Developmental changes due to long-distance movement of a homeobox fusion transcript in tomato

Movement of ACC oxidase 3 mRNA from seeds to flesh promotes fruit ripening in apple

Xenia, the phenomenon in which the pollen genotype directly affects the phenotypic characteristics of maternal tissues (i.e., fruit ripening), has applications in crop production and breeding. However, the underlying molecular mechanism has yet to be elucidated. Here, we investigated whether mobile mRNAs from the pollen affect the ripening and quality-related characteristics of the fruit using cross-pollination between distinct Malus domestica (apple) cultivars. We demonstrated that hundreds of mobile mRNAs originating from the seeds are delivered to the fruit. We found that the movement of one of these mRNAs, ACC oxidase 3 (MdACO3), is coordinated with fruit ripening. Salicylic acid treatment, which can cause plasmodesmal closure, blocks MdACO3 movement, indicating that MdACO3 transcripts may move through the plasmodesmata. To assess the role of mobile MdACO3 transcripts in apple fruit, we created MdACO3-GFP-expressing apple seeds using MdACO3-GFP-overexpressing pollen for pollination and showed that MdACO3 transcripts in the transgenic seeds move to the flesh, where they promote fruit ripening. Furthermore, we demonstrated that MdACO3 can be transported from the seeds to fruit in the fleshy-fruited species tomato and strawberry. These results underscore the potential of mobile mRNAs from seeds to influence fruit characteristics, providing an explanation for the xenia phenomenon. Notably, our findings highlight the feasibility of leveraging diverse pollen genomic resources, without resorting to genome editing, to improve fruit quality.

Arabidopsis leaf-expressed AGAMOUS-LIKE 24 mRNA systemically specifies floral meristem differentiation

Plants can record external stimuli in mobile mRNAs and systemically deliver them to distal tissues to adjust development. Despite the identification of thousands of mobile mRNAs, the functional relevance of mobile mRNAs remains limited. Many mobile mRNAs are synthesized in the source cells that perceive environmental stimuli, but specifically exert their functions upon transportation to the recipient cells. However, the translation of mobile mRNA-encoded protein in the source cells could locally activate downstream target genes. How plants avoid ectopic functions of mobile mRNAs in the source cells to achieve tissue specificity remains to be elucidated. Here, we show that Arabidopsis AGAMOUS-LIKE 24 (AGL24) is a mobile mRNA whose movement is necessary and sufficient to specify floral organ identity. Although AGL24 mRNA is expressed in vegetative tissues, AGL24 protein exclusively accumulates in the shoot apex. In leaves, AGL24 proteins are degraded to avoid ectopically activating its downstream target genes. Our results reveal how selective protein degradation in source cells provides a strategy to limit the local effects associated with proteins encoded by mobile mRNAs, which ensures that mobile mRNAs specifically trigger systemic responses only in recipient tissues.

Arabidopsis cyclophilins direct intracellular transport of mobile mRNA via organelle hitchhiking

Plants convert external cues into mobile mRNAs to synchronize meristematic differentiation with environmental dynamics. These mRNAs are selectively transported to intercellular pores, plasmodesmata (PD), for cell-to-cell movement. However, how plants recognize and deliver mobile mRNAs to PD remains unknown. Here we show that mobile mRNAs hitchhike on organelle trafficking to transport towards PD. Perturbed cytoskeleton organization or organelle trafficking severely disrupts the subcellular distribution of mobile mRNAs. Arabidopsis rotamase cyclophilins (ROCs), which are organelle-localized RNA-binding proteins, specifically bind mobile mRNAs on the surface of organelles to direct intracellular transport. Arabidopsis roc mutants exhibit phenotype alterations and disruptions in the transport of mobile mRNAs. These findings suggest that ROCs play a crucial role in facilitating the systemic delivery of mobile mRNAs. Our results highlight that an RNA-binding protein-mediated hitchhiking system is specifically recruited to orient plant mobile mRNAs for intercellular transport.

BEL transcription factors in prominent Solanaceae crops: the missing pieces of the jigsaw in plant development

MAIN CONCLUSION

Understanding BEL transcription factors roles in potato and tomato varies considerably with little overlap. The review suggests reciprocal use of gained results to proceed with the knowledge in both crops The proper development of organs that plants use for reproduction, like fruits or tubers, is crucial for the survival and competitiveness of the species and thus subject to strict regulations. Interestingly, the controls of potato (Solanum tuberosum) tuber and tomato (S. lycopersicum) fruit development use common mechanisms, including the action of the BEL transcription factors (TFs). Although more than ten BEL genes have been identified in either genome, only a few of them have been characterized. The review summarizes knowledge of BEL TFs' roles in these closely related Solanaceae species, focusing on those that are essential for tuberization in potato, namely StBEL5, StBEL11 and StBEL29, and for fruit development in tomato - SlBEL11, SlBL2 and SIBL4. Comprehension of the roles of individual BEL TFs, however, is not yet sufficient. Different levels of understanding of important characteristics are described, such as BEL transcript accumulation patterns, their mobility, BEL protein interaction with KNOX partners, subcellular localisation, and their target genes during initiation and development of the organs in question. A comparison of the knowledge on BEL TFs and their mechanisms of action in potato and tomato may provide inspiration for faster progress in the study of both models through the exchange of information and ideas. Both crops are extremely important for human nutrition. In addition, their production is likely to be threatened by the upcoming climate change, so there is a particular need for breeding using a deep knowledge of control mechanisms.

A cryptic natural variant allele of BYPASS2 suppresses the bypass1 mutant phenotype

The Arabidopsis (Arabidopsis thaliana) BYPASS1 (BPS1) gene encodes a protein with no functionally characterized domains, and loss-of-function mutants (e.g. bps1-2 in Col-0) present a severe growth arrest phenotype that is evoked by a root-derived graft-transmissible small molecule that we call dalekin. The root-to-shoot nature of dalekin signaling suggests it could be an endogenous signaling molecule. Here, we report a natural variant screen that allowed us to identify enhancers and suppressors of the bps1-2 mutant phenotype (in Col-0). We identified a strong semi-dominant suppressor in the Apost-1 accession that largely restored shoot development in bps1 and yet continued to overproduce dalekin. Using bulked segregant analysis and allele-specific transgenic complementation, we showed that the suppressor is the Apost-1 allele of a BPS1 paralog, BYPASS2 (BPS2). BPS2 is one of four members of the BPS gene family in Arabidopsis, and phylogenetic analysis demonstrated that the BPS family is conserved in land plants and the four Arabidopsis paralogs are retained duplicates from whole genome duplications. The strong conservation of BPS1 and paralogous proteins throughout land plants, and the similar functions of paralogs in Arabidopsis, suggests that dalekin signaling might be retained across land plants.

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

Organismal communication entails encoding a message that is sent over space or time to a recipient cell, where that message is decoded to activate a downstream response. Defining what qualifies as a functional signal is essential for understanding intercellular communication. In this review, we delve into what is known and unknown in the field of long-distance messenger RNA (mRNA) movement and draw inspiration from the field of information theory to provide a perspective on what defines a functional signaling molecule. Although numerous studies support the long-distance movement of hundreds to thousands of mRNAs through the plant vascular system, only a small handful of these transcripts have been associated with signaling functions. Deciphering whether mobile mRNAs generally serve a role in plant communication has been challenging, due to our current lack of understanding regarding the factors that influence mRNA mobility. Further insight into unsolved questions regarding the nature of mobile mRNAs could provide an understanding of the signaling potential of these macromolecules.

