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

Brassinosteroids-Induced Systemic Stress Tolerance was Associated with Increased Transcripts of Several Defence-Related Genes in the Phloem in Cucumis sativus

Brassinosteroids (BRs), a group of naturally occurring plant steroidal compounds, are essential for plant growth, development and stress tolerance. Recent studies showed that BRs could induce systemic tolerance to biotic and abiotic stresses; however, the molecular mechanisms by which BRs signals lead to responses in the whole plant are largely unknown. In this study, 24-epibrassinosteroid (EBR)-induced systemic tolerance in Cucumis sativus L. cv. Jinyan No. 4 was analyzed through the assessment of symptoms of photooxidative stress by chlorophyll fluorescence imaging pulse amplitude modulation. Expression of defense/stress related genes were induced in both treated local leaves and untreated systemic leaves by local EBR application. With the suppressive subtractive hybridization (SSH) library using cDNA from the phloem sap of EBR-treated plants as the tester and distilled water (DW)-treated plants as the driver, 14 transcripts out of 260 clones were identified. Quantitative Real Time-Polymerase Chain Reaction (RT-qPCR) validated the specific up-regulation of these transcripts. Of the differentially expressed transcripts with known functions, transcripts for the selected four cDNAs, which encode an auxin-responsive protein (IAA14), a putative ankyrin-repeat protein, an F-box protein (PP2), and a major latex, pathogenesis-related (MLP)-like protein, were induced in local leaves, systemic leaves and roots after foliar application of EBR onto mature leaves. Our results demonstrated that EBR-induced systemic tolerance is accompanied with increased transcript of genes in the defense response in other organs. The potential role of phloem mRNAs as signaling components in mediating BR-regulated systemic resistance is discussed.

Inter-species grafting caused extensive and heritable alterations of DNA methylation in Solanaceae plants

BACKGROUND

Grafting has been extensively used to enhance the performance of horticultural crops. Since Charles Darwin coined the term "graft hybrid" meaning that asexual combination of different plant species may generate products that are genetically distinct, highly discrepant opinions exist supporting or against the concept. Recent studies have documented that grafting enables exchanges of both RNA and DNA molecules between the grafting partners, thus providing a molecular basis for grafting-induced genetic variation. DNA methylation is known as prone to alterations as a result of perturbation of internal and external conditions. Given characteristics of grafting, it is interesting to test whether the process may cause an alteration of this epigenetic marker in the grafted organismal products.

METHODOLOGY/PRINCIPAL FINDINGS

We analyzed relative global DNA methylation levels and locus-specific methylation patterns by the MSAP marker and locus-specific bisulfite-sequencing in the seed plants (wild-type controls), self- and hetero-grafted scions/rootstocks, selfed progenies of scions and their seed-plant controls, involving three Solanaceae species. We quantified expression of putative genes involved in establishing and/or maintaining DNA methylation by q-(RT)-PCR. We found that (1) hetero-grafting caused extensive alteration of DNA methylation patterns in a locus-specific manner, especially in scions, although relative methylation levels remain largely unaltered; (2) the altered methylation patterns in the hetero-grafting-derived scions could be inherited to sexual progenies with some sites showing further alterations or revisions; (3) hetero-grafting caused dynamic changes in steady-state transcript abundance of genes encoding for a set of enzymes functionally relevant to DNA methylation.

CONCLUSIONS/SIGNIFICANCE

Our results demonstrate that inter-species grafting in plants could produce extensive and heritable alterations in DNA methylation. We suggest that these readily altered, yet heritable, epigenetic modifications due to interspecies hetero-grafting may shed one facet of insight into the molecular underpinnings for the still contentious concept of graft hybrid.

The plant vascular system: evolution, development and functions

The emergence of the tracheophyte-based vascular system of land plants had major impacts on the evolution of terrestrial biology, in general, through its role in facilitating the development of plants with increased stature, photosynthetic output, and ability to colonize a greatly expanded range of environmental habitats. Recently, considerable progress has been made in terms of our understanding of the developmental and physiological programs involved in the formation and function of the plant vascular system. In this review, we first examine the evolutionary events that gave rise to the tracheophytes, followed by analysis of the genetic and hormonal networks that cooperate to orchestrate vascular development in the gymnosperms and angiosperms. The two essential functions performed by the vascular system, namely the delivery of resources (water, essential mineral nutrients, sugars and amino acids) to the various plant organs and provision of mechanical support are next discussed. Here, we focus on critical questions relating to structural and physiological properties controlling the delivery of material through the xylem and phloem. Recent discoveries into the role of the vascular system as an effective long-distance communication system are next assessed in terms of the coordination of developmental, physiological and defense-related processes, at the whole-plant level. A concerted effort has been made to integrate all these new findings into a comprehensive picture of the state-of-the-art in the area of plant vascular biology. Finally, areas important for future research are highlighted in terms of their likely contribution both to basic knowledge and applications to primary industry.

Heavy traffic in the fast lane: long-distance signalling by macromolecules

The two major vascular conduits in plants, the xylem and phloem, theoretically provide opportunities for the long-distance translocation of almost any type of water-borne molecule. This review focuses on the signalling functions conveyed by the movement of macromolecules. Here, a signal is defined as the communication of information from source to destination, where it modifies development, physiology or defence through altered gene expression or by direct influences on other cellular processes. Xylem and phloem sap both contain diverse classes of proteins; in addition, phloem contains many full-length and small RNA species. Only a few of these mobile molecules have proven functions in signalling. The transduction of signals typically depends on connection to appropriate signalling pathways. Incoming protein signals require specific detection systems, generally via receptors. Mobile RNAs require either the translation or presence of a homologous target. Given that phloem sieve elements are enucleate and lack translation machinery, RNA function requires subsequent unloading at least into adjacent companion cells. The binding of RNA by proteins in ribonucleoprotein complexes enables the translocation of some signals, with evidence for both sequence-specific and size-specific binding. Several examples of long-distance macromolecular signalling are highlighted, including the FT protein signal which regulates flowering time and other developmental switches.

Intercellular and systemic spread of RNA and RNAi in plants

Plants possess dynamic networks of intercellular communication that are crucial for plant development and physiology. In plants, intercellular communication involves a combination of ligand-receptor-based apoplasmic signaling, and plasmodesmata and phloem-mediated symplasmic signaling. The intercellular trafficking of macromolecules, including RNAs and proteins, has emerged as a novel mechanism of intercellular communication in plants. Various forms of regulatory RNAs move over distinct cellular boundaries through plasmodesmata and phloem. This plant-specific, non-cell-autonomous RNA trafficking network is also involved in development, nutrient homeostasis, gene silencing, pathogen defense, and many other physiological processes. However, the mechanism underlying macromolecular trafficking in plants remains poorly understood. Current progress made in RNA trafficking research and its biological relevance to plant development will be summarized. Diverse plant regulatory mechanisms of cell-to-cell and systemic long-distance transport of RNAs, including mRNAs, viral RNAs, and small RNAs, will also be discussed.

