The mRNA mobileome: challenges and opportunities for deciphering signals from the noise

RNA signaling in medicinal plants: An overlooked mechanism for phytochemical regulation

Background/objective

Medicinal plants are invaluable sources of bioactive phytochemicals critical for global health. This mini review explores the role of RNA signaling in regulating phytochemical production in medicinal plants, highlighting its potential for optimizing their therapeutic potential.

Methods

This mini review integrates insights from recent studies published in Scopus and Web of Science (2019-2025) on RNA-mediated signaling, including small RNAs (sRNAs), long non-coding RNAs (lncRNAs), and messenger RNAs (mRNAs).

Results

RNA signaling is revealed as a pivotal mechanism in secondary metabolite regulation, mediating stress-induced compound synthesis and environmental interactions. Notable findings include the role of siRNAs in activating alkaloid pathways and lncRNAs in regulating phenolic compound biosynthesis. RNA-directed DNA methylation and systemic RNA signaling further highlight its versatility in phytochemical regulation.

Conclusion

RNA signaling enhances medicinal plant research, unlocking therapeutic potential through bioactive compound production. The study calls for focused research to bridge knowledge gaps and translate laboratory findings into field applications.

On the overinterpretation of mass screening data - the example of mobile mRNA

The mathematics of mass screening is crucial for understanding results from imperfect detection methods in large datasets. Although this framework is well-established, it is not commonly applied in plant biology. Here, we view the identification of messenger RNAs that travel over long distances in plants (mobile mRNAs) through the lens of mass screening statistics. RNA-Seq analyses have identified thousands of mobile mRNAs. Consideration of the detection accuracy and prevalence, however, cast doubt on these numbers. The presented methodology is relevant to all areas of research where detection tests with less than 100% accuracy are applied to find rare events in large datasets.

Here comes the sun: integration of light, temperature, and auxin during herbaceous plant grafting

MAIN CONCLUSION

Light and temperature can regulate auxin production which has been recently shown to be key during graft healing, suggesting that abiotic factors may be vital variables for future graft studies. Grafting is an important horticultural tool used to combine advantageous plant traits. Despite its broad usage, the mechanisms that underlie graft healing remain poorly understood. Recent work has highlighted the influence of high temperature-mediated auxin flow on graft success. Light and temperature sensing utilize partially overlapping mechanisms to regulate auxin biosynthesis, signaling, and transport. In this review, we explore the sensors and transcriptional regulators that modulate auxin response, specifically emphasizing how these components regulate graft success and vascular reconnection. We also discuss areas of graft biology regulated by auxin and underexplored areas of photobiology that may be key to a better understanding of graft mechanisms. This review underscores the importance of translating genetic findings from model systems into horticultural crops to expand our knowledge of economically valuable techniques like grafting.

Re-analysis of mobile mRNA datasets raises questions about the extent of long-distance mRNA communication

Short-read RNA-seq studies of grafted plants have led to the proposal that thousands of messenger RNAs (mRNAs) move over long distances between plant tissues1-7, potentially acting as signals8-12. Transport of mRNAs between cells and tissues has been shown to play a role in several physiological and developmental processes in plants, such as tuberization13, leaf development14 and meristem maintenance15; yet for most mobile mRNAs, the biological relevance of transport remains to be determined16-19. Here we perform a meta-analysis of existing mobile mRNA datasets and examine the associated bioinformatic pipelines. Taking technological noise, biological variation, potential contamination and incomplete genome assemblies into account, we find that a high percentage of currently annotated graft-mobile transcripts are left without statistical support from available RNA-seq data. This meta-analysis challenges the findings of previous studies and current views on mRNA communication.

m5C and m6A modifications regulate the mobility of pumpkin CHOLINE KINASE 1 mRNA under chilling stress

Mobile messenger RNAs (mRNAs) serve as crucial long-distance signaling molecules, responding to environmental stimuli in plants. Although many mobile transcripts have been identified, only a limited subset has been characterized as functional long-distance signals within specific plant species, raising an intriguing question about whether the prevalence of species specificity in mobile transcripts implies a divergence in the mechanisms governing mRNA mobility across distinct plant species. Our study delved into the notable case of CHOLINE KINASE 1 (CK1), an extensively studied instance of mobile mRNAs regulated by a transfer RNA-like sequence (TLS) in Arabidopsis (Arabidopsis thaliana). We established an association between mRNA mobility and length, independent of TLS numbers. Notably, neither the mobile mRNAs nor the mechanisms underpinning their mobility proved to be conserved across different plant species. The exclusive mobility of pumpkin CK1 mRNA under chilling stress was pivotal in enhancing the chilling tolerance of cucumber/pumpkin heterografts. Distinct from the TLS-mediated mobility of AtCK1 mRNA, the mobility of CmoCK1 mRNA is orchestrated by both m5C and m6A modifications, adding dimensions to our understanding of mRNA transport mechanisms.

