contribution of microRNAs (miRNAs) to branching in different species, highlighting the action of such evolutionarily conserved factors. We underline some possible pathways by which light may modulate miRNA-dependent regulation of branching. In the second part, we exploit the strict light dependence of rosebush for branching to identify putative miRNAs that could contribute to the photocontrol of branching. For this, we first performed a profiling of the miRNAs expressed in early light-induced rosebush buds and next tested whether they were predicted to target recognized regulators of branching. Thus, we identified seven miRNAs (miR156, miR159, miR164, miR166, miR399, miR477, and miR8175) that could target nine genes (CKX1/6, EXPA3, MAX4, CYCD3;1, SUSY, 6PFK, APX1, and RBOHB1). Because these genes are affecting branching through different hormonal or metabolic pathways and because expression of some of these genes is photoregulated, our bioinformatic analysis suggests that miRNAs may trigger a rearrangement of the regulatory network to modulate branching in response to light environment.

Genome-wide identification of microRNAs involved in the regulation of fruit ripening and climacteric stages in melon (Cucumis melo)

Fruit ripening is influenced by multiple plant hormones and the regulation of genes. However, studies on posttranscriptional regulators (e.g., miRNAs) of fruit growth and ripening are limited. We used miRNA sequencing and degradome methods to identify miRNAs and their target genes in melon (Cucumis melo cv. Hetao melon). A total of 61 conserved miRNAs and 36 novel miRNAs were identified from fruit growth, ripening, climacteric, and postclimacteric developmental stage samples, of which 32 conserved miRNAs were differentially expressed between developmental stage samples. Sixty-two target genes of 43 conserved miRNAs and 1 novel miRNA were identified from degradome sequencing. To further investigate miRNA influencing fruit ripening, transgenic melon plants overexpressing pre-cme-miR393 (cme-miR393-OE) were generated and characterized. The results showed that fruit ripening was delayed in cme-miR393-OE transgenic lines compared to nontransgenic fruits. The target of cme-miR393 was also identified, and the expression of CmAFB2 was repressed in transgenic plants. These results provide evidence that miRNA regulates melon fruit ripening and provide potential targets to improve the horticultural traits of melon fruit.

Transcriptome-wide identification of novel circular RNAs in soybean in response to low-phosphorus stress

Low-phosphorus (LP) stress is a major factor limiting the growth and yield of soybean. Circular RNAs (circRNAs) are novel noncoding RNAs that play a crucial role in plant responses to abiotic stress. However, how LP stress mediates the biogenesis of circRNAs in soybean remains unclear. Here, to explore the response mechanisms of circRNAs to LP stress, the roots of two representative soybean genotypes with different P-use efficiency, Bogao (a LP-sensitive genotype) and Nannong 94156 (a LP-tolerant genotype), were used for the construction of RNA sequencing (RNA-seq) libraries and circRNA identification. In total, 371 novel circRNA candidates, including 120 significantly differentially expressed (DE) circRNAs, were identified across different P levels and genotypes. More DE circRNAs were significantly regulated by LP stress in Bogao than in NN94156, suggesting that the tolerant genotype was less affected by LP stress than the sensitive genotype was; in other words, NN94156 may have a better ability to maintain P homeostasis under LP stress. Moreover, a positive correlation was observed between the expression patterns of P stress-induced circRNAs and their circRNA-host genes. Gene Ontology (GO) enrichment analysis of these circRNA-host genes and microRNA (miRNA)-targeted genes indicated that these DE circRNAs were involved mainly in defense responses, ADP binding, nucleoside binding, organic substance catabolic processes, oxidoreductase activity, and signal transduction. Together, our results revealed that LP stress can significantly alter the genome-wide profiles of circRNAs and indicated that the regulation of circRNAs was both genotype and environment specific in response to LP stress. LP-induced circRNAs might provide a rich resource for LP-responsive circRNA candidates for future studies.

Sugar Signaling and Post-transcriptional Regulation in Plants: An Overlooked or an Emerging Topic?

Plants are autotrophic organisms that self-produce sugars through photosynthesis. These sugars serve as an energy source, carbon skeletons, and signaling entities throughout plants' life. Post-transcriptional regulation of gene expression plays an important role in various sugar-related processes. In cells, it is regulated by many factors, such as RNA-binding proteins (RBPs), microRNAs, the spliceosome, etc. To date, most of the investigations into sugar-related gene expression have been focused on the transcriptional level in plants, while only a few studies have been conducted on post-transcriptional mechanisms. The present review provides an overview of the relationships between sugar and post-transcriptional regulation in plants. It addresses the relationships between sugar signaling and RBPs, microRNAs, and mRNA stability. These new items insights will help to reach a comprehensive understanding of the diversity of sugar signaling regulatory networks, and open onto new investigations into the relevance of these regulations for plant growth and development.

Systematic Analysis of Alkaline/Neutral Invertase Genes Reveals the Involvement of Smi-miR399 in Regulation of SmNINV3 and SmNINV4 in Salvia miltiorrhiza

Alkaline/neutral invertases (NINVs), which irreversibly catalyze the hydrolysis of sucrose into fructose and glucose, play crucial roles in carbohydrate metabolism and plant development. Comprehensive insights into NINV genes are lacking in Salvia miltiorrhiza, a well-known traditional Chinese medicinal (TCM) plant with significant medicinal and economic value. Through genome-wide prediction, nine putative SmNINV genes, termed SmNINV1-SmNINV9, were identified. Integrated analysis of gene structures, sequence features, conserved domains, conserved motifs and phylogenetic trees revealed the conservation and divergence of SmNINVs. The identified SmNINVs were differentially expressed in roots, stems, leaves, flowers, and different root tissues. They also responded to drought, salicylic acid, yeast extract, and methyl jasmonate treatments. More importantly, computational prediction and experimental validation showed that SmNINV3 and SmNINV4 were targets of Smi-miR399, a conserved miRNA previously shown to affect Pi uptake and translocation through the cleavage of PHOSPHATE2 (PHO2). Consistently, analysis of 43 NINV genes and 26 miR399 sequences from Arabidopsis thaliana, Populus trichocarpa, Manihot esculenta, and Solanum lycopersicum showed that various AtNINV, PtNINV, MeNINV, and SlNINV genes were regulated by miR399. It indicates that the miR399-NINV module exists widely in plants. Furthermore, Smi-miR399 also cleaved SmPHO2 transcripts in S. miltiorrhiza, suggesting the complexity of NINVs, PHO2, and miR399 networks.