A chaperonin containing T-complex polypeptide-1 facilitates the formation of the PbWoxT1-PbPTB3 ribonucleoprotein complex for long-distance RNA trafficking in Pyrus betulaefolia

Numerous plant endogenous mRNAs move via phloem and thus affect the growth and development of long-distant organs. mRNAs are transported with RNA-binding proteins forming a ribonucleoprotein complex. However, it remains elusive how such RNP complex assembles and facilitates mRNA trafficking. Protease digestion and RNA immunoprecipitation were used to investigate the RNP assembly function of the complete Chaperonin Containing T-complex Polypeptide-1. In situ hybridization, hairy root transformation, microprojectile bombardment, and grafting experiments demonstrate the role of CCT complex in the transport of a PbWoxT1-PbPTB3 RNP complex in Pyrus betulaefolia. PbCCT5 silenced caused defective movement of GFP-PbPTB3 and GFP-PbWoxT1 from hairy roots to new leaves via the phloem. PbCCT5 is shown to interact with PbPTB3. PbCCT complex enhanced PbPTB3 stabilization and permitted assembly of PbWoxT1 and PbPTB3 into an RNP complex. Furthermore, silencing of individual CCT subunits inhibited the intercellular movement of GFP-PbPTB3 and long-distance trafficking of PbWoxT1 and PbPTB3 in grafted plants. Taken together, the CCT complex assembles PbPTB3 and PbWoxT1 into an RNP complex in the phloem in order to facilitate the long-distance trafficking of PbWoxT1 in P. betulaefolia. This study therefore provides important insights into the mechanism of RNP complex formation and transport.

Long distance signalling and epigenetic changes in crop grafting

Humans have used grafting for more than 4000 years to improve plant production, through physically joining two different plants, which can continue to grow as a single organism. Today, grafting is becoming increasingly more popular as a technique to increase the production of herbaceous horticultural crops, where rootstocks can introduce traits such as resistance to several pathogens and/or improving the plant vigour. Research in model plants have documented how long-distance signalling mechanisms across the graft junction, together with epigenetic regulation, can produce molecular and phenotypic changes in grafted plants. Yet, most of the studied examples rely on proof-of-concept experiments or on limited specific cases. This review explores the link between research findings in model plants and crop species. We analyse studies investigating the movement of signalling molecules across the graft junction and their implications on epigenetic regulation. The improvement of genomics analyses and the increased availability of genetic resources has allowed to collect more information on potential benefits of grafting in horticultural crop models. Ultimately, further research into this topic will enhance our ability to use the grafting technique to exploit genetic and epigenetic variation in crops, as an alternative to traditional breeding.

The role of shoot-derived RNAs transported to plant root in response to abiotic stresses

A large number of RNA molecules are transported over long-distance between shoots and roots via phloem in higher plants. Mobile RNA signals are important for plants to tackle abiotic stresses. Shoot-derived mobile RNAs can be involved in the response to different developmental or environmental signals in the root. Some environmental conditions such as climate change, water deficit, nutrient deficiency challenge modern agriculture with more expeditious abiotic stress conditions. Root architecture determines the ability of water and nutrient uptake and further abiotic stress tolerance, and shoot tissue also determines the balance between shoot-root relationship in plant growth and adaptations. Thus, it is necessary to understand the roles of shoot-derived RNA signals and their potential function in roots upon abiotic stresses in the model plants (Arabidopsis thaliana and Nicotiana benthamiana) and agricultural crops. In this review, we summarize the so-far discovered shoot-derived mobile RNA transportation to the root under abiotic stress conditions, e.g. drought, cold stress and nutrient deficiencies. Furthermore, we will focus on the biological relevance and the potential roles of these RNAs in root development and stress responses which will be an asset for the future breeding strategies.

Light and temperature regulate m6A-RNA modification to regulate growth in plants

N6-methyladenosine is a highly dynamic, abundant mRNA modification which is an excellent potential mechanism for fine tuning gene expression. Plants adapt to their surrounding light and temperature environment using complex gene regulatory networks. The role of m6A in controlling gene expression in response to variable environmental conditions has so far been unexplored. Here, we map the transcriptome-wide m6A landscape under various light and temperature environments. Identified m6A-modifications show a highly specific spatial distribution along transcripts with enrichment occurring in 5'UTR regions and around transcriptional end sites. We show that the position of m6A modifications on transcripts might influence cellular transcript localization and the presence of m6A-modifications is associated with alternative polyadenylation, a process which results in multiple RNA isoforms with varying 3'UTR lengths. RNA with m6A-modifications exhibit a higher preference for shorter 3'UTRs. These shorter 3'UTR regions might directly influence transcript abundance and localization by including or excluding cis-regulatory elements. We propose that environmental stimuli might change the m6A landscape of plants as one possible way of fine tuning gene regulation through alternative polyadenylation and transcript localization.

Effects of Pollen Sources on Fruit Set and Fruit Characteristics of 'Fengtangli' Plum (Prunus salicina Lindl.) Based on Microscopic and Transcriptomic Analysis

Adequate yield and fruit quality are required in commercial plum production. The pollen source has been shown to influence fruit set and fruit characteristics. In this study, 'Siyueli', 'Fenghuangli' and 'Yinhongli' were used as pollinizers of 'Fengtangli' plum. Additionally, self-pollination, mixed pollination, and open pollination were performed. We characterized the differences in pollen tube growth, fruit set and fruit quality among pollination combinations. 'Fengtangli' flowers pollinated by 'Fenghuangli' had more pistils with pollen tubes penetrating the ovary and the highest fruit set rate, while the lowest fruit set rate was obtained from self-pollination. In self-pollinated flowers, 33% of pistils had at least one pollen tube reaching the ovary, implying that 'Fengtangli' is partially self-compatible. Pollen sources affected 'Fengtangli' fruit size, weight, pulp thickness, soluble solids, and sugar content. Transcriptome analysis of 'Siyueli'-pollinated and 'Yinhongli'-pollinated fruits revealed 2762 and 1018 differentially expressed genes (DEGs) involved in the response to different pollen sources. DEGs were enriched in plant hormone signal transduction, starch and sucrose metabolism, and MAPK signaling pathways. Our findings provide a reference for the selection of suitable pollinizers for 'Fengtangli' plum and promote future research on the metaxenia effect at the molecular level.

Intrinsically disordered plant protein PARCL colocalizes with RNA in phase-separated condensates whose formation can be regulated by mutating the PLD

In higher plants, long-distance RNA transport via the phloem is crucial for communication between distant plant tissues to align development with stress responses and reproduction. Several recent studies suggest that specific RNAs are among the potential long-distance information transmitters. However, it is yet not well understood how these RNAs enter the phloem stream, how they are transported, and how they are released at their destination. It was proposed that phloem RNA-binding proteins facilitate RNA translocation. In the present study, we characterized two orthologs of the phloem-associated RNA chaperone-like (PARCL) protein from Arabidopsis thaliana and Brassica napus at functional and structural levels. Microscale thermophoresis showed that these phloem-abundant proteins can bind a broad spectrum of RNAs and show RNA chaperone activity in FRET-based in vitro assays. Our SAXS experiments revealed a high degree of disorder, typical for RNA-binding proteins. In agroinfiltrated tobacco plants, eYFP-PARCL proteins mainly accumulated in nuclei and nucleoli and formed cytosolic and nuclear condensates. We found that formation of these condensates was impaired by tyrosine-to-glutamate mutations in the predicted prion-like domain (PLD), while C-terminal serine-to-glutamate mutations did not affect condensation but reduced RNA binding and chaperone activity. Furthermore, our in vitro experiments confirmed phase separation of PARCL and colocalization of RNA with the condensates, while mutation as well as phosphorylation of the PLD reduced phase separation. Together, our results suggest that RNA binding and condensate formation of PARCL can be regulated independently by modification of the C-terminus and/or the PLD.