A census of cells in time: quantitative genetics meets developmental biology

Quantitative genetics has become a popular method for determining the genetic basis of natural variation. Combined with genomic methods, it provides a tool for discerning the genetic basis of gene expression. So-called genetical genomics approaches yield a wealth of genomic information, but by necessity, because of cost and time, fail to resolve the differences between organs, tissues, and/or cell types. Similarly, quantitative approaches in development that might potentially address these issues are seldom applied to quantitative genetics. We discuss recent advances in cell type-specific isolation methods, the quantitative analysis of phenotype, and developmental modeling that are compatible with quantitative genetics and, with time, promise to bridge the gap between these two powerful disciplines yielding unprecedented biological insight.

A critical appraisal of phloem-mobile signals involved in tuber induction

The identification of FLOWERING LOCUS T (FT) and several FT homologs as phloem-mobile proteins that regulate flowering has sparked the search for additional homologs involved in the long-distance regulation of other developmental processes. Given that flowering and tuber induction share regulatory pathways, the quest for long-distance tuberization signals has been further stimulated. Several tuberization regulators have been proposed as mobile molecules, including the FT family protein StSP6A, the plant growth regulators gibberellins and the microRNA miR172. Although some of these hypotheses are attractive and plausible, evidence that these molecules are transmissible in potato has yet to be obtained. Two mRNAs encoding transcription factors, StBEL5 and POTATO HOMEOBOX 1 (POTH1), are mobile and correlate with tuber induction. However, evidence that StBEL5 or POTH1 are required for tuberization is not available yet. Therefore, there are several good candidates for long-distance molecules in the tuberization process. Further research should test their role as systemic tuberization signals.

Phloem-mobile messenger RNAs and root development

Numerous signal molecules move through the phloem to regulate development, including proteins, secondary metabolites, small RNAs and full-length transcripts. Several full-length mRNAs have been identified that move long distances in a shootward or rootward direction through the plant vasculature to modulate both floral and vegetative processes of growth. Here we discuss two recently discovered examples of long-distance transport of full-length mRNAs into roots and the potential target genes and pathways for these mobile signals. In both cases, the mobile RNAs regulate root growth. Previously, RNA movement assays demonstrated that transcripts of StBEL5, a transcription factor from the three-amino-loop-extension superclass, move through the phloem to stolon tips to enhance tuber formation in potato (Solanum tuberosum L.). StBEL5 mRNA originates in the leaf and its movement to stolons is induced by a short-day photoperiod. Movement of StBEL5 RNA to roots correlated with increased growth and the accumulation of several transcripts associated with hormone metabolism, including GA2-oxidase1, YUCCA1a and -c, several Aux/IAA types, and PIN1, -2, and -4 was observed. In another example, heterografting techniques were used to identify phloem-mobile Aux/IAA transcripts in Arabidopsis. Movement assays confirmed that these Aux/IAA transcripts are transported into the root system where they suppress lateral root formation. Phloem transport of both StBEL5 and Aux/IAA RNAs are linked to hormone metabolism and both target auxin synthesis genes or auxin signaling processes. The mechanisms of transport for these mobile RNAs, the impact they have on controlling root growth, and a potential transcriptional connection between the BEL1/KNOX complex and Aux/IAA genes are discussed.

The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions

Watermelon, Citrullus lanatus, is an important cucurbit crop grown throughout the world. Here we report a high-quality draft genome sequence of the east Asia watermelon cultivar 97103 (2n = 2× = 22) containing 23,440 predicted protein-coding genes. Comparative genomics analysis provided an evolutionary scenario for the origin of the 11 watermelon chromosomes derived from a 7-chromosome paleohexaploid eudicot ancestor. Resequencing of 20 watermelon accessions representing three different C. lanatus subspecies produced numerous haplotypes and identified the extent of genetic diversity and population structure of watermelon germplasm. Genomic regions that were preferentially selected during domestication were identified. Many disease-resistance genes were also found to be lost during domestication. In addition, integrative genomic and transcriptomic analyses yielded important insights into aspects of phloem-based vascular signaling in common between watermelon and cucumber and identified genes crucial to valuable fruit-quality traits, including sugar accumulation and citrulline metabolism.

Phloem-mobile Aux/IAA transcripts target to the root tip and modify root architecture

In plants, the phloem is the component of the vascular system that delivers nutrients and transmits signals from mature leaves to developing sink tissues. Recent studies have identified proteins, mRNA, and small RNA within the phloem sap of several plant species. It is now of considerable interest to elucidate the biological functions of these potential long-distance signal agents, to further our understanding of how plants coordinate their developmental programs at the whole-plant level. In this study, we developed a strategy for the functional analysis of phloem-mobile mRNA by focusing on IAA transcripts, whose mobility has previously been reported in melon (Cucumis melo cv. Hale's Best Jumbo). Indoleacetic acid (IAA) proteins are key transcriptional regulators of auxin signaling, and are involved in a broad range of developmental processes including root development. We used a combination of vasculature-enriched sampling and hetero-grafting techniques to identify IAA18 and IAA28 as phloem-mobile transcripts in the model plant Arabidopsis thaliana. Micro-grafting experiments were used to confirm that these IAA transcripts, which are generated in vascular tissues of mature leaves, are then transported into the root system where they negatively regulate lateral root formation. Based on these findings, we present a model in which auxin distribution, in combination with phloem-mobile Aux/IAA transcripts, can determine the sites of auxin action.

Overexpression of Arabidopsis plasmodesmata germin-like proteins disrupts root growth and development

In plants, a population of non-cell-autonomous proteins (NCAPs), including numerous transcription factors, move cell to cell through plasmodesmata (PD). In many cases, the intercellular trafficking of these NCAPs is regulated by their interaction with specific PD components. To gain further insight into the functions of this NCAP pathway, coimmunoprecipitation experiments were performed on a tobacco (Nicotiana tabacum) plasmodesmal-enriched cell wall protein preparation using as bait the NCAP, pumpkin (Cucurbita maxima) PHLOEM PROTEIN16 (Cm-PP16). A Cm-PP16 interaction partner, Nt-PLASMODESMAL GERMIN-LIKE PROTEIN1 (Nt-PDGLP1) was identified and shown to be a PD-located component. Arabidopsis thaliana putative orthologs, PDGLP1 and PDGLP2, were identified; expression studies indicated that, postgermination, these proteins were preferentially expressed in the root system. The PDGLP1 signal peptide was shown to function in localization to the PD by a novel mechanism involving the endoplasmic reticulum-Golgi secretory pathway. Overexpression of various tagged versions altered root meristem function, leading to reduced primary root but enhanced lateral root growth. This effect on root growth was corrected with an inability of these chimeric proteins to form stable PD-localized complexes. PDGLP1 and PDGLP2 appear to be involved in regulating primary root growth by controlling phloem-mediated allocation of resources between the primary and lateral root meristems.

