Friedrich Kragler

• Dr.
• Group Leader at Max Planck Institute of Molecular Plant Physiology

Short-read RNA-Seq analyses of grafted plants have led to the proposal that large numbers of mRNAs move over long distances between plant tissues, acting as potential signals. The detection of transported transcripts by RNA-Seq is both experimentally and computationally challenging, requiring successful grafting, delicate harvesting, rigorous conta...

In Arabidopis a high number of distinct mRNAs move from shoot to root. We previously reported on the correlation of m ⁵ C-methylation and lack of mRNA transport in juvenile plants depending on the RNA methyltransferases DNMT2 NSUN2B . However, to our surprise we uncovered that lack of DNMT2 NSUN2B (writer) activity did not abolished transport of TC...

In grapevines, incompatibility manifests in short-term graft failure or long-term decline of vineyards both causing economic losses to nurseries and growers. Here, we assessed the suitability of in vitro systems coupled with histochemistry analysis as early detection methods for grapevine incompatibility using certified homografted (i.e., a graft b...

In vineyards to control phylloxera (Daktulosphaira vitifolia Ficth) attacks in Vitis vinifera L., heterografted vines are planted using American vines hybrids as rootstocks. However, graft incompatibilities can affect grape yield and plant longevity. Thus, to identify early graft incompatibility factors, we established in vitro micrografting protoc...

In this study we present callus-grafting - a method for reproducibly generating tissue chimeras from callus cultures of Arabidopsis thaliana. In this way, callus cultures of different genetic backgrounds may be co-cultivated such that cell-to-cell connectivity is achieved as a chimeric tissue is formed. To track intercellular connectivity and trans...

The HSC70/HSP70 family of heat shock proteins are evolutionarily conserved chaperones involved in protein folding, protein transport, and RNA binding. Arabidopsis HSC70 chaperones are thought to act as housekeeping chaperones and as such are involved in many growth‐related pathways. Whether Arabidopsis HSC70 binds RNA and whether this interaction i...

Generation of stable gene-edited plant lines using clustered regularly interspaced short palindromic repeats (CRISPR)–CRISPR-associated protein 9 (Cas9) requires a lengthy process of outcrossing to eliminate CRISPR–Cas9-associated sequences and produce transgene-free lines. We have addressed this issue by designing fusions of Cas9 and guide RNA tra...

The long-distance transport of messenger RNAs (mRNAs) has been shown to be important for several developmental processes in plants. A popular method for identifying travelling mRNAs is to perform RNA-Seq on grafted plants. This approach depends on the ability to correctly assign sequenced mRNAs to the genetic background from which they originated....

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 e...

Grafting is a method for plant propagation and improvement. In the European viticulture, grafting is the sole control strategy against Phylloxera injuries and thus is of crucial importance for sustainable grape production. Despite its benefits, grafting is also a source for disease dissemination and graft incompatibility sometimes detected long aft...

Mitochondria in animals are associated with development, as well as physiological and pathological behaviors. Several conserved mitochondrial genes exist between plants and higher eukaryotes. Yet, the similarities in mitochondrial function between plant and animal species is poorly understood. Here, we show that FMT (FRIENDLY MITOCHONDRIA) from Ara...

A callus is a semi-disorganized tissue that can be induced to develop from diverse tissues by the addition of exogenous hormones. The fast growth and ease of propagation have made callus cultures useful for creating a wide variety of different experimental systems.Here, we describe a detailed and simple procedure by which different, non-clonal call...

Although several large-scale single-cell RNA sequencing (scRNAseq) studies addressing the root of Arabidopsis (Arabidopsis thaliana) have been published, there is still need for a de novo reference map for both root and especially above-ground cell types. As the plants’ transcriptome substantially changes throughout the day, shaped by the circadian...

Pericentromeric DNA, consisting of high-copy-number tandem repeats and transposable elements, is normally silenced through DNA methylation and histone modifications to maintain chromosomal integrity and stability. Although histone deacetylase 6 (HDA6) has been known to participate in pericentromeric silencing, the mechanism is still yet unclear. He...

