C-Type LECTIN receptor-like kinase 1 and ACTIN DEPOLYMERIZING FACTOR 3 are key components of plasmodesmata callose modulation

Plasmodesmata (PDs) are intercellular organelles carrying multiple membranous nanochannels that allow the trafficking of cellular signalling molecules. The channel regulation of PDs occurs dynamically and is required in various developmental and physiological processes. It is well known that callose is a critical component in regulating PD permeability or symplasmic connectivity, but the understanding of the signalling pathways and mechanisms of its regulation is limited. Here, we used the reverse genetic approach to investigate the role of C-type lectin receptor-like kinase 1 (CLRLK1) in the aspect of PD callose-modulated symplasmic continuity. Here, we found that loss-of-function mutations in CLRLK1 resulted in excessive PD callose deposits and reduced symplasmic continuity, resulting in an accelerated gravitropic response. The protein interactome study also found that CLRLK1 interacted with actin depolymerizing factor 3 (ADF3) in vitro and in plants. Moreover, mutations in ADF3 result in elevated PD callose deposits and faster gravitropic response. Our results indicate that CLRLK1 and ADF3 negatively regulate PD callose accumulation, contributing to fine-tuning symplasmic opening apertures. Overall, our studies identified two key components involved in the deposits of PD callose and provided new insights into how symplasmic connectivity is maintained by the control of PD callose homoeostasis.

Arabidopsis MCTP family member QUIRKY regulates the formation of the STRUBBELIG receptor kinase complex

Intercellular communication plays a central role in organogenesis. Tissue morphogenesis in Arabidopsis (Arabidopsis thaliana) requires signaling mediated by a cell surface complex containing the atypical receptor kinase STRUBBELIG (SUB) and the multiple C2 domains and transmembrane region protein QUIRKY (QKY). QKY is required to stabilize SUB at the plasma membrane. However, it is unclear what the in vivo architecture of the QKY/SUB signaling complex is, how it is controlled, and how it relates to the maintenance of SUB at the cell surface. We addressed these questions using a combination of genetics, yeast 2-hybrid assays, and Förster resonance energy transfer (FRET)/fluorescence lifetime imaging microscopy (FLIM) in epidermal cells of seedling roots. We found that QKY promotes the formation of SUB homooligomers in vivo. Homooligomerization of SUB appeared to involve its extracellular domain. We also showed that QKY and SUB physically interact and form a complex at the cell surface in vivo. In addition, the data showed that the N-terminal C2A-B region of QKY interacts with the intracellular domain of SUB. They further revealed that this interaction is essential to maintain SUB levels at the cell surface. Finally, we provided evidence that QKY forms homomultimers in vivo in a SUB-independent manner. We suggest a model in which the physical interaction of QKY with SUB mediates the oligomerization of SUB and attenuates its internalization, thereby maintaining sufficiently high levels of SUB at the cell surface required for the control of tissue morphogenesis.

Leaf vein patterning is regulated by the aperture of plasmodesmata intercellular channels

To form tissue networks, animal cells migrate and interact through proteins protruding from their plasma membranes. Plant cells can do neither, yet plants form vein networks. How plants do so is unclear, but veins are thought to form by the coordinated action of the polar transport and signal transduction of the plant hormone auxin. However, plants inhibited in both pathways still form veins. Patterning of vascular cells into veins is instead prevented in mutants lacking the function of the GNOM (GN) regulator of auxin transport and signaling, suggesting the existence of at least one more GN-dependent vein-patterning pathway. Here we show that in Arabidopsis such a pathway depends on the movement of auxin or an auxin-dependent signal through plasmodesmata (PDs) intercellular channels. PD permeability is high where veins are forming, lowers between veins and nonvascular tissues, but remains high between vein cells. Impaired ability to regulate PD aperture leads to defects in auxin transport and signaling, ultimately leading to vein patterning defects that are enhanced by inhibition of auxin transport or signaling. GN controls PD aperture regulation, and simultaneous inhibition of auxin signaling, auxin transport, and regulated PD aperture phenocopies null gn mutants. Therefore, veins are patterned by the coordinated action of three GN-dependent pathways: auxin signaling, polar auxin transport, and movement of auxin or an auxin-dependent signal through PDs. Such a mechanism of tissue network formation is unprecedented in multicellular organisms.

How do plants form vein networks, in the absence of cellular migration or direct cell-cell interaction? This study shows that a GNOM-dependent combination of polar auxin transport, auxin signal transduction, and movement of an auxin signal through plasmodesmata patterns leaf vascular cells into veins.