Control of root-to-shoot long-distance flow by a key ROS-regulating factor in Arabidopsis

Inter-tissue communication is instrumental to coordinating the whole-body level behaviour for complex multicellular organisms. However, little is known about the regulation of inter-tissue information exchange. Here we carried out genetic screens for root-to-shoot mobile silencing in Arabidopsis plants with a compromised small RNA-mediated gene silencing movement rate and identified radical-induced cell death 1 (RCD1) as a critical regulator of root-shoot communication. RCD1 belongs to a family of poly (ADP-ribose) polymerase proteins, which are highly conserved across land plants. We found that RCD1 coordinates symplastic and apoplastic movement by modulating the sterol level of lipid rafts. The higher superoxide production in rcd1-knockout plants resulted in lower plasmodesmata (PD) frequency and altered PD structure in the symplasm of the hypocotyl cortex. Furthermore, the mutants showed increased lateral area of tracheary pits, which reduced axial movement. Our study highlights a novel mechanism through which root-to-shoot long-distance signalling can be modulated both symplastically and apoplastically.

Long-Distance Transported RNAs: From Identity to Function

There is now a wealth of data, from different plants and labs and spanning more than two decades, which unequivocally demonstrates that RNAs can be transported over long distances, from the cell where they are transcribed to distal cells in other tissues. Different types of RNA molecules are transported, including micro- and messenger RNAs. Whether these RNAs are selected for transport and, if so, how they are selected and transported remain, in general, open questions. This aspect is likely not independent of the biological function and relevance of the transported RNAs, which are in most cases still unclear. In this review, we summarize the experimental data supporting selectivity or nonselectivity of RNA translocation and review the evidence for biological functions. After discussing potential issues regarding the comparability between experiments, we propose criteria that need to be critically evaluated to identify important signaling RNAs.

Long-distance mobile mRNA CAX3 modulates iron uptake and zinc compartmentalization

Iron deficiency in plants can lead to excessive absorption of zinc; however, important details of this mechanism have yet to be elucidated. Here, we report that MdCAX3 mRNA is transported from the leaf to the root, and that MdCAX3 is then activated by MdCXIP1. Suppression of MdCAX3 expression leads to an increase in the root apoplastic pH, which is associated with the iron deficiency response. Notably, overexpression of MdCAX3 does not affect the apoplastic pH in a MdCXIP1 loss-of-function Malus baccata (Mb) mutant that has a deletion in the MdCXIP1 promoter. This deletion in Mb weakens MdCXIP1 expression. Co-expression of MdCAX3 and MdCXIP1 in Mb causes a decrease in the root apoplastic pH. Furthermore, suppressing MdCAX3 in Malus significantly reduces zinc vacuole compartmentalization. We also show that MdCAX3 activated by MdCXIP1 is not only involved in iron uptake, but also in regulating zinc detoxification by compartmentalizing zinc in vacuoles to avoid iron starvation-induced zinc toxicity. Thus, mobile MdCAX3 mRNA is involved in the regulation of iron and zinc homeostasis in response to iron starvation.

PbANK facilitates the long-distance movement of the PbWoxT1-PbPTB3 RNP complex by degrading deposited callose

Grafting horticultural crops can result in phenotypic changes in the grafted materials due to the movement of macromolecular signals, including RNAs and proteins, across the graft union; however, little is known about the composition of trafficking ribonucleoprotein (RNP) complexes or how these macromolecules are transported. Here, we used the core of PbPTB3-PbWoxT1 RNP complex, PbPTB3, as bait to screen Pyrus betulaefolia cDNA library for its interaction partners. We identified an ankyrin protein, PbANK, that interacts with PbPTB3 to facilitate its transport through the phloem alongside PbWoxT1 mRNA. Heterografting experiments showed that silencing PbANK in rootstock prevented the transport of PbPTB3 and PbWoxT1 mRNA from the rootstock to the scion. Similarly, heterologous grafting experiments demonstrated that PbANK itself cannot be transported over long distances through a graft union. Fluorescence microscopy showed that silencing ANK affected the intercellular diffusion of PbPTB3 and increased callose deposition at plasmodesmata. Collectively, these findings demonstrate that PbANK mediates the long-distance movement of PbPTB3 and PbWoxT1 by degrading callose to increase the efficiency of cell-to-cell movement.

Grafting: a potential method to reveal the differential accumulation mechanism of secondary metabolites

Plant secondary metabolites make a great contribution to the agricultural and pharmaceutical industries. Their accumulation is determined by the integrated transport of target compounds and their biosynthesis-related RNA, protein, or DNA. However, it is hard to track the movement of these biomolecules in vivo. Grafting may be an ideal method to solve this problem. The differences in genetic and metabolic backgrounds between rootstock and scion, coupled with multiple omics approaches and other molecular tools, make it feasible to determine the movement of target compounds, RNAs, proteins, and DNAs. In this review, we will introduce methods of using the grafting technique, together with molecular biological tools, to reveal the differential accumulation mechanism of plant secondary metabolites at different levels. Details of the case of the transport of one diterpene alkaloid, fuziline, will be further illustrated to clarify how the specific accumulation model is shaped with the help of grafting and multiple molecular biological tools.

Mobile Messenger RNAs in Grafts of Salix matsudana Are Associated with Plant Rooting

Messenger RNAs exchanged between scions and rootstocks of grafted plants seriously affect their traits performance. The study goals were to identify the long-distance mRNA transmission events in grafted willows using a transcriptome analysis and to reveal the possible effects on rooting traits. The results showed that the Salix matsudana variety 9901 has better rooting ability than YJ, which reasonably improved the rooting performance of the heterologous grafts 9901 (scion)/YJ (rootstock). A transcriptome analysis showed that 2948 differentially expressed genes (DEGs) were present in the rootstock of 9901/YJ grafted plants in comparison with YJ/YJ. Among them, 692 were identified as mRNAs moved from 9901 scion based on SNP analysis of two parents. They were mostly 1001–1500 bp, had 40–45% GC contents, or had expression abundance values less than 10. However, mRNAs over 4001 bp, having 50–55% GC contents, or having expression abundance values of 10–20 were preferentially transferred. Eight mRNAs subjected to long-distance trafficking were involved in the plant hormone pathways and may significantly promote the root growth of grafted plants. In summary, heterologous grafts of Salix matsudana could efficiently influence plant rooting of the mRNAs transport from scion to rootstock.

Rootstock-scion exchanging mRNAs participate in the pathways of amino acids and fatty acid metabolism in cucumber under early chilling stress

Cucumber (Cucumis sativus L.) often experiences chilling stress that limits their growth and productivity. Grafting is widely used to improve abiotic stress resistance by alternating a vigorous root system, suggesting there exists systemic signals communication between distant organs. mRNAs are reported to be evolving in fortification strategies by long-distance signaling when plants suffering from chilling stress. However, the potential function of mobile mRNAs alleviating chilling stress in grafted cucumber is still unknown. Here, the physiological changes, mobile mRNAs profiling, transcriptomic and metabolomic changes in above- and underground tissues of all graft combinations of cucumber and pumpkin responding to chilling stress were established and analyzed comprehensively. The co-relationship between the cluster of chilling-induced pumpkin mobile mRNAs with Differentially Expressed Genes (DEGs) and Differentially Intensive Metabolites (DIMs) revealed that four key chilling-induced pumpkin mobile mRNAs were highly related to glycine, serine and threonine synthesis and fatty acid β-oxidative degradation metabolism in cucumber tissues of heterografts. The verification of mobile mRNAs, potential transport of metabolites and exogenous application of key metabolites of glycerophospholipid metabolism pathway in cucumber seedlings confirmed that the role of mobile mRNAs in regulating chilling responses in grafted cucumber. Our results build a link between the long-distance mRNAs of chilling-tolerant pumpkin and the fatty acid β-oxidative degradation metabolism of chilling-sensitive cucumber. It helps to uncover the mechanism of signaling interaction between scion and stock responding to chilling tolerant in grafted cucumber.

Inter-species mRNA transfer among green peach aphids, dodder parasites, and cucumber host plants

mRNAs are transported within a plant through phloem. Aphids are phloem feeders and dodders (Cuscuta spp.) are parasites which establish phloem connections with host plants. When aphids feed on dodders, whether there is trafficking of mRNAs among aphids, dodders, and host plants and if aphid feeding affects the mRNA transfer between dodders and hosts are unclear. We constructed a green peach aphid (GPA, Myzus persicae)-dodder (Cuscuta australis)-cucumber (Cucumis sativus) tritrophic system by infesting GPAs on C. australis, which parasitized cucumber hosts. We found that GPA feeding activated defense-related phytohormonal and transcriptomic responses in both C. australis and cucumbers and large numbers of mRNAs were found to be transferred between C. australis and cucumbers and between C. australis and GPAs; importantly, GPA feeding on C. australis greatly altered inter-species mobile mRNA profiles. Furthermore, three cucumber mRNAs and three GPA mRNAs could be respectively detected in GPAs and cucumbers. Moreover, our statistical analysis indicated that mRNAs with high abundances and long transcript lengths are likely to be mobile. This study reveals the existence of inter-species and even inter-kingdom mRNA movement among insects, parasitic plants, and parasite hosts, and suggests complex regulation of mRNA trafficking.

Studies on Viroid Shed Light on the Role of RNA Three-Dimensional Structural Motifs in RNA Trafficking in Plants

RNAs play essential roles in various biological processes. Mounting evidence has demonstrated that RNA subcellular localization and intercellular/systemic trafficking govern their functions in coordinating plant growth at the organismal level. While numerous types of RNAs (i.e., mRNAs, small RNAs, rRNAs, tRNAs, and long noncoding RNAs) have been found to traffic in a non-cell-autonomous fashion within plants, the underlying regulatory mechanism remains unclear. Viroids are single-stranded circular noncoding RNAs, which entirely rely on their RNA motifs to exploit cellular machinery for organelle entry and exit, cell-to-cell movement through plasmodesmata, and systemic trafficking. Viroids represent an excellent model to dissect the role of RNA three-dimensional (3D) structural motifs in regulating RNA movement. Nearly two decades of studies have found multiple RNA 3D motifs responsible for viroid nuclear import as well as trafficking across diverse cellular boundaries in plants. These RNA 3D motifs function as "keys" to unlock cellular and subcellular barriers and guide RNA movement within a cell or between cells. Here, we summarize the key findings along this line of research with implications for future studies on RNA trafficking in plants.

Mobile Host mRNAs Are Translated to Protein in the Associated Parasitic Plant Cuscuta campestris

Cuscuta spp. are obligate parasites that connect to host vascular tissue using a haustorium. In addition to water, nutrients, and metabolites, a large number of mRNAs are bidirectionally exchanged between Cuscuta spp. and their hosts. This trans-specific movement of mRNAs raises questions about whether these molecules function in the recipient species. To address the possibility that mobile mRNAs are ultimately translated, we built upon recent studies that demonstrate a role for transfer RNA (tRNA)-like structures (TLSs) in enhancing mRNA systemic movement. C. campestris was grown on Arabidopsis that expressed a β-glucuronidase (GUS) reporter transgene either alone or in GUS-tRNA fusions. Histochemical staining revealed localization in tissue of C. campestris grown on Arabidopsis with GUS-tRNA fusions, but not in C. campestris grown on Arabidopsis with GUS alone. This corresponded with detection of GUS transcripts in Cuscuta on Arabidopsis with GUS-tRNA, but not in C. campestris on Arabidopsis with GUS alone. Similar results were obtained with Arabidopsis host plants expressing the same constructs containing an endoplasmic reticulum localization signal. In C. campestris, GUS activity was localized in the companion cells or phloem parenchyma cells adjacent to sieve tubes. We conclude that host-derived GUS mRNAs are translated in C. campestris and that the TLS fusion enhances RNA mobility in the host-parasite interactions.

Long-distance communication through systemic macromolecular signaling mediates stress defense responses in plants

Land plants have a unique vascular bundle system that ranges in length from a few centimeters to hundreds of meters. These systems integrate the various organs of the whole plant, perform material exchange between different plant tissues and mediate the transmission of signals between cells or over long distances. Grafting and parasitism can reshape the vascular tissues of different ecotypes or species and represent two important systems for studying plant systemic signaling. In recent years, with the advancement of genomics and sequencing technology, the transportation, identification, and function of systemic plant macromolecules have been extensively studied. Here, we review the current body of knowledge of the transport pathways and regulatory mechanisms of macromolecules in plants and assess systemic, long-distance signal trafficking that mediates stress responses, and plant-environment or plant-insect community interactions. Additionally, we propose several methods for identifying mobile mRNAs and proteins. Finally, we discuss the challenges facing systemic signaling research and put forth the most urgent questions that need to be answered to advance our understanding of plant systemic signaling.

Unveiling the Complexity of Red Clover (Trifolium pratense L.) Transcriptome and Transcriptional Regulation of Isoflavonoid Biosynthesis Using Integrated Long- and Short-Read RNAseq

Red clover (Trifolium pratense L.) is used as forage and contains a high level of isoflavonoids. Although isoflavonoids in red clover were discovered a long time ago, the transcriptional regulation of isoflavonoid biosynthesis is virtually unknown because of the lack of accurate and comprehensive characterization of the transcriptome. Here, we used a combination of long-read (PacBio Iso-Seq) and short-read (Illumina) RNAseq sequencing to develop a more comprehensive full-length transcriptome in four tissues (root, stem, leaf, and flower) and to identify transcription factors possibly involved in isoflavonoid biosynthesis in red clover. Overall, we obtained 50,922 isoforms, including 19,860 known genes and 2817 novel isoforms based on the annotation of RefGen Tp_v2.0. We also found 1843 long non-coding RNAs, 1625 fusion genes, and 34,612 alternatively spliced events, with some transcript isoforms validated experimentally. A total of 16,734 differentially expressed genes were identified in the four tissues, including 43 isoflavonoid-biosynthesis-related genes, such as stem-specific expressed TpPAL, TpC4H, and Tp4CL and root-specific expressed TpCHS, TpCHI1, and TpIFS. Further, weighted gene co-expression network analysis and a targeted compound assay were combined to investigate the association between the isoflavonoid content and the transcription factors expression in the four tissues. Twelve transcription factors were identified as key genes for isoflavonoid biosynthesis. Among these transcription factors, the overexpression of TpMYB30 or TpRSM1-2 significantly increased the isoflavonoid content in tobacco. In particular, the glycitin was increased by 50-100 times in the plants overexpressing TpRSM1-2, in comparison to that in the WT plants. Our study provides a comprehensive and accurate annotation of the red clover transcriptome and candidate genes to improve isoflavonoid biosynthesis and accelerate research into molecular breeding in red clover or other crops.

Cold Stress in Citrus: A Molecular, Physiological and Biochemical Perspective

Due to climate change, we are forced to face new abiotic stress challenges like cold and heat waves that currently result from global warming. Losses due to frost and low temperatures force us to better understand the physiological, hormonal, and molecular mechanisms of response to such stress to face losses, especially in tropical and subtropical crops like citrus fruit, which are well adapted to certain weather conditions. Many of the responses to cold stress that are found are also conserved in citrus. Hence, this review also intends to show the latest work on citrus. In addition to basic research, there is a great need to employ and cultivate new citrus rootstocks to better adapt to environmental conditions.

Transcriptome sequencing and differential expression analysis of seed starch accumulation in Chinese chestnut Metaxenia

Background

Chestnut seeds are important kinds of edible nuts rich in starch and protein. The characteristics and nutrient contents of chestnut have been found to show obvious metaxenia effects in previous studies. To improve the understanding of the effect of metaxenia on chestnut starch and sucrose metabolism, this study used three varieties of chestnut, ‘Yongfeng 1’, ‘YongRen Zao’ and ‘Yimen 1’, as male parents to pollinate the female parent, ‘Yongfeng 1’, and investigated the mechanisms of starch and sucrose metabolism in three starch accumulation stages (70 (S1), 82 (S2), and 94 (S3) days after pollination, DAP) in chestnut seed kernels.

Result

Most carbohydrate metabolism genes were highly expressed in YFF (self-pollinated ‘Yongfeng 1’) in stage S2 and in YFR (‘Yongfeng 1’ × ‘Yongren Zao’) and YFM (‘Yongfeng 1’ × ‘Yimen 1’) in stage S3. In stage S3, hub genes encoding HSF_DNA-binding, ACT, Pkinase, and LIM proteins and four transcription factors were highly expressed, with YFF showing the highest expression, followed by YFR and YFM. In addition, transcriptome analysis of the kernels at 70, 82 and 94 DAP showed that the starch granule-bound starch synthase (EC 2.4.1.242) and ADP-glucose pyrophosphorylase (EC 2.7 .7.27) genes were actively expressed at 94 DAF. Chestnut seeds regulate the accumulation of soluble sugars, reducing sugars and starch by controlling glycosyl transferase and hydrolysis activity during development.

Conclusion

These results and resources have important guiding significance for further research on starch and sucrose metabolism and other types of metabolism related to chestnut metaxenia.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07923-5.

Effect of Transgenic Rootstock Grafting on the Omics Profiles in Tomato

Grafting of non-transgenic scion onto genetically modified (GM) rootstocks provides superior agronomic traits in the GM rootstock, and excellent fruits can be produced for consumption. In such grafted plants, the scion does not contain any foreign genes, but the fruit itself is likely to be influenced directly or indirectly by the foreign genes in the rootstock. Before market release of such fruit products, the effects of grafting onto GM rootstocks should be determined from the perspective of safety use. Here, we evaluated the effects of a transgene encoding β-glucuronidase (GUS) on the grafted tomato fruits as a model case. An edible tomato cultivar, Stella Mini Tomato, was grafted onto GM Micro-Tom tomato plants that had been transformed with the GUS gene. The grafted plants showed no difference in their fruit development rate and fresh weight regardless of the presence or absence of the GUS gene in the rootstock. The fruit samples were subjected to transcriptome (NGS-illumina), proteome (shotgun LC-MS/MS), metabolome (LC-ESI-MS and GC-EI-MS), and general food ingredient analyses. In addition, differentially detected items were identified between the grafted plants onto rootstocks with or without transgenes (more than two-fold). The transcriptome analysis detected approximately 18,500 expressed genes on average, and only 6 genes were identified as differentially expressed. Principal component analysis of 2,442 peaks for peptides in proteome profiles showed no significant differences. In the LC-ESI-MS and GC-EI-MS analyses, a total of 93 peak groups and 114 peak groups were identified, respectively, and only 2 peak groups showed more than two-fold differences. The general food ingredient analysis showed no significant differences in the fruits of Stella scions between GM and non-GM Micro-Tom rootstocks. These multiple omics data showed that grafting on the rootstock harboring the GUS transgene did not induce any genetic or metabolic variation in the scion.

Trans-species small RNAs move long distances in a parasitic plant complex

Parasitic plants exchange various types of RNAs with their host plants, including mRNA, and small non-coding RNA. Among small non-coding RNAs, miRNA production is known to be induced at the haustorial interface. The induced miRNAs transfer to the host plant and activate secondary siRNA production to silence target genes in the host. In addition to interfacial transfer, long-distance movement of the small RNAs has also been known to mediate signaling and regulate biological processes. In this study, we tested the long-distance movement of trans-species small RNAs in a parasitic-plant complex. Small RNA-Seq was performed using a complex of a stem parasitic plant, Cuscuta campestris, and a host, Arabidopsis thaliana. In the host plant's parasitized stem, genes involved in the production of secondary siRNA, AtSGS3 and AtRDR6, were upregulated, and 22-nt small RNA was enriched concomitantly, suggesting the activation of secondary siRNA production. Stem-loop RT-PCR and subsequent sequencing experimentally confirmed the mobility of the small RNAs. Trans-species mobile small RNAs were detected in the parasitic interface and also in distant organs. To clarify the mode of long-distance translocation, we examined whether C. campestris-derived small RNA moves long distances in A. thaliana sgs3 and rdr6 mutants or not. Mobility of C. campestris-derived small RNA in sgs3 and rdr6 mutants suggested the occurrence of direct long-distance transport without secondary siRNA production in the recipient plant.

A historical overview of long-distance signalling in plants

Be it a small herb or a large tree, intra- and intercellular communication and long-distance signalling between distant organs are crucial for every aspect of plant development. The vascular system, comprising xylem and phloem, acts as a major conduit for the transmission of long-distance signals in plants. In addition to expanding our knowledge of vascular development, numerous reports in the past two decades revealed that selective populations of RNAs, proteins, and phytohormones function as mobile signals. Many of these signals were shown to regulate diverse physiological processes, such as flowering, leaf and root development, nutrient acquisition, crop yield, and biotic/abiotic stress responses. In this review, we summarize the significant discoveries made in the past 25 years, with emphasis on key mobile signalling molecules (mRNAs, proteins including RNA-binding proteins, and small RNAs) that have revolutionized our understanding of how plants integrate various intrinsic and external cues in orchestrating growth and development. Additionally, we provide detailed insights on the emerging molecular mechanisms that might control the selective trafficking and delivery of phloem-mobile RNAs to target tissues. We also highlight the cross-kingdom movement of mobile signals during plant-parasite relationships. Considering the dynamic functions of these signals, their implications in crop improvement are also discussed.

The interplay of phloem-mobile signals in plant development and stress response

Plants integrate a variety of biotic and abiotic factors for optimal growth in their given environment. While some of these responses are local, others occur distally. Hence, communication of signals perceived in one organ to a second, distal part of the plant and the coordinated developmental response require an intricate signaling system. To do so, plants developed a bipartite vascular system that mediates the uptake of water, minerals, and nutrients from the soil; transports high-energy compounds and building blocks; and traffics essential developmental and stress signals. One component of the plant vasculature is the phloem. The development of highly sensitive mass spectrometry and molecular methods in the last decades has enabled us to explore the full complexity of the phloem content. As a result, our view of the phloem has evolved from a simple transport path of photoassimilates to a major highway for pathogens, hormones and developmental signals. Understanding phloem transport is essential to comprehend the coordination of environmental inputs with plant development and, thus, ensure food security. This review discusses recent developments in its role in long-distance signaling and highlights the role of some of the signaling molecules. What emerges is an image of signaling paths that do not just involve single molecules but rather, quite frequently an interplay of several distinct molecular classes, many of which appear to be transported and acting in concert.

Threat at One End of the Plant: What Travels to Inform the Other Parts?

Adaptation and response to environmental changes require dynamic and fast information distribution within the plant body. If one part of a plant is exposed to stress, attacked by other organisms or exposed to any other kind of threat, the information travels to neighboring organs and even neighboring plants and activates appropriate responses. The information flow is mediated by fast-traveling small metabolites, hormones, proteins/peptides, RNAs or volatiles. Electric and hydraulic waves also participate in signal propagation. The signaling molecules move from one cell to the neighboring cell, via the plasmodesmata, through the apoplast, within the vascular tissue or-as volatiles-through the air. A threat-specific response in a systemic tissue probably requires a combination of different traveling compounds. The propagating signals must travel over long distances and multiple barriers, and the signal intensity declines with increasing distance. This requires permanent amplification processes, feedback loops and cross-talks among the different traveling molecules and probably a short-term memory, to refresh the propagation process. Recent studies show that volatiles activate defense responses in systemic tissues but also play important roles in the maintenance of the propagation of traveling signals within the plant. The distal organs can respond immediately to the systemic signals or memorize the threat information and respond faster and stronger when they are exposed again to the same or even another threat. Transmission and storage of information is accompanied by loss of specificity about the threat that activated the process. I summarize our knowledge about the proposed long-distance traveling compounds and discuss their possible connections.

Epigenetic Changes and Transcriptional Reprogramming Upon Woody Plant Grafting for Crop Sustainability in a Changing Environment

Plant grafting is an ancient agricultural practice widely employed in crops such as woody fruit trees, grapes, and vegetables, in order to improve plant performance. Successful grafting requires the interaction of compatible scion and rootstock genotypes. This involves an intricate network of molecular mechanisms operating at the graft junction and associated with the development and the physiology of the scion, ultimately leading to improved agricultural characteristics such as fruit quality and increased tolerance/resistance to abiotic and biotic factors. Bidirectional transfer of molecular signals such as hormones, nutrients, proteins, and nucleic acids from the rootstock to the scion and vice versa have been well documented. In recent years, studies on rootstock-scion interactions have proposed the existence of an epigenetic component in grafting reactions. Epigenetic changes such as DNA methylation, histone modification, and the action of small RNA molecules are known to modulate chromatin architecture, leading to gene expression changes and impacting cellular function. Mobile small RNAs (siRNAs) migrating across the graft union from the rootstock to the scion and vice versa mediate modifications in the DNA methylation pattern of the recipient partner, leading to altered chromatin structure and transcriptional reprogramming. Moreover, graft-induced DNA methylation changes and gene expression shifts in the scion have been associated with variations in graft performance. If these changes are heritable they can lead to stably altered phenotypes and affect important agricultural traits, making grafting an alternative to breeding for the production of superior plants with improved traits. However, most reviews on the molecular mechanisms underlying this process comprise studies related to vegetable grafting. In this review we will provide a comprehensive presentation of the current knowledge on the epigenetic changes and transcriptional reprogramming associated with the rootstock-scion interaction focusing on woody plant species, including the recent findings arising from the employment of advanced-omics technologies as well as transgrafting methodologies and their potential exploitation for generating superior quality grafts in woody species. Furthermore, will discuss graft-induced heritable epigenetic changes leading to novel plant phenotypes and their implication to woody crop improvement for yield, quality, and stress resilience, within the context of climate change.

To move or not to move: roles and specificity of plant RNA mobility

Intercellular communication in plants coordinates cellular functions during growth and development, and in response to environmental cues. RNAs figure prominently among the mobile signaling molecules used. Many hundreds of RNA species move over short and long distances, and can be mutually exchanged in biotic interactions. Understanding the specificity determinants of RNA mobility and the physiological relevance of this phenomenon are areas of active research. Here, we highlight the recent progress in our knowledge of small RNA and messenger RNA movement. Particular emphasis is given to novel insight into the specificity determinants of messenger RNA mobility, the role of small RNA movement in development, and the specificity of RNA exchange in plant-plant and plant-microbe interactions.

Identification of Long-Distance Transmissible mRNA between Scion and Rootstock in Cucurbit Seedling Heterografts

Grafting has been widely used to improve plant growth and tolerance in crop production, as well as for clarifying systemic mRNA signaling from donor to recipient tissues in organ-to-organ communication. In this study, we investigated graft partner interaction mechanisms of Cucumis sativus (Csa) and Cucurbita moschata (Cmo) using a large-scale endogenous mRNA transport. The results indicated that most mobile transcripts followed an allocation pathway from source to sink. Gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that mRNA mobility functions are universally common and individually specific. Identification of mRNA mobility between distant tissues in heterografts with RT-PCR (reverse transcription PCR), RT-qPCR (reverse transcriptional quantitative real time PCR), and clone sequencing were used to estimate 78.75% of selected mobile transcripts. Integration of bioinformatic analysis and RT-qPCR identification allowed us to hypothesize a scion-to-rootstock-to-scion feedback signal loop of Csa move-down and Cmo move-up mRNAs, where Csa scion move-down mRNAs were involved in carbon fixation and biosynthesis of amino acid pathways, and Cmo root received Csa move-down mRNA and then delivered the corresponding Cmo upward mRNA to scion to improve photosynthesis of cucumber scion. This formed a feedback signal loop of scion-to-rootstock-to scion to explain why pumpkin rootstock enhanced cucumber production in the industry, which was utilized for organ communication and mediates photosynthesis processes in heterograft cucurbit crops.

Long-Distance Movement of mRNAs in Plants

Long-distance transport of information molecules in the vascular tissues could play an important role in regulating plant growth and enabling plants to cope with adverse environments. Various molecules, including hormones, proteins, small peptides and small RNAs have been detected in the vascular system and proved to have systemic signaling functions. Sporadic studies have shown that a number of mRNAs produced in the mature leaves leave their origin cells and move to distal tissues to exert important physiological functions. In the last 3-5 years, multiple heterograft systems have been developed to demonstrate that a large quantity of mRNAs are mobile in plants. Further comparison of the mobile mRNAs identified from these systems showed that the identities of these mRNAs are very diverse. Although species-specific mRNAs may regulate the unique physiological characteristic of the plant, mRNAs with conserved functions across multiple species are worth more effort in identifying universal physiological mechanisms existing in the plant kingdom.

Systemic Long-Distance Signaling and Communication Between Rootstock and Scion in Grafted Vegetables

Grafting is widely used in fruit, vegetable, and flower propagation to improve biotic and abiotic stress resistance, yield, and quality. At present, the systemic changes caused by grafting, as well as the mechanisms and effects of long-distance signal transport between rootstock and scion have mainly been investigated in model plants (Arabidopsis thaliana and Nicotiana benthamiana). However, these aspects of grafting vary when different plant materials are grafted, so the study of model plants provides only a theoretical basis and reference for the related research of grafted vegetables. The dearth of knowledge about the transport of signaling molecules in grafted vegetables is inconsistent with the rapid development of large-scale vegetable production, highlighting the need to study the mechanisms regulating the rootstock-scion interaction and long-distance transport. The rapid development of molecular biotechnology and "omics" approaches will allow researchers to unravel the physiological and molecular mechanisms involved in the rootstock-scion interaction in vegetables. We summarize recent progress in the study of the physiological aspects (e.g., hormones and nutrients) of the response in grafted vegetables and focus in particular on long-distance molecular signaling (e.g., RNA and proteins). This review provides a theoretical basis for studies of the rootstock-scion interaction in grafted vegetables, as well as provide guidance for rootstock breeding and selection to meet specific demands for efficient vegetable production.

Extensive Inter-plant Protein Transfer between Cuscuta Parasites and Their Host Plants

Cuscuta species (dodders) are holoparasites that totally rely on host plants to survive. Although various mobile proteins have been identified to travel within a plant, whether and to what extent protein transfer between Cuscuta and host plants remain unclear. We found that hundreds to more than 1500 proteins were transferred between Cuscuta and the host plants Arabidopsis and soybean, and hundreds of inter-plant mobile proteins were even detected in the seeds of Cuscuta and the host soybean. Different hosts bridge-connected by dodder were also found to exchange hundreds of proteins. Quantitatively, the mobile proteins represent a few to more than 10% of the proteomes of foreign plants. Using Arabidopsis plants expressing different reporter proteins, we further showed that these reporter proteins could travel between plants and, importantly, retained their activity in the foreign plants. Comparative analysis between the inter-plant mobile proteins and mRNAs indicated that the majority of mobile proteins were not de novo synthesized from the translocated mRNAs, but bona fide mobile proteins. We propose that large-scale inter-plant protein translocation may play an important role in the interactions between host plants and dodder and even among the dodder bridge-connected hosts.