MicroRNAs and their diverse functions in plants

microRNAs (miRNAs) are an extensive class of newly identified small RNAs, which regulate gene expression at the post-transcriptional level by mRNA cleavage or translation inhibition. Currently, there are 3,070 miRNAs deposited in the public available miRNA database; these miRNAs were obtained from 43 plant species using both computational (comparative genomics) and experimental (direct cloning and deep sequencing) approaches. Like other signaling molecules, plant miRNAs can also be moved from one tissue to another through the vascular system. These mobile miRNAs may play an important role in plant nutrient homeostasis and response to environmental biotic and abiotic stresses. In addition, miRNAs also control a wide range of biological and metabolic processes, including developmental timing, tissue-specific development, and stem cell maintenance and differentiation. Currently, a majority of plant miRNA-related researches are purely descriptive, and provide no further detailed mechanistic insight into miRNA-mediated gene regulation and other functions. To better understand the function and regulatory mechanisms of plant miRNAs, more strategies need to be employed to investigate the functions of miRNAs and their associated signaling pathways and gene networks. Elucidating the evolutionary mechanism of miRNAs is also important. It is possible to develop a novel miRNA-based biotechnology for improving plant yield, quality and tolerance to environmental biotic and abiotic stresses besides focusing on basic genetic studies.

The peach (Prunus persica L. Batsch) genome harbours 10 KNOX genes, which are differentially expressed in stem development, and the class 1 KNOPE1 regulates elongation and lignification during primary growth

The KNOTTED-like (KNOX) genes encode homeodomain transcription factors and regulate several processes of plant organ development. The peach (Prunus persica L. Batsch) genome was found to contain 10 KNOX members (KNOPE genes); six of them were experimentally located on the Prunus reference map and the class 1 KNOPE1 was found to link to a quantitative trait locus (QTL) for the internode length in the peach×Ferganensis population. All the KNOPE genes were differentially transcribed in the internodes of growing shoots; the KNOPE1 mRNA abundance decreased progressively from primary (elongation) to secondary growth (radial expansion). During primary growth, the KNOPE1 mRNA was localized in the cortex and in the procambium/metaphloem zones, whereas it was undetected in incipient phloem and xylem fibres. KNOPE1 overexpression in the Arabidopsis bp4 loss-of-function background (35S:KNOPE1/bp genotype) restored the rachis length, suggesting, together with the QTL association, a role for KNOPE1 in peach shoot elongation. Several lignin biosynthesis genes were up-regulated in the bp4 internodes but repressed in the 35S:KNOPE1/bp lines similarly to the wild type. Moreover, the lignin deposition pattern of the 35S:KNOPE1/bp and the wild-type internodes were the same. The KNOPE1 protein was found to recognize in vitro one of the typical KNOX DNA-binding sites that recurred in peach and Arabidopsis lignin genes. KNOPE1 expression was inversely correlated with that of lignin genes and lignin deposition along the peach shoot stems and was down-regulated in lignifying vascular tissues. These data strongly support that KNOPE1 prevents cell lignification by repressing lignin genes during peach stem primary growth.

The mRNA of a Knotted1-like transcription factor of potato is phloem mobile

Potato Homeobox1 (POTH1) is a Knotted1-like transcription factor from the Three Amino Acid Loop Extension (TALE) superfamily that is involved in numerous aspects of development in potato (Solanum tuberosum L). POTH1 interacts with its protein partner, StBEL5, to facilitate binding to specific target genes to modulate hormone levels, mediate leaf architecture, and enhance tuber formation. In this study, promoter analyses show that the upstream sequence of POTH1 drives β-glucuronidase activity in response to light and in association with phloem cells in both petioles and stems. Because POTH1 transcripts have previously been detected in phloem cells, long-distance movement of its mRNA was tested. Using RT-PCR and transgenic potato lines over-expressing POTH1, in vitro micrografts demonstrated unilateral movement of POTH1 RNA in a rootward direction. Movement across a graft union into leaves from newly arising axillary shoots and roots of wild type stocks was verified using soil-grown tobacco heterografts. Leaves from the wild type stock containing the mobile POTH1 RNA exhibited a reduction in leaf size relative to leaves from wild type grafts. Both untranslated regions of POTH1 when fused to an expression marker β-glucuronidase, repressed its translation in tobacco protoplasts. RNA/protein binding assays demonstrated that the UTRs of POTH1 bind to two RNA-binding proteins, a polypyrimidine tract-binding protein and an alba-domain type. Conserved glycerol-responsive elements (GRE), specific to alba-domain interaction, are duplicated in both the 5' and 3' untranslated regions of POTH1. These results suggest that POTH1 functions as a mobile signal in regulating development.

Graft-union development: a delicate process that involves cell-cell communication between scion and stock for local auxin accumulation

Grafting is an ancient cloning method that has been used widely for thousands of years in agricultural practices. Graft-union development is also an intricate process that involves substantial changes such as organ regeneration and genetic material exchange. However, the molecular mechanisms for graft-union development are still largely unknown. Here, a micrografting method that has been used widely in Arabidopsis was improved to adapt it a smooth procedure to facilitate sample analysis and to allow it to easily be applied to various dicotyledonous plants. The developmental stage of the graft union was characterized based on this method. Histological analysis suggested that the transport activities of vasculature were recovered at 3 days after grafting (dag) and that auxin modulated the vascular reconnection at 2 dag. Microarray data revealed a signal-exchange process between cells of the scion and stock at 1 dag, which re-established the communication network in the graft union. This process was concomitant with the clearing of cell debris, and both processes were initiated by a wound-induced programme. The results demonstrate the feasibility and potential power of investigating various plant developmental processes by this method, and represent a primary and significant step in interpretation of the molecular mechanisms underlying graft-union development.

Mobility of Transgenic Nucleic Acids and Proteins within Grafted Rootstocks for Agricultural Improvement

Grafting has been used in agriculture for over 2000 years. Disease resistance and environmental tolerance are highly beneficial traits that can be provided through use of grafting, although the mechanisms, in particular for resistance, have frequently been unknown. As information emerges that describes plant disease resistance mechanisms, the proteins, and nucleic acids that play a critical role in disease management can be expressed in genetically engineered (GE) plant lines. Utilizing transgrafting, the combination of a GE rootstock with a wild-type (WT) scion, or the reverse, has the potential to provide pest and pathogen resistance, impart biotic and abiotic stress tolerance, or increase plant vigor and productivity. Of central importance to these potential benefits is the question of to what extent nucleic acids and proteins are transmitted across a graft junction and whether the movement of these molecules will affect the efficacy of the transgrafting approach. Using a variety of specific examples, this review will report on the movement of organellar DNA, RNAs, and proteins across graft unions. Attention will be specifically drawn to the use of small RNAs and gene silencing within transgrafted plants, with a particular focus on pathogen resistance. The use of GE rootstocks or scions has the potential to extend the horticultural utility of grafting by combining this ancient technique with the molecular strategies of the modern era.