In viticulture, grafting is used to propagate Phylloxera-susceptible European grapevines, thereby using resistant American rootstocks. Although scion–rootstock reciprocal signaling is essential for the formation of a proper vascular union and for coordinated growth, our knowledge of graft partner interactions is very limited. In order to elucidate...

In plants, the shoot apical meristem (SAM) is essential for the growth of above-ground organs. However, little is known about its molecular responses to abiotic stresses. Here, we show that the SAM of Arabidopsis thaliana displays an autonomous heat stress (HS) memory of a previous non-lethal HS, allowing the SAM to regain growth after exposure to...

In flowering plants, sugars act as carbon sources providing energy for developing embryos and seeds. Although most studies focus on carbon metabolism in whole seeds, knowledge about how particular sugars contribute to the developmental transitions during embryogenesis is scarce. To develop a quantitative understanding of how carbon composition chan...

Although we have a good understanding of the development of shoot apical meristems (SAM) in higher plants, and the function of the stem cells (SCs) embedded in the SAM, there is surprisingly little known of its molecular responses to abiotic stresses. Here, we show that the SAM of Arabidopsis thaliana senses heat stress (HS) and retains an autonomo...

Mitochondria in animals are associated with development, as well as physiological and pathological behaviors. Several conserved mitochondrial genes exist between plants and higher eukaryotes. Yet, comparative mitochondrial function among plant and animal species is poorly understood. Here, we show that FMT (FRIENDLY MITOCHONDRIA) from Arabidopsis t...

Grafting is the most used propagation method in viticulture and is the unique control strategy against Phylloxera. Nevertheless, its practice remains limited mainly due to inconsistent graft success and difficulties in predicting graft compatibility responses of proposed scion–rootstock combinations, slowing down the selection of elite rootstocks....

Secondary base modifications on RNA, such as m 5 C, affect the structure and function of the modified RNA molecules. Methylated RNA Immunoprecipitation and sequencing (MeRIP-seq) is a method that aims to enrich for methylated RNA and ultimately identify modified transcripts. Briefly, sonicated RNA is incubated with an antibody for 5-methylated cyto...

Short title: Expression atlas of Selaginella moellendorffii One-sentence summary: Analysis of the gene expression atlas of Selaginella moellendorffii reveals transcriptional programs that arose in vascular plants over the course of one billion of years of evolution. ABSTRACT Selaginella moellendorffii is a representative of the lycophyte lineage th...

The lycophyte Selaginella moellendorffii represents early vascular plants and is studied to understand the evolution of higher plant traits such as the vasculature, leaves, stems, roots, and secondary metabolism. However, little is known about the gene expression and transcriptional coordination of Selaginella genes, which precludes us from underst...

In plants, transcripts move to distant body parts to potentially act as systemic signals regulating development and growth. Thousands of messenger RNAs (mRNAs) are transported across graft junctions via the phloem to distinct plant parts. Little is known regarding features, structural motifs, and potential base modifications of transported transcri...

High throughput studies identified approximately one fifth of Arabidopsis protein encoding transcripts to be graft transmissible and to move over long distances in phloem. In roots, one fifth of transcription factors were annotated as non-cell-autonomous moving between cells. Is this massive transport a way of inter-organ and cell-to-cell communica...

Contents Summary 29 I. Introduction 29 II. Phloem as a conduit for macromolecules 30 III. Classes of phloem transported RNAs and their function 32 IV. Mode of RNA transport 35 V. Conclusions 37 Acknowledgements 37 References 37 Summary In higher plants, small noncoding RNA s and large messenger RNA ( mRNA ) molecules are transported betwee...

We used Phytotyping4D to investigate the contribution of clock- and light-signaling to diurnal regulation of rosette expansion growth and leaf movement in Arabidopsis. Wild-type plants and clock mutants with a short (lhycca1) and long (prr7prr9) period were analyzed in a T24 cycle and in T-cycles that were closer to the mutants' period. Wild-types...