A constitutive and drought-responsive mRNA undergoes long-distance transport in pear (Pyrus betulaefolia) phloem

Pear is one of the most commercially important fruit trees worldwide and is widely cultivated in temperate zones. Drought stress can greatly limit pear fruit yield and quality. Pyrus betulaefolia Bunge, a drought-resistant pear rootstock that is commonly used in northern China, confers favourable characteristics to pear scions, allowing them to respond rapidly to drought stress via the transport of macromolecules such as phloem-mobile mRNAs. How drought-responsive mRNAs function as phloem-mobile signals remains unknown, however. Here, we used RNA sequencing (RNA-seq) combined with SNP analysis to identify mobile mRNAs in P. betulaefolia. We focused on mobile mRNAs that respond to drought stress and found that the abundance of a novel mRNA named PbDRM (P. betulaefoliaDROUGHT-RESPONSIVE MOBILE GENE) significantly increased in several different scion cultivars when they were grafted onto P. betulaefolia rootstock under drought conditions. In addition, downregulating PbDRM by virus-induced gene silencing (VIGS) increased the drought sensitivity of P. betulaefolia. CAPS RT-PCR analysis confirmed that PbDRM mRNA moves from rootstock to scion in micrografting systems. Therefore, PbDRM mRNA acts as a phloem-mobile signal in pear under drought stress.

Identification of Phloem Mobile mRNAs Using the Solanaceae Heterograft System

Large numbers of mRNAs move in the phloem and some may function as signals to exert important physiological functions in the distal recipient organs. Generating an authentic list of phloem mobile mRNA is a prerequisite for elucidating their physiological functions. Nicotiana benthamiana can be used as a scion to graft on a tomato (Solanum lycopersicum) rootstock. Thereby, shoot-to-root mobile N. benthamiana mRNAs transported via the phloem can be identified from the root of the tomato rootstock. Due to the close relationship and similar genome sequences of the two species, stringent informatics procedures should be applied to avoid false identification. This heterograft system can be used to study physiological processes associated with mRNAs that are mobile under either normal or adverse growth condition.

The role of microRNAs in the legume-Rhizobium nitrogen-fixing symbiosis

Under nitrogen starvation, most legume plants form a nitrogen-fixing symbiosis with Rhizobium bacteria. The bacteria induce the formation of a novel organ called the nodule in which rhizobia reside as intracellular symbionts and convert atmospheric nitrogen into ammonia. During this symbiosis, miRNAs are essential for coordinating the various plant processes required for nodule formation and function. miRNAs are non-coding, endogenous RNA molecules, typically 20-24 nucleotides long, that negatively regulate the expression of their target mRNAs. Some miRNAs can move systemically within plant tissues through the vascular system, which mediates, for example, communication between the stem/leaf tissues and the roots. In this review, we summarize the growing number of miRNAs that function during legume nodulation focusing on two model legumes, Lotus japonicus and Medicago truncatula, and two important legume crops, soybean (Glycine max) and common bean (Phaseolus vulgaris). This regulation impacts a variety of physiological processes including hormone signaling and spatial regulation of gene expression. The role of mobile miRNAs in regulating legume nodule number is also highlighted.

Utilizing Potato Virus X to Monitor RNA Movement

Mobility assays coupled with RNA profiling have revealed the presence of hundreds of full-length non-cell-autonomous messenger RNAs that move through the whole plant via the phloem cell system. Monitoring the movement of these RNA signals can be difficult and time consuming. Here we describe a simple, virus-based system for surveying RNA movement by replacing specific sequences within the viral RNA genome of potato virus X (PVX) that are critical for movement with other sequences that facilitate movement. PVX is a RNA virus dependent on three small proteins that facilitate cell-to-cell transport and a coat protein (CP) required for long-distance spread of PVX. Deletion of the CP blocks movement, whereas replacing the CP with phloem-mobile RNA sequences reinstates mobility. Two experimental models validating this assay system are discussed. One involves the movement of the flowering locus T RNA that regulates floral induction and the second involves movement of StBEL5, a long-distance RNA signal that regulates tuber formation in potato.

In Vivo Imaging of Mobile mRNAs in Plants Using MS2

Multicellular organisms rely on systemic signals to orchestrate diverse developmental and physiological programs. To transmit environmental stimuli that perceived in the leaves, plants recruit many mobile molecules including mobile mRNAs as systemic signals for interorgan communication. The mobile mRNAs provide an efficient and specific remote control system for plants to cope with environmental dynamics. Upon being transcribed in local tissues, mobile mRNAs are selectively targeted to plasmodesmata for cell-to-cell and long-distance translocation. The mRNA labeling system based on the RNA-binding protein MS2 provides a useful tool to investigate intracellular trafficking of mobile mRNAs in plants. Here we describe the detailed protocol to visualize intracellular trafficking of plant mobile mRNAs by using the MS2 live-cell imaging system.

A three-dimensional RNA motif mediates directional trafficking of Potato spindle tuber viroid from epidermal to palisade mesophyll cells in Nicotiana benthamiana

Potato spindle tuber viroid (PSTVd) is a circular non-coding RNA of 359 nucleotides that replicates and spreads systemically in host plants, thus all functions required to establish an infection are mediated by sequence and structural elements in the genome. The PSTVd secondary structure contains 26 Watson-Crick base-paired stems and 27 loops. Most of the loops are believed to form three-dimensional (3D) structural motifs through non-Watson-Crick base pairing, base stacking, and other local interactions. Homology-based prediction using the JAR3D online program revealed that loop 27 (nucleotides 177-182) most likely forms a 3D structure similar to the loop of a conserved hairpin located in the 3' untranslated region of histone mRNAs in animal cells. This stem-loop, which is involved in 3'-end maturation, is not found in polyadenylated plant histone mRNAs. Mutagenesis showed that PSTVd genomes containing base substitutions in loop 27 predicted by JAR3D to disrupt the 3D structure were unable to replicate in Nicotiana benthamiana leaves following mechanical rub inoculation, with one exception: a U178G/U179G double mutant was replication-competent and able to spread within the upper epidermis of inoculated leaves, but was confined to this cell layer. Remarkably, direct delivery of the U178G/U179G mutant into the vascular system by needle puncture inoculation allowed it to spread systemically and enter mesophyll cells and epidermal cells of upper leaves. These findings highlight the importance of RNA 3D structure for PSTVd replication and intercellular trafficking and indicate that loop 27 is required for epidermal exit, but not epidermal entry or transit between other cell types. Thus, requirements for RNA trafficking between epidermal and underlying palisade mesophyll cells are unique and directional. Our findings further suggest that 3D structure and RNA-protein interactions constrain RNA sequence evolution, and validate JAR3D as a tool to predict RNA 3D structure.

Systemic signalling through translationally controlled tumour protein controls lateral root formation in Arabidopsis

The plant body plan and primary organs are established during embryogenesis. However, in contrast to animals, plants have the ability to generate new organs throughout their whole life. These give them an extraordinary developmental plasticity to modulate their size and architecture according to environmental constraints and opportunities. How this plasticity is regulated at the whole-organism level is elusive. Here we provide evidence for a role for translationally controlled tumour protein (TCTP) in regulating the iterative formation of lateral roots in Arabidopsis. AtTCTP1 modulates root system architecture through a dual function: as a general constitutive growth promoter enhancing root elongation and as a systemic signalling agent via mobility in the vasculature. AtTCTP1 encodes mRNAs with long-distance mobility between the shoot and roots. Mobile shoot-derived TCTP1 gene products act specifically to enhance the frequency of lateral root initiation and emergence sites along the primary root pericycle, while root elongation is controlled by local constitutive TCTP1 expression and scion size. These findings uncover a novel type for an integrative signal in the control of lateral root initiation and the compromise for roots between branching more profusely or elongating further. They also provide the first evidence in plants of an extracellular function of the vital, highly expressed ubiquitous TCTP1.