Functional characterization of the apple MhGAI1 gene through ectopic expression and grafting experiments in tomatoes

DELLA proteins are essential components of GA signal transduction. MhGAI1 was isolated from the tea crabapple (Malus hupehensis Redh. var. pingyiensis), and it was found to encode a DELLA protein. Mhgai1 is a GA-insensitive allele that was artificially generated via a bridge-PCR approach. Ectopic expression of Mhgai1 reduced plant stature, decreased spontaneous fruit-set-ratio and enhanced drought-tolerance in transgenic tomatoes. In addition, we examined the long-distance movement of Mhgai1 mRNAs by grafting experiments and SqRT-PCR analysis. It was found that the wild-type scions accumulated Mhgai1 transcripts trafficked from the transgenic rootstocks and therefore exhibited dwarf phenotypes. Furthermore, transgenic tomato plants produced more soluble solids, sugars and organic acids compared to wild-type tomatoes, suggesting an involvement of GA signaling in the regulation of fruit quality. Despite noticeable accumulation in the leaves and stems of WT scions, Mhgai1 transcripts were undetectable in flowers and fruit. Therefore, fruit quality was less influenced by the grafting of WT scions onto transgenic rootstocks than they were by the ectopic expression of Mhgai1 in transgenic rootstocks. Taken together, MhGAI1, which functions as a repressor in the GA signaling pathway, and its GA-insensitive allele, Mhgai1, could turn out to be useful targets for the genetic improvement of dwarfing rootstocks in apples.

Developmental plasticity, morphological variation and evolvability: a multilevel analysis of morphometric integration in the shape of compound leaves

The structure of compound leaves provides flexibility for morphological change by variation in the shapes, sizes and arrangement of leaflets. Here, we conduct a multilevel analysis of shape variation in compound leaves to explore the developmental plasticity and evolutionary potential that are the basis of diversification in leaf shape. We use the methods of geometric morphometrics to study the shapes of individual leaflets and whole leaves in 20 taxa of Potentilla (sensu lato). A newly developed test based on the bootstrap approach suggests that uncertainty in the molecular phylogeny precludes firm conclusions whether there is a phylogenetic signal in the data on leaf shape. For variation among taxa, variation within taxa, as well as fluctuating asymmetry, there is evidence of strong morphological integration. The patterns of variation are similar across all three levels, suggesting that integration within taxa may act as a constraint on evolutionary change.

(Questions)n on phloem biology. 2. Mass flow, molecular hopping, distribution patterns and macromolecular signalling

This review speculates on correlations between mass flow in sieve tubes and the distribution of photoassimilates and macromolecular signals. Since micro- (low-molecular compounds) and macromolecules are withdrawn from, and released into, the sieve-tube sap at various rates, distribution patterns of these compounds do not strictly obey mass-flow predictions. Due to serial release and retrieval transport steps executed by sieve tube plasma membranes, micromolecules are proposed to "hop" between sieve element/companion cell complexes and phloem parenchyma cells under source-limiting conditions (apoplasmic hopping). Under sink-limiting conditions, micromolecules escape from sieve tubes via pore-plasmodesma units and are temporarily stored. It is speculated that macromolecules "hop" between sieve elements and companion cells using plasmodesmal trafficking mechanisms (symplasmic hopping). We explore how differential tagging may influence distribution patterns of macromolecules and how their bidirectional movement could arise. Effects of exudation techniques on the macromolecular composition of sieve-tube sap are discussed.

Mobile FT mRNA contributes to the systemic florigen signalling in floral induction

In inducing photoperiodic conditions, plants produce a signal dubbed "florigen" in leaves. Florigen moves through the phloem to the shoot apical meristem (SAM) where it induces flowering. In Arabidopsis, the FLOWERING LOCUS T (FT) protein acts as a component of this phloem-mobile signal. However whether the transportable FT mRNA also contributes to systemic florigen signalling remains to be elucidated. Using non-conventional approaches that exploit virus-induced RNA silencing and meristem exclusion of virus infection, we demonstrated that the ArabidopsisFT mRNA, independent of the FT protein, can move into the SAM. Viral ectopic expression of a non-translatable FT mRNA promoted earlier flowering in the short-day (SD) Nicotiana tabacum Maryland Mammoth tobacco in SD. These data suggest a possible role for FT mRNA in systemic floral signalling, and also demonstrate that cis-transportation of cellular mRNA into SAM and meristem exclusion of pathogenic RNAs are two mechanistically distinct processes.

[Progress in research on plant graft-induced genetic variation]

Inheritable variation induced by plant grafting is a universal phenomenon; however, its mechanism has always been a controversial subject. In recent years, research on horizontal transfer of genetic materials between stock and scion has made great progress. The latest studies have found that genetic information in grafted plants is transported through plasmodesma and phloem to modulate the growth and development of the scion plants. Furthermore, non-coding RNAs could induce epigenetic modification, which facilitates plants to adapt to the grafting-caused stress. This article focuses on the review of recent advances in the induction and maintenance of the graft-induced genetic variation and could be helpful in thoroughly understanding the mechanism.

CmRBP50 protein phosphorylation is essential for assembly of a stable phloem-mobile high-affinity ribonucleoprotein complex

RNA-binding proteins (RBPs) form ribonucleoprotein (RNP) complexes that play crucial roles in RNA processing for gene regulation. The angiosperm sieve tube system contains a unique population of transcripts, some of which function as long-distance signaling agents involved in regulating organ development. These phloem-mobile mRNAs are translocated as RNP complexes. One such complex is based on a phloem RBP named Cucurbita maxima RNA-binding protein 50 (CmRBP50), a member of the polypyrimidine track binding protein family. The core of this RNP complex contains six additional phloem proteins. Here, requirements for assembly of this CmRBP50 RNP complex are reported. Phosphorylation sites on CmRBP50 were mapped, and then coimmunoprecipitation and protein overlay studies established that the phosphoserine residues, located at the C terminus of CmRBP50, are critical for RNP complex assembly. In vitro pull-down experiments revealed that three phloem proteins, C. maxima phloem protein 16, C. maxima GTP-binding protein, and C. maxima phosphoinositide-specific phospholipase-like protein, bind directly with CmRBP50. This interaction required CmRBP50 phosphorylation. Gel mobility-shift assays demonstrated that assembly of the CmRBP50-based protein complex results in a system having enhanced binding affinity for phloem-mobile mRNAs carrying polypyrimidine track binding motifs. This property would be essential for effective long-distance translocation of bound mRNA to the target tissues.

Macromolecular composition of phloem exudate from white lupin (Lupinus albus L.)

BACKGROUND

Members of the legume genus Lupinus exude phloem 'spontaneously' from incisions made to the vasculature. This feature was exploited to document macromolecules present in exudate of white lupin (Lupinus albus [L.] cv Kiev mutant), in particular to identify proteins and RNA molecules, including microRNA (miRNA).