Nature Plants 1 , 15025 (2015); published 23 March 2015; corrected 21 November 2016. In the version of this Article originally published, the x -axis scale in Fig. 4b was incorrectly labelled and should have ranged from −10 to 10.

In plants, various phloem-mobile macromolecules including noncoding RNAs, mRNAs and proteins are suggested to act as important long-distance signals in regulating crucial physiological and morphological transition processes such as flowering, plant growth and stress responses. Given recent advances in high-throughput sequencing technologies, numero...

Phloem serves as a highway for mobile signals in plants. Apart from sugars and hormones, proteins and RNAs are transported via the phloem and contribute to the intercellular communication coordinating growth and development. Different classes of RNAs have been found mobile and in the phloem exudate such as viral RNAs, small interfering RNAs (siRNAs...

In plants, protein-coding messenger RNAs (mRNAs) can move via the phloem vasculature to distant tissues, where they may act as non-cell-autonomous signals. Emerging work has identified many phloem-mobile mRNAs, but little is known regarding RNA motifs triggering mobility, the extent of mRNA transport, and the potential of transported mRNAs to be tr...

A comprehensive analysis of transcripts in grafted cucumber–watermelon plants substantiates specific transcript transport to diverse tissues and provides new insights into phosphate starvation responses.

Background The genus Cuscuta is a group of parasitic plants that are distributed world-wide. The process of parasitization starts with a Cuscuta plant coiling around the host stem. The parasite’s haustorial organs then establish a vascular connection allowing for access to the phloem content. The host and the parasite form new cellular connections,...

Pressure microinjection can be used to introduce fluorescent dyes and labeled macromolecules into single cells. The method allows measuring transport activity of macromolecules such as proteins and RNA molecules within and between cells. Routinely, plant mesophyll cells are injected with fluorescent dextran molecules of specific sizes to measure an...

Mitogen-activated protein kinase (MAPK) cascades are universal signal transduction modules present in all eukaryotes. In plants, MAPK cascades were shown to regulate cell division, developmental processes, stress responses, and hormone pathways. The subgroup A of Arabidopsis MAPKs consists of AtMPK3, AtMPK6, and AtMPK10. AtMPK3 and AtMPK6 are activ...

The concept that proteins and small RNAs can move to and function in distant body parts is well established. However, non-cell-autonomy of small RNA molecules raises the question: To what extent are protein-coding messenger RNAs (mRNAs) exchanged between tissues in plants? Here we report the comprehensive identification of 2,006 genes producing mob...

Integrative studies of plant growth require spatially- and temporally-resolved information from high-throughput imaging systems. However, analysis and interpretation of conventional two-dimensional images is complicated by the three-dimensional nature of shoot architecture and by changes in leaf position over time, named hyponasty. To solve this pr...

Plants often experience low oxygen conditions as the consequence of reduced oxygen availability in their environment or due to a high activity of respiratory metabolism. Recently, an oxygen sensing pathway was described in Arabidopsis thaliana which involves the migration of an ERF transcription factor (RAP2.12) from the plasma membrane to the nucl...

Mitogen-activated protein kinase (MAPK) cascades are universal signal transduction modules present in all eukaryotes. In plants, MAPK cascades were shown to regulate cell division, developmental processes, stress responses and hormone pathways. The subgroup A of Arabidopsis MAPKs consists of AtMPK3, AtMPK6, and AtMPK10. AtMPK3 and AtMPK6 are activa...

In plants small interfering RNAs (siRNA) and micro RNAs move to distant tissues where they control numerous developmental and physiological processes such as morphogenesis and stress responses. Grafting techniques and transient expression systems have been employed to show that sequence-specific siRNAs with a size of 21 to 24 nucleotides traffic to...