Comprehensive transcriptome profiling and phenotyping of rootstock and scion in a tomato/potato heterografting system

Tomato/potato heterografting-triggered phenotypic variations are well documented, yet the molecular mechanisms underlying grafting-induced phenotypic processes remain unknown. To investigate the phenotypic and transcriptomic responses of grafting parents in heterografting in comparison with self-grafting, tomato (Sl) was grafted onto potato rootstocks (St), and comparative phenotyping and transcriptome profiling were performed. Phenotypic analysis showed that Sl/St heterografting induced few phenotypic changes in the tomato scion. A total of 209 upregulated genes were identified in the tomato scion, some of which appear to be involved in starch and sucrose biosynthesis. Sl/St heterografting induced several modifications in the potato rootstocks (St-R), stolon number, stolon length and tuber number decreased significantly, together with an increase in GA₃ content of stolon and tuber, compared with self-grafted potato (St-WT). These results indicate that the tomato scion is less effective at producing substances or signals to induce tuberization but promotes stolon development into aerial stems and sprouting. RNA-Seq data analysis showed that 1529 genes were upregulated and 1329 downregulated between St-WT and St-R; some of these genes are involved in plant hormone signal transduction, with GID1-like gibberellin receptor (StGID1) and DELLA protein (StDELLA) being upregulated. Several genes in auxin, abscisic acid and ethylene pathways were differentially expressed as well. Various hormone signals engage in crosstalk to regulate diverse phenotypic events after grafting. This work provides abundant transcriptome profile data and lays a foundation for further research on the molecular mechanisms underlying RNA-based interactions between rootstocks and scions after tomato/potato heterografting.

Connecting the pieces: uncovering the molecular basis for long-distance communication through plant grafting

Vascular plants are wired with a remarkable long-distance communication system. This network can span from as little as a few centimeters (or less) in species like Arabidopsis, up to 100 m in the tallest giant sequoia, linking distant organ systems into a unified, multicellular organism. Grafting is a fundamental technique that allows researchers to physically break apart and reassemble the long-distance transport system, enabling the discovery of molecular signals that underlie intraorganismal communication. In this review, we highlight how plant grafting has facilitated the discovery of new long-distance signaling molecules that function in coordinating developmental transitions, abiotic and biotic responses, and cross-species interactions. This rapidly expanding area of research offers sustainable approaches for improving plant performance in the laboratory, the field, the orchard, and beyond.

Rootstock effects on scion phenotypes in a 'Chambourcin' experimental vineyard

Understanding how root systems modulate shoot system phenotypes is a fundamental question in plant biology and will be useful in developing resilient agricultural crops. Grafting is a common horticultural practice that joins the roots (rootstock) of one plant to the shoot (scion) of another, providing an excellent method for investigating how these two organ systems affect each other. In this study, we used the French-American hybrid grapevine 'Chambourcin' (Vitis L.) as a model to explore the rootstock-scion relationship. We examined leaf shape, ion concentrations, and gene expression in 'Chambourcin' grown ungrafted as well as grafted to three different rootstocks ('SO4', '1103P' and '3309C') across 2 years and three different irrigation treatments. We found that a significant amount of the variation in leaf shape could be explained by the interaction between rootstock and irrigation. For ion concentrations, the primary source of variation identified was the position of a leaf in a shoot, although rootstock and rootstock by irrigation interaction also explained a significant amount of variation for most ions. Lastly, we found rootstock-specific patterns of gene expression in grafted plants when compared to ungrafted vines. Thus, our work reveals the subtle and complex effect of grafting on 'Chambourcin' leaf morphology, ionomics, and gene expression.

Plant lncRNAs are enriched in and move systemically through the phloem in response to phosphate deficiency

In response to phosphate (Pi) deficiency, it has been shown that micro-RNAs (miRNAs) and mRNAs are transported through the phloem for delivery to sink tissues. Growing evidence also indicates that long non-coding RNAs (lncRNAs) are critical regulators of Pi homeostasis in plants. However, whether lncRNAs are present in and move through the phloem, in response to Pi deficiency, remains to be established. Here, using cucumber as a model plant, we show that lncRNAs are enriched in the phloem translocation stream and respond, systemically, to an imposed Pi-stress. A well-known lncRNA, IPS1, the target mimic (TM) of miRNA399, accumulates to a high level in the phloem, but is not responsive to early Pi deficiency. An additional 24 miRNA TMs were also detected in the phloem translocation stream; among them miRNA171 TMs and miR166 TMs were induced in response to an imposed Pi stress. Grafting studies identified 22 lncRNAs which move systemically into developing leaves and root tips. A CU-rich PTB motif was further identified in these mobile lncRNAs. Our findings revealed that lncRNAs respond to Pi deficiency, non-cell-autonomously, and may act as systemic signaling agents to coordinate early Pi deficiency signaling, at the whole-plant level.

PbTTG1 forms a ribonucleoprotein complex with polypyrimidine tract-binding protein PbPTB3 to facilitate the long-distance trafficking of PbWoxT1 mRNA

The grafting of horticultural crops enables breeders to induce phenotypic changes in rootstocks and scions. A number of signaling molecules, including RNAs and proteins, were recently shown to underlie these changes; however, little is known about the composition of ribonucleoprotein (RNP) complexes or how these macromolecules are transported. Here, we used a polypyrimidine tract-binding protein, PbPTB3, as a bait to screen a library of phloem cDNA from a pear variety 'Du Li' (Pyrus betulaefolia). We identified a new protein constituent of the RNP complex, TRANSPARENT TESTA GLABRA1 (PbTTG1), a WD40 protein that interacts with PbPTB3 to facilitate its transport with PbWoxT1 mRNA through the phloem. Overexpression experiments indicated that PbTTG1 binds to PbPTB3, facilitating its transmission from the leaf through the petiole, while silencing of PbTTG1 expression prevented their translocation. Heterografting experiments also showed that silencing of PbTTG1 prevented the transport of PbPTB3 from the rootstock to the scion. Collectively, these findings established that PbTTG1 binds to PbPTB3 and PbWoxT1 to form an RNP complex, which facilitates their long-distance movement.

The developmental dynamics of the Populus stem transcriptome

The Populus shoot undergoes primary growth (longitudinal growth) followed by secondary growth (radial growth), which produces biomass that is an important source of energy worldwide. We adopted joint PacBio Iso-Seq and RNA-seq analysis to identify differentially expressed transcripts along a developmental gradient from the shoot apex to the fifth internode of Populus Nanlin895. We obtained 87 150 full-length transcripts, including 2081 new isoforms and 62 058 new alternatively spliced isoforms, most of which were produced by intron retention, that were used to update the Populus annotation. Among these novel isoforms, there are 1187 long non-coding RNAs and 356 fusion genes. Using this annotation, we found 15 838 differentially expressed transcripts along the shoot developmental gradient, of which 1216 were transcription factors (TFs). Only a few of these genes were reported previously. The differential expression of these TFs suggests that they may play important roles in primary and secondary growth. AP2, ARF, YABBY and GRF TFs are highly expressed in the apex, whereas NAC, bZIP, PLATZ and HSF TFs are likely to be important for secondary growth. Overall, our findings provide evidence that long-read sequencing can complement short-read sequencing for cataloguing and quantifying eukaryotic transcripts and increase our understanding of the vital and dynamic process of shoot development.