RESULTS

Proteomic analysis tentatively identified 86 proteins from 130 spots collected from 2D gels analysed by partial amino acid sequence determination using MS/MS. Analysis of a cDNA library constructed from exudate identified 609 unique transcripts. Both proteins and transcripts were classified into functional groups. The largest group of proteins comprised those involved in metabolism (24%), followed by protein modification/turnover (9%), redox regulation (8%), cell structural components (6%), stress and defence response (6%) with fewer in other groups. More prominent proteins were cyclophilin, ubiquitin, a glycine-rich RNA-binding protein, a group of proteins that comprise a glutathione/ascorbate-based mechanism to scavenge oxygen radicals, enzymes of glycolysis and other metabolism including methionine and ethylene synthesis. Potential signalling macromolecules such as transcripts encoding proteins mediating calcium level and the Flowering locus T (FT) protein were also identified. From around 330 small RNA clones (18-25 nt) 12 were identified as probable miRNAs by homology with those from other species. miRNA composition of exudate varied with site of collection (e.g. upward versus downward translocation streams) and nutrition (e.g. phosphorus level).

CONCLUSIONS

This is the first inventory of macromolecule composition of phloem exudate from a species in the Fabaceae, providing a basis to identify systemic signalling macromolecules with potential roles in regulating development, growth and stress response of legumes.

Macromolecules in phloem exudates--a review

Proteomic and transcriptomic analyses using the growing resources of genomic information have been applied to identification of macromolecules in exudates collected from phloem. Most of the analyses rely on collection of exudate following incisions made to the vasculature, but some limited data are available for exudates collected from excised aphid stylets. Species examined, to date, include a number of cereals (rice, barley, and wheat), a number of cucurbits, castor bean, members of the genus Lupinus, brassicas, and Arabidopsis. As many as 1,100 proteins, some hundreds of transcripts, and a growing number of small ribonucleic acids (RNAs), including micro-RNAs, have been identified across the species with a high degree of commonality. Questions relating to the nature and extent of contamination of sieve element contents with those of surrounding companion cells and nonvascular cells are addressed together with likely functions of identified macromolecules. The review considers likely translocation and systemic signaling functions among the macromolecular inventory of phloem exudates.

A three-dimensional RNA motif in Potato spindle tuber viroid mediates trafficking from palisade mesophyll to spongy mesophyll in Nicotiana benthamiana

Cell-to-cell trafficking of RNA is an emerging biological principle that integrates systemic gene regulation, viral infection, antiviral response, and cell-to-cell communication. A key mechanistic question is how an RNA is specifically selected for trafficking from one type of cell into another type. Here, we report the identification of an RNA motif in Potato spindle tuber viroid (PSTVd) required for trafficking from palisade mesophyll to spongy mesophyll in Nicotiana benthamiana leaves. This motif, called loop 6, has the sequence 5'-CGA-3'...5'-GAC-3' flanked on both sides by cis Watson-Crick G/C and G/U wobble base pairs. We present a three-dimensional (3D) structural model of loop 6 that specifies all non-Watson-Crick base pair interactions, derived by isostericity-based sequence comparisons with 3D RNA motifs from the RNA x-ray crystal structure database. The model is supported by available chemical modification patterns, natural sequence conservation/variations in PSTVd isolates and related species, and functional characterization of all possible mutants for each of the loop 6 base pairs. Our findings and approaches have broad implications for studying the 3D RNA structural motifs mediating trafficking of diverse RNA species across specific cellular boundaries and for studying the structure-function relationships of RNA motifs in other biological processes.

Lights at the end of the tunnel: new views of plasmodesmal structure and function

Plasmodesmata (PDs), tiny channels connecting neighboring plant cells, play big roles in the transport of metabolites, viral movement, cell fate specification and development. Many recent studies are opening our eyes to the composition and formation of PDs, as well as the function and regulation of trafficking through them. Both proteomic and genetic approaches have revealed the central importance of callose in modulating PD connectivity. Moreover, many new developmental regulators, including transcription factors as well as small RNAs (sRNAs), have been found to be mobile and essential for specifying cell fate and tissue patterning.

Characterisation of microRNAs from apple (Malus domestica 'Royal Gala') vascular tissue and phloem sap

BACKGROUND

Plant microRNAs (miRNAs) are a class of small, non-coding RNAs that play an important role in development and environmental responses. Hundreds of plant miRNAs have been identified to date, mainly from the model species for which there are available genome sequences. The current challenge is to characterise miRNAs from plant species with agricultural and horticultural importance, to aid our understanding of important regulatory mechanisms in crop species and enable improvement of crops and rootstocks.

RESULTS

Based on the knowledge that many miRNAs occur in large gene families and are highly conserved among distantly related species, we analysed expression of twenty-one miRNA sequences in different tissues of apple (Malus x domestica 'Royal Gala'). We identified eighteen sequences that are expressed in at least one of the tissues tested. Some, but not all, miRNAs expressed in apple tissues including the phloem tissue were also detected in the phloem sap sample derived from the stylets of woolly apple aphids. Most of the miRNAs detected in apple phloem sap were also abundant in the phloem sap of herbaceous species. Potential targets for apple miRNAs were identified that encode putative proteins shown to be targets of corresponding miRNAs in a number of plant species. Expression patterns of potential targets were analysed and correlated with expression of corresponding miRNAs.

CONCLUSIONS

This study validated tissue-specific expression of apple miRNAs that target genes responsible for plant growth, development, and stress response. A subset of characterised miRNAs was also present in the apple phloem translocation stream. A comparative analysis of phloem miRNAs in herbaceous species and woody perennials will aid our understanding of non-cell autonomous roles of miRNAs in plants.

Characterisation of microRNAs from apple (Malus domestica 'Royal Gala') vascular tissue and phloem sap

BACKGROUND

Plant microRNAs (miRNAs) are a class of small, non-coding RNAs that play an important role in development and environmental responses. Hundreds of plant miRNAs have been identified to date, mainly from the model species for which there are available genome sequences. The current challenge is to characterise miRNAs from plant species with agricultural and horticultural importance, to aid our understanding of important regulatory mechanisms in crop species and enable improvement of crops and rootstocks.

RESULTS

Based on the knowledge that many miRNAs occur in large gene families and are highly conserved among distantly related species, we analysed expression of twenty-one miRNA sequences in different tissues of apple (Malus x domestica 'Royal Gala'). We identified eighteen sequences that are expressed in at least one of the tissues tested. Some, but not all, miRNAs expressed in apple tissues including the phloem tissue were also detected in the phloem sap sample derived from the stylets of woolly apple aphids. Most of the miRNAs detected in apple phloem sap were also abundant in the phloem sap of herbaceous species. Potential targets for apple miRNAs were identified that encode putative proteins shown to be targets of corresponding miRNAs in a number of plant species. Expression patterns of potential targets were analysed and correlated with expression of corresponding miRNAs.

CONCLUSIONS

This study validated tissue-specific expression of apple miRNAs that target genes responsible for plant growth, development, and stress response. A subset of characterised miRNAs was also present in the apple phloem translocation stream. A comparative analysis of phloem miRNAs in herbaceous species and woody perennials will aid our understanding of non-cell autonomous roles of miRNAs in plants.

The phloem pathway: new issues and old debates

The phloem is a central actor in plant development and nutrition, providing nutrients and energy to sink organs and integrating interorgan communication. A comprehensive picture of the molecules trafficking in phloem sap is being made available, with recent surveys of proteins, RNAs, sugars, and other metabolites, some of which are potentially acting as signals. In this review, we focus on recent breakthroughs on phloem transport and signalling. A case study was phloem loading of sucrose, acting both as a nutrient and as a signal, whose activity was shown to be tightly regulated. Recent advances also described actors of macromolecular trafficking in sieve elements, including chaperones and RNA binding proteins, involved potentially in the formation of ribonucleoprotein complexes. Likewise, long distance signalling appeared to integrate electrical potential waves, calcium bursts and potentially the generation of reactive oxygen species. The ubiquitin-proteasome system was also proposed to be on action in sieve elements for signalling and protein turnover. Surprisingly, several basic processes of phloem physiology are still under debate. Hence, the absence in phloem sap of reducing sugar species, such as hexoses, was recently challenged with observations based on an analysis of the sap from Ranunculaceae and Papaveraceae. The possibility that protein synthesis might occur in sieve elements was again questioned with the identification of components of the translational machinery in Pumpkin phloem sap. Altogether, these new findings strengthen the idea that phloem is playing a central role in interorgan nutrient exchanges and communication and demonstrate that the ways by which this is achieved can obey various patterns among species.

Effects of transgenic rootstocks on growth and development of non-transgenic scion cultivars in apple

Although cultivation of genetic modified (GM) annual crops has been steadily increasing in the recent 10 years, the commercial cultivation of GM fruit tree is still very limited and reports of field trials on GM fruit trees are rare. This is probably because development and evaluation of GM fruit trees require a long period of time due to long life cycles of trees. In this study, we report results from a field trial on three rolB transgenic dwarfing apple rootstocks of M26 and M9 together with non-transgenic controls grafted with five non-transgenic scion cultivars. We intended to investigate the effects of transgenic rootstock on non-transgenic scion cultivars under natural conditions as well as to evaluate the potential value of using the rolB gene to modify difficult-to-root rootstocks of fruit trees. The results showed that all rolB transgenic rootstocks significantly reduced vegetative growth including tree height regardless of scion cultivar, compared with the non-transgenic rootstocks. Flowering and fruiting were also decreased for cultivars grown on the transgenic rootstocks in most cases, but the fruit quality was not clearly affected by the transgenic rootstocks. Cutting experiment and RT-PCR analysis showed that the rolB gene was stably expressed under field conditions. PCR and RT-PCR analyses displayed that the rolB gene or its mRNA were not detectable in the scion cultivars, indicating no translocation of the transgene or its mRNA from rootstock to scion. Our results suggest that rolB modified rootstocks should be used in combination with vigorous scion cultivars in order to obtain sufficient vegetative growth and good yield. Alternatively, the rolB gene could be used to dwarf vigorous rootstocks of fruit trees or produce bonzai plants as it can significantly reduce the vegetative growth of plants.

cDNA-AFLP analysis of gene expression in hickory (Carya cathayensis) during graft process

The graft technique is a valid method for propagating plants. A better elucidation of the graft mechanism is helpful in improving the production efficiency and fruit quality in hickory. In this study, cDNA-amplified fragment length polymorphism analysis was used to examine the gene expression in hickory at four time points (at 0, 3, 7 and 14 days) during the graft process. Forty-nine unique genes involved in the graft mechanism were obtained. The expression patterns of these genes were confirmed by real-time reverse transcription-polymerase chain reaction analysis based on 12 selected genes representing different patterns. The 49 genes composed 19 genes of known function, nine genes of unknown function and 21 novel genes. These 19 genes of known functions were involved in the indole-3-acetic acid transport protein, cell cycle, signal transduction, water metabolism, nuclear metabolism, amino acid metabolism, protein metabolism, carbon metabolism and secretion of substances, suggesting that Carya cathayensis Sarg. undergoes a complex metabolism process during the grafting.

A model system of development regulated by the long-distance transport of mRNA

BEL1-like transcription factors are ubiquitous in plants and interact with KNOTTED1-types to regulate numerous developmental processes. In potato, the RNA of several BEL1-like transcription factors has been identified in phloem cells. One of these, StBEL5, and its Knox protein partner regulate tuber formation by targeting genes that control growth. RNA detection methods and grafting experiments demonstrated that StBEL5 transcripts move across a graft union to localize in stolon tips, the site of tuber induction. This movement of RNA originates in source leaf veins and petioles and is induced by a short-day photoperiod, regulated by the untranslated regions, and correlated with enhanced tuber production. Addition of the StBEL5 untranslated regions to another BEL1-like mRNA resulted in its preferential transport to stolon tips leading to increased tuber production. Upon fusion of the untranslated regions of StBEL5 to a beta-glucuronidase marker, translation in tobacco protoplasts was repressed by those constructs containing the 3' untranslated sequence. The untranslated regions of the StBEL5 mRNA are involved in mediating its long-distance transport and in controlling translation. The 3' untranslated sequence contains an abundance of conserved motifs that may serve as binding motifs for RNA-binding proteins. Because of their presence in the phloem sieve tube system, their unique untranslated region sequences and their diverse RNA accumulation patterns, the family of BEL1-like RNAs from potato represents a valuable model for studying the long-distance transport of full-length mRNAs and their role in development.

Viroids: small probes for exploring the vast universe of RNA trafficking in plants

Cell-to-cell and long-distance trafficking of RNA is a rapidly evolving frontier of integrative plant biology that broadly impacts studies on plant growth and development, spread of infectious agents and plant defense responses. The fundamental questions being pursued at the forefronts revolve around function, mechanism and evolution. In the present review, we will first use specific examples to illustrate the biological importance of cell-to-cell and long-distance trafficking of RNA. We then focus our discussion on research findings obtained using viroids that have advanced our understanding of the underlying mechanisms involved in RNA trafficking. We further use viroid examples to illustrate the great diversity of trafficking machinery evolved by plants, as well as the promise for new insights in the years ahead. Finally, we discuss the prospect of integrating findings from different experimental systems to achieve a systems-based understanding of RNA trafficking function, mechanism and evolution.

The sequences of Arabidopsis GA-INSENSITIVE RNA constitute the motifs that are necessary and sufficient for RNA long-distance trafficking

In higher plants a number of physiological processes are regulated by systemic RNA signaling molecules. This phloem-mediated remote-control system provides specific and efficient regulation to fine-tune many plant developmental programs. However, the molecular mechanism underlying long-distance movement of RNA remains to be elucidated. To this end, we examined the long-distance movement of GA-insensitive (GAI) RNA by Arabidopsis inflorescence grafting and RT-PCR analysis. Our results demonstrated that long-distance movement of RNA only occurred in specific transcripts. In addition, the sequences of GAI RNA are necessary and sufficient to target GREEN FLUORESCENT PROTEIN (GFP) RNA for long-distance movement, which indicates that the trafficking of GAI RNA is mediated by specific RNA motifs. Further analyses revealed that the motifs at coding sequences and 3' untranslated regions of GAI RNA play important roles during RNA movement. In addition, the structure of the RNA rather than its specific sequence may also be important in GAI RNA trafficking. However, the secondary structure of GAI RNA is not the only factor to target RNA for long-distance movement, because recovery of the secondary structure of movement-defective GAI RNA only partially rescued RNA movement. Taken together, our results show that long-distance movement of non-cell autonomous RNA operates by specific RNA mobile elements.

Viroid intercellular trafficking: RNA motifs, cellular factors and broad impacts

Viroids are noncoding RNAs that infect plants. In order to establish systemic infection, these RNAs must traffic from an initially infected host cell into neighboring cells and ultimately throughout a whole plant. Recent studies have identified structural motifs in a viroid that are required for trafficking, enabling further studies on the mechanisms of their function. Some cellular proteins interact with viroids in vivo and may play a role in viroid trafficking, which can now be directly tested by using a virus-induced gene silencing system that functions efficiently in plant species from which these factors were identified. This review discusses these recent advances, unanswered questions and the use of viroid infection as an highly productive model to elucidate mechanisms of RNA trafficking that is of broad biological significance.

Rootstock-induced dwarfing in cherries is caused by differential cessation of terminal meristem growth and is triggered by rootstock-specific gene regulation

Use of dwarfing rootstocks has dramatically increased the profitability of fruit production by reducing production costs, reduced chemical use and higher density plantings. Despite the importance of rootstock-induced dwarfing, the cause of this phenomenon is not known. Using two commercially available graft combinations consisting of a sweet cherry scion, 'Bing', on a dwarfing rootstock (Gi5) or a semi-vigorous rootstock (Gi6), we discovered that the difference in grafted tree height was due to a significantly earlier cessation of terminal meristem growth of the scion on Gi5 compared to Gi6 rootstock, rather than shorter metamer length. We then carried out cDNA-AFLP analysis to investigate differential gene expression between the two graft combinations. Transcript-derived fragments (TDFs) identified as differentially expressed were cloned and printed on microarrays for further confirmation of the differential expression. A total of 99 TDFs were identified as differentially expressed between the 'Bing'/Gi5 and 'Bing'/Gi6 samples, including genes involved in transcription regulation, brassinosteroid signaling, flavonoid metabolism and cell wall biosynthesis or modification. Rootstock vigor has a significant effect on gene expression at the scion and the graft union. Timing of the differential gene expression in the dwarf trees coincides with the earlier cessation of terminal shoot growth, suggesting that these differentially expressed genes may be involved in the dwarfing phenomenon.

RNA translocation between parasitic plants and their hosts

Recent research indicates that RNA translocation occurs between certain parasitic plant species and their hosts. The movement of at least 27 mRNAs has been demonstrated between hosts and Cuscuta pentagona Engelm., with the largest proportion of these being regulatory genes. Movement of RNAi signals has been documented from hosts to the parasites Triphysaria versicolor (Frisch & CA Mey) and Orobanche aegyptiaca (Pers.), demonstrating that the regulation of genes in one species can be influenced by transfer of RNA signals through a parasitic association. This review considers the implications of these findings in light of present understanding of host-parasite connections and the growing body of evidence that RNAs are able to act as signal molecules that convey regulatory information in a cell- and tissue-specific manner. Together, this suggests that parasitic plants can exchange RNAs with their hosts, and that this may be part of the coordinated growth and development that occurs during the process of parasitism. This phenomenon offers promise for new insights into parasitic plants, and new opportunities for the control of parasitic weeds.

Long-distance transport of macromolecules through the phloem

Long-distance phloem transport of small metabolites has long been the subject of many different studies concentrating on resource allocation and signalling between plant organs. Also, phloem movement of viruses has long been examined as the route for systemic infection of the plant. Only recently, the transport of macromolecules, such as proteins and nucleic acids, has received increasing attention because they are regarded as being a new class of potential information-transmitter. A set of recent publications allows the first insights into the important roles that phloem-mobile macromolecules might play in the regulation of development and the responses to stress. Furthermore, they start to shed light on the mechanisms involved in systemic macromolecule transport.

A cis element within flowering locus T mRNA determines its mobility and facilitates trafficking of heterologous viral RNA

The Arabidopsis flowering locus T (FT) gene encodes the mobile florigen essential for floral induction. While movement of the FT protein has been shown to occur within plants, systemic spread of FT mRNA remains to be unequivocally demonstrated. Utilizing novel RNA mobility assay vectors based on two distinct movement-defective viruses, Potato virus X and Turnip crinkle virus, and an agroinfiltration assay, we demonstrate that nontranslatable FT mRNA, independent of the FT protein, moves throughout Nicotiana benthamiana and mutant Arabidopsis plants and promotes systemic trafficking of viral and green fluorescence protein RNAs. Viral ectopic expression of FT induced flowering in the short-day N. tabacum Maryland Mammoth tobacco under long-day conditions. Recombinant Potato virus X bearing FT RNA spread and established systemic infection more quickly than the parental virus. The cis-acting element essential for RNA movement was mapped to the nucleotides 1 to 102 of the FT mRNA coding sequence. These data demonstrate that a plant self-mobile RNA molecule can mediate long-distance trafficking of heterologous RNAs and raise the possibility that FT RNA, along with the FT protein, may be involved in the spread of the floral stimulus throughout the plant.

Adaptation of a seedling micro-grafting technique to the study of long-distance signaling in flowering of Arabidopsis thaliana

Long-distance signaling via phloem tissues is an important mechanism for inter-organ communication. Such communication allows plants to integrate environmental information into physiological and developmental responses. Grafting has provided persuasive evidence of long-distance signaling involved in various processes, including flowering, tuberization, nodulation, shoot branching, post-transcriptional gene silencing, and disease resistance. A micro-grafting technique to generate two-shoot grafts is available for young seedlings of Arabidopsis thaliana and was adapted for use in the study of flowering. Histological analysis using transgenic plants expressing beta-glucuronidase (GUS) in phloem tissues showed that phloem continuity between a stock and a scion was established between 7 and 10 days after grafting. Experiments using tracer dyes and enhanced green fluorescent protein (EGFP) showed that the phloem connection was functional and capable of effecting macromolecular transmission. Successful grafts can be obtained at high frequency (10-30%) and selected after 2-3 weeks of post-surgery growth. This method was applied successfully to the study of flowering, one of the important events regulated by long-distance signaling. This grafting technique will facilitate the study of the long-distance action of genes involved in various aspects of growth and development, and in transport of signal molecules.

A polypyrimidine tract binding protein, pumpkin RBP50, forms the basis of a phloem-mobile ribonucleoprotein complex

RNA binding proteins (RBPs) are integral components of ribonucleoprotein (RNP) complexes and play a central role in RNA processing. In plants, some RBPs function in a non-cell-autonomous manner. The angiosperm phloem translocation stream contains a unique population of RBPs, but little is known regarding the nature of the proteins and mRNA species that constitute phloem-mobile RNP complexes. Here, we identified and characterized a 50-kD pumpkin (Cucurbita maxima cv Big Max) phloem RNA binding protein (RBP50) that is evolutionarily related to animal polypyrimidine tract binding proteins. In situ hybridization studies indicated a high level of RBP50 transcripts in companion cells, while immunolocalization experiments detected RBP50 in both companion cells and sieve elements. A comparison of the levels of RBP50 present in vascular bundles and phloem sap indicated that this protein is highly enriched in the phloem sap. Heterografting experiments confirmed that RBP50 is translocated from source to sink tissues. Collectively, these findings established that RBP50 functions as a non-cell-autonomous RBP. Protein overlay, coimmunoprecipitation, and cross-linking experiments identified the phloem proteins and mRNA species that constitute RBP50-based RNP complexes. Gel mobility-shift assays demonstrated that specificity, with respect to the bound mRNA, is established by the polypyrimidine tract binding motifs within such transcripts. We present a model for RBP50-based RNP complexes within the pumpkin phloem translocation stream.

Plant responses to photoperiod

Photoperiod controls many developmental responses in animals, plants and even fungi. The response to photoperiod has evolved because daylength is a reliable indicator of the time of year, enabling developmental events to be scheduled to coincide with particular environmental conditions. Much progress has been made towards understanding the molecular mechanisms involved in the response to photoperiod in plants. These mechanisms include the detection of the light signal in the leaves, the entrainment of circadian rhythms, and the production of a mobile signal which is transmitted throughout the plant. Flowering, tuberization and bud set are just a few of the many different responses in plants that are under photoperiodic control. Comparison of what is known of the molecular mechanisms controlling these responses shows that, whilst common components exist, significant differences in the regulatory mechanisms have evolved between these responses.

Phloem transport: cellular pathways and molecular trafficking

The phloem transports nutrients, defensive compounds, and informational signals throughout vascular plants. Sampling the complex components of mobile phloem sap is difficult because of the damage incurred when the pressurized sieve tubes are breached. In this review we discuss sampling methods, the artifacts that can be introduced by different sampling procedures, the intricate pathways by which materials enter and exit the phloem, and the major types of compounds transported. Loading and unloading patterns are largely determined by the conductivity and number of plasmodesmata and the position-dependent function of solute-specific, plasma membrane transport proteins. Recent evidence indicates that mobile proteins and RNA are part of the plant's long-distance communication signaling system. Evidence also exists for the directed transport and sorting of macromolecules as they pass through plasmodesmata. A future challenge is to dissect the molecular and cellular aspects of long-distance macromolecular trafficking in the signal transduction pathways of the whole plant.

Accumulation of BEL1-like transcripts in solanaceous species

Although numerous RNAs have been detected in the phloem, only a few have been confirmed to move long distances. In potato, full-length mRNA of the BEL1-like transcription factor, StBEL5, moves from leaf veins through the phloem to stolon tips to activate tuber formation. BEL1-like transcription factors are ubiquitous in plants and interact with KNOTTED1-types to regulate numerous developmental processes. To explore the range of KNOTTED1- and BEL1-like mRNAs present in phloem, an analysis of the transcript profile of phloem sap was undertaken. Using a modified technique for the collection of phloem-enriched exudate from excised stems, numerous RNAs encoding these transcription factors were detected in the phloem sap from several solanceous species. All seven known BEL1-like RNAs of potato were detected in the phloem-enriched exudates of stem, whereas several stolon-abundant RNAs were not. After refining the technique to minimize the contamination from RNA arising from wounded cells, KNOTTED1-like RNAs were detected in phloem-enriched sap of potato and BEL5 RNA was detected in the sap collected from two closely related nontuber-bearing potato species and tomato. BEL5 RNA was also detected in RNA extracted from leaf veins of tobacco. The detection of these full-length mRNAs from the KNOTTED1- and BEL1-like families in phloem sap indicates that their potential role as long-distance signals seems to be much more extensive than previously known.

Analysis of the pumpkin phloem proteome provides insights into angiosperm sieve tube function

Increasing evidence suggests that proteins present in the angiosperm sieve tube system play an important role in the long distance signaling system of plants. To identify the nature of these putatively non-cell-autonomous proteins, we adopted a large scale proteomics approach to analyze pumpkin phloem exudates. Phloem proteins were fractionated by fast protein liquid chromatography using both anion and cation exchange columns and then either in-solution or in-gel digested following further separation by SDS-PAGE. A total of 345 LC-MS/MS data sets were analyzed using a combination of Mascot and X!Tandem against the NCBI non-redundant green plant database and an extensive Cucurbit maxima expressed sequence tag database. In this analysis, 1,209 different consensi were obtained of which 1,121 could be annotated from GenBank and BLAST search analyses against three plant species, Arabidopsis thaliana, rice (Oryza sativa), and poplar (Populus trichocarpa). Gene ontology (GO) enrichment analyses identified sets of phloem proteins that function in RNA binding, mRNA translation, ubiquitin-mediated proteolysis, and macromolecular and vesicle trafficking. Our findings indicate that protein synthesis and turnover, processes that were thought to be absent in enucleate sieve elements, likely occur within the angiosperm phloem translocation stream. In addition, our GO analysis identified a set of phloem proteins that are associated with the GO term "embryonic development ending in seed dormancy"; this finding raises the intriguing question as to whether the phloem may exert some level of control over seed development. The universal significance of the phloem proteome was highlighted by conservation of the phloem proteome in species as diverse as monocots (rice), eudicots (Arabidopsis and pumpkin), and trees (poplar). These results are discussed from the perspective of the role played by the phloem proteome as an integral component of the whole plant communication system.

Adaptation of aphid stylectomy for analyses of proteins and mRNAs in barley phloem sap

Sieve tubes are transport conduits not only for photoassimilates but also for macromolecules and other compounds that are involved in sieve tube maintenance and systemic signalling. In order to gain sufficient amounts of pure phloem exudates from barley plants for analyses of the protein and mRNA composition, a previously described stylectomy set-up was optimized. Aphids were placed in sealed cages, which, immediately after microcauterization of the stylets, were flooded with water-saturated silicon oil. The exuding phloem sap was collected with a capillary connected to a pump. Using up to 30 plants and 600 aphids (Rhopalosiphum padi) in parallel, an average of 10 mul of phloem sap could be obtained within 6 h of sampling. In first analyses of the macromolecular content, eight so far unknown phloem mRNAs were identified by cDNA-amplified fragment length polymorphism. Transcripts in barley phloem exudates are related to metabolism, signalling, and pathogen defence, for example coding for a protein kinase and a pathogen- and insect-responsive WIR1A (wheat-induced resistance 1A)-like protein. Further, one-dimensional gel electrophoresis and subsequent partial sequencing by mass spectrometry led to the identification of seven major proteins with putative functions in stress responses and transport of mRNAs, proteins, and sugars. Two of the discovered proteins probably represent isoforms of a new phloem-mobile sucrose transporter. Notably, two-dimensional electrophoresis confirmed that there are >250 phloem proteins awaiting identification in future studies.