Transport of endogenous macromolecules within and between tissues serves as a signaling pathway to regulate numerous aspects of plant growth. The florigenic FT gene product moves via the phloem from leaves to apical tissues and induces the flowering program in meristems. Similarly, short interfering RNA (siRNA) signals produced in source or sink ti...

In plants, intercellular structures named plasmodesmata (PD) form a continuous cytoplasmic network between neighboring cells. PD pores provide channels for intercellular symplasmic (cell-to-cell) transport throughout most tissues of the plant body. Cell-defining proteins, such as transcription factors, and regulatory non-coding sequences, such as s...

The homeodomain transcription factor KNOTTED1 (KN1) functions in shoot meristem maintenance and is thought to move from cell to cell in a similar fashion as viral movement proteins. Both types of transported proteins bind to RNA, and associate with intercellular bridges formed by plasmodesmata. In a mutant screen for KN1 transport deficiency, a com...

Numerous studies revealed that beside viral RNAs also plant endogenous RNAs are transported from source tissue towards apical tissues in plants. Surprisingly a high number of distinct transcripts including protein coding and non-coding RNAs were shown to allocate from cell to cell and via the phloem to distant organs. These mobile RNA molecules see...

The ability of plants to exchange RNA molecules and transcription factors between cells and tissues is a relatively recent discovery. However, all areas of research such as plant development, metabolism, and plant pathogen interactions now realize the importance of this phenomenon. In this book, experts from the field of intercellular transport dea...

The organization of eukaryotic cells into membrane-bound compartments must be faithfully sustained for survival of the cell. A subtle equilibrium exists between the degradation and the proliferation of organelles. Commonly, proliferation is initiated by a membrane remodeling process. Here, we dissect the function of proteins driving organelle proli...

Dynamic changes of membrane structure are intrinsic to organelle morphogenesis and homeostasis. Ectopic expression of proteins of the PEX11 family from yeast, plant or human lead to the formation of juxtaposed elongated peroxisomes (JEPs),which is evocative of an evolutionary conserved function of these proteins in membrane tubulation. Microscopic...

It has long been known that the phloem facilitates long-distance transport of sugars, hormones and amino acids in plants. In the last decade, messenger RNAs (mRNA) and small interfering RNAs (siRNA)/micro-RNAs (miRNA) were found to use the same systemic source–sink pathway. It is thought that these RNA macromolecules are selectively delivered via p...

In plants, the vascular tissue contains the enucleated sieve tubes facilitating long-distance transport of nutrients, hormones, and proteins. In addition, several mRNAs and small interfering RNAs/microRNAs were shown to be delivered via sieve tubes whose content is embodied by the phloem sap (PS). A number of these phloem transcripts are transporte...

Trichome patterning in Arabidopsis serves as a model system to study how single cells are selected within a field of initially equivalent cells. Current models explain this pattern by an activator-inhibitor feedback loop. Here, we report that also a newly discovered mechanism is involved by which patterning is governed by the removal of the trichom...

IntroductionComponents of the PD transport pathwayIdentifying PD transport signal(s)Conclusions and future prospectsAcknowledgements

Plasmodesmata establish a pathway for the intercellular trafficking of viral movement proteins and endogenous non-cell-autonomous proteins, such as the two closely related meristem-maintaining KNOTTED1-like homeobox (KNOX) proteins Zea mays KNOTTED1 (KN1) and Arabidopsis thaliana SHOOTMERISTEMLESS (STM). KNOX family members are DNA binding proteins...

Non-cell-autonomous signals in the form of microRNAs and transcription factors could have important developmental functions. Plasmodesmata (PD) form a cytoplasmic network throughout the plant body and provide the means of symplasmic cell-to-cell transport in plants. Homeodomain transcription factors, small RNA molecules and viral genomic informatio...

Systemic translocation of RNA exerts non-cell-autonomous control over plant development and defense. Long-distance delivery of mRNA has been proven, but transport of small interfering RNA and microRNA remains to be demonstrated. Analyses performed on phloem sap collected from a range of plants identified populations of small RNA species. The dynami...

The movement protein of tobacco mosaic virus, MP30, mediates viral cell-to-cell transport via plasmodesmata. The complex MP30 intra- and intercellular distribution pattern includes localization to the endoplasmic reticulum, cytoplasmic bodies, microtubules, and plasmodesmata and likely requires interaction with plant endogenous factors. We have ide...

Plasmodesmata establish a pathway for the trafficking of non-cell-autonomously acting proteins and ribonucleoprotein complexes. Plasmodesmal enriched cell fractions and the contents of enucleate sieve elements, in the form of phloem sap, were used to isolate and characterize heat shock cognate 70 (Hsc70) chaperones associated with this cell-to-cell...

The eukaryotic glyoxylate cycle has been previously hypothesized to occur in the peroxisomal compartment, which in the yeast Saccharomyces cerevisiae additionally represents the sole site for fatty acid beta-oxidation. The subcellular location of the key glyoxylate-cycle enzyme malate synthase 1 (Mls1p), an SKL-terminated protein, was examined in y...

A new paradigm is emerging in plant biology in which proteins and ribonucleoprotein (RNP) complexes play non-cell-autonomous roles in contributing to the control over developmental and physiological processes. Plasmodesmata (PD), the intercellular organelle(s) of the plant kingdom, create the pathway for the cell-to-cell trafficking of these inform...

A role for RNA as a non-cell-autonomous information macromolecule is emerging as a new model in biology. Studies on higher plants have shown the operation of cell-to-cell and long-distance communication networks that mediate the selective transport of RNA. The evolution and function of these systems are discussed in terms of an RNA-based signalling...

In plants, cell-to-cell transport of endogenous and viral proteins and ribonucleoprotein complexes (RNPCs) occurs via plasmodesmata. Specificity of this transport pathway appears to involve interaction between such proteins/RNPCs and plasmodesmal chaperones/receptors. Here, KN1 and the cucumber mosaic virus movement protein (CMV-MP) were used, in a...

Protein translocation into peroxisomes takes place via recognition of a peroxisomal targeting signal present at either the extreme C termini (PTS1) or N termini (PTS2) of matrix proteins. In mammals and yeast, the peroxisomal targeting signal receptor, Pex5p, recognizes the PTS1 consisting of -SKL or variants thereof. Although many plant peroxisoma...

Plasmodesmata and the nuclear pore complex (NPC) mediate the selective trafficking of proteins and protein-nucleic acid complexes. The events underlying the translocation of endogenous and viral proteins through plasmodesmata were investigated to further explore the parallels between these cell-to-cell and intracellular communication systems. Studi...

Although it has long been known that plasmodesmata establish cytoplasmic continuity between most cells within the body of the plant, it is only recently that these special structures have been viewed as dynamic intercellular organelles (Lucas and Wolf, Trends in Cell Biology 3 : 308–315, 1993) involved in the transport of macromolecules. Ultrastruc...

The PAS10 gene was found in a two-hybrid screen for the isolation of genes encoding proteins which interact with the C-terminal peroxisomal targeting signal -SKL. The PAS10 protein is known to be involved in import of proteins into peroxisomes and to contain a tetratricopeptide repeat (TPR) domain. All TPR-containing proteins involved in diverse pr...

In contrast to many other peroxisomal proteins catalase A contains at least two peroxisomal targeting signals each sufficient to direct reporter proteins to peroxisomes. One of them resides at the extreme carboxy terminus constituting a new variant of this signal, -SSNSKF, not active in monkey kidney cells (Gould, S. J., G. A. Keller, N. Hosken, J....

In contrast to many other peroxisomal proteins catalase A contains at least two peroxisomal targeting signals each sufficient to direct reporter proteins to peroxisomes. One of them resides at the extreme carboxy terminus constituting a new variant of this signal, -SSNSKF, not active in monkey kidney cells (Gould, S. J., G. A. Keller, N. Hosken, J....