Gene silencing in broomrapes and other parasitic plants of the Orobanchaceae family: mechanisms, considerations, and future directions

Holoparasites of the Orobanchaceae family are devastating pests causing severe damage to many crop species, and are nearly impossible to control with conventional methods. During the past few decades, RNAi has been seen as a promising approach to control various crop pests. The exchange of small RNAs (sRNAs) between crops and parasitic plants has been documented, indicating potential for the development of methods to protect them via the delivery of the sRNAs to parasites, a method called host-induced gene silencing (HIGS). Here we describe various approaches used for gene silencing in plants and suggest solutions to improve the long-distance movement of the silencing triggers to increase the efficiency of HIGS in parasitic plants. We also investigate the important biological processes during the life cycle of the parasites, with a focus on broomrape species, providing several appropriate target genes that can be used, in particular, in multiplex gene silencing experiments. We also touch on how the application of nanoparticles can improve the stability and delivery of the silencing triggers, highlighting its potential for control of parasitic plants. Finally, suggestions for further research and possible directions for RNAi in parasitic plants are provided.

Plasmodesmata: Channels Under Pressure

Multicellularity has emerged multiple times in evolution, enabling groups of cells to share a living space and reducing the burden of solitary tasks. While unicellular organisms exhibit individuality and independence, cooperation among cells in multicellular organisms brings specialization and flexibility. However, multicellularity also necessitates intercellular dependence and relies on intercellular communication. In plants, this communication is facilitated by plasmodesmata: intercellular bridges that allow the direct (cytoplasm-to-cytoplasm) transfer of information between cells. Plasmodesmata transport essential molecules that regulate plant growth, development, and stress responses. They are embedded in the extracellular matrix but exhibit flexibility, adapting intercellular flux to meet the plant's needs.In this review, we delve into the formation and functionality of plasmodesmata and examine the capacity of the plant communication network to respond to developmental and environmental cues. We illustrate how environmental pressure shapes cellular interactions and aids the plant in adapting its growth.

Tracking the messengers: Emerging advances in mRNA-based plant communication

Messenger RNAs (mRNAs) are the templates for protein translation but can also act as non-cell-autonomous signaling molecules. Plants input endogenous and exogenous cues to mobile mRNAs and output them to local or systemic target cells and organs to support specific plant responses. Mobile mRNAs form ribonucleoprotein (RNP) complexes with proteins during transport. Components of these RNP complexes could interact with plasmodesmata (PDs), a major mediator of mRNA transport, to ensure mRNA mobility and transport selectivity. Based on advances in the last two to three years, this review summarizes mRNA transport mechanisms in local and systemic signaling from the perspective of RNP complex formation and PD transport. We also discuss the physiological roles of endogenous mRNA transport and the recently revealed roles of non-cell-autonomous mRNAs in inter-organism communication.

Frontiers in plant RNA research in ICAR2023: from lab to innovative agriculture

The recent growth in global warming, soil contamination, and climate instability have widely disturbed ecosystems, and will have a significant negative impact on the growth of plants that produce grains, fruits and woody biomass. To conquer this difficult situation, we need to understand the molecular bias of plant environmental responses and promote development of new technologies for sustainable maintenance of crop production. Accumulated molecular biological data have highlighted the importance of RNA-based mechanisms for plant stress responses. Here, we report the most advanced plant RNA research presented in the 33rd International Conference on Arabidopsis Research (ICAR2023), held as a hybrid event on June 5-9, 2023 in Chiba, Japan, and focused on "Arabidopsis for Sustainable Development Goals". Six workshops/concurrent sessions in ICAR2023 targeted plant RNA biology, and many RNA-related topics could be found in other sessions. In this meeting report, we focus on the workshops/concurrent sessions targeting RNA biology, to share what is happening now at the forefront of plant RNA research.

Traveling with purpose: cell-to-cell transport of plant mRNAs

Messenger RNAs (mRNAs) in multicellular organisms can act as signals transported cell-to-cell and over long distances. In plants, mRNAs traffic cell-to-cell via plasmodesmata (PDs) and over long distances via the phloem vascular system to control diverse biological processes - such as cell fate and tissue patterning - in destination organs. Research on long-distance transport of mRNAs in plants has made remarkable progress, including the cataloguing of many mobile mRNAs, characterization of mRNA features important for transport, identification of mRNA-binding proteins involved in their transport, and understanding of the physiological roles of mRNA transport. However, information on short-range mRNA cell-to-cell transport is still limited. This review discusses the regulatory mechanisms and physiological functions of mRNA transport at the cellular and whole plant levels.