Histidine kinase inhibitors impair shoot regeneration in Arabidopsis thaliana via cytokinin signaling and SAM patterning determinants

Reversible protein phosphorylation is a post-translational modification involved in virtually all plant processes, as it mediates protein activity and signal transduction. Here, we probe dynamic protein phosphorylation during de novo shoot organogenesis in Arabidopsis thaliana. We find that application of three kinase inhibitors in various time intervals has different effects on root explants. Short exposures to the putative histidine (His) kinase inhibitor TCSA during the initial days on shoot induction medium (SIM) are detrimental for regeneration in seven natural accessions. Investigation of cytokinin signaling mutants, as well as reporter lines for hormone responses and shoot markers, suggests that TCSA impedes cytokinin signal transduction via AHK3, AHK4, AHP3, and AHP5. A mass spectrometry-based phosphoproteome analysis further reveals profound deregulation of Ser/Thr/Tyr phosphoproteins regulating protein modification, transcription, vesicle trafficking, organ morphogenesis, and cation transport. Among TCSA-responsive factors are prior candidates with a role in shoot apical meristem patterning, such as AGO1, BAM1, PLL5, FIP37, TOP1ALPHA, and RBR1, as well as proteins involved in polar auxin transport (e.g., PIN1) and brassinosteroid signaling (e.g., BIN2). Putative novel regeneration determinants regulated by TCSA include RD2, AT1G52780, PVA11, and AVT1C, while NAIP2, OPS, ARR1, QKY, and aquaporins exhibit differential phospholevels on control SIM. LC-MS/MS data are available via ProteomeXchange with identifier PXD030754.

Characterization and phylogenetic analysis of multiple C2 domain and transmembrane region proteins in maize

BACKGROUND

Multiple C2 domain and transmembrane region proteins (MCTPs) are evolutionarily conserved and important signaling molecules. However, the MCTP gene family has not been comprehensively analyzed in maize.

RESULTS

In this study, 385 MCTP genes were identified in all surveyed 38 species. Moreover, gene duplication mode exploration showed that whole genome duplication (WGD) mainly contributed to the expansion of MCTP genes in angiosperms. Phylogeny reconstruction with all surveyed species by the maximum-likelihood (ML) method showed five clades of MCTPs, Clades I to V. Each clade of MCTPs had conservative structures and motifs. Focusing on maize, 17 MCTPs were identified, and a neighborjoining (NJ) phylogenetic tree with only ZmMCTPs was also constructed. As expected, 17 MCTPs showed similar phylogenetic relationships in the neighbor-joining (NJ) tree with those in the maximum-likelihood (ML) tree and could also be divided into five subclades. Moreover, ZmMCTP members in different clades showed specific gene structure, conserved motif, and domain structure compositions. Intriguingly, most ZmMCTP genes were intronless. Analyses of isoelectric points (pIs) and grand averages of hydropathicity (GRAVYs) indicated that the N-terminus was more dispersive than the C-terminus. Further tissue-specific expression analysis indicated that duplicated ZmMCTP pairs involved in whole genome duplication (WGD) had similar expression trends. Finally, ZmMCTPs were transcriptionally altered under diverse abiotic stresses and hormone treatments.

CONCLUSIONS

Our results contribute to deciphering the evolutionary history of MCTPs in maize and other plants, facilitating further functional analysis of these factors, and provide a basis for further clarification of the molecular mechanism of stress responses.

A comparative meta-proteomic pipeline for the identification of plasmodesmata proteins and regulatory conditions in diverse plant species

BACKGROUND

A major route for cell-to-cell signalling in plants is mediated by cell wall-embedded pores termed plasmodesmata forming the symplasm. Plasmodesmata regulate the plant development and responses to the environment; however, our understanding of what factors or regulatory cues affect their structure and permeability is still limited. In this paper, a meta-analysis was carried out for the identification of conditions affecting plasmodesmata transport and for the in silico prediction of plasmodesmata proteins in species for which the plasmodesmata proteome has not been experimentally determined.

RESULTS

Using the information obtained from experimental proteomes, an analysis pipeline (named plasmodesmata in silico proteome 1 or PIP1) was developed to rapidly generate candidate plasmodesmata proteomes for 22 plant species. Using the in silico proteomes to interrogate published transcriptomes, gene interaction networks were identified pointing to conditions likely affecting plasmodesmata transport capacity. High salinity, drought and osmotic stress regulate the expression of clusters enriched in genes encoding plasmodesmata proteins, including those involved in the metabolism of the cell wall polysaccharide callose. Experimental determinations showed restriction in the intercellular transport of the symplasmic reporter GFP and enhanced callose deposition in Arabidopsis roots exposed to 75-mM NaCl and 3% PEG (polyethylene glycol). Using PIP1 and transcriptome meta-analyses, candidate plasmodesmata proteins for the legume Medicago truncatula were generated, leading to the identification of Medtr1g073320, a novel receptor-like protein that localises at plasmodesmata. Expression of Medtr1g073320 affects callose deposition and the root response to infection with the soil-borne bacteria rhizobia in the presence of nitrate.

CONCLUSIONS

Our study shows that combining proteomic meta-analysis and transcriptomic data can be a valuable tool for the identification of new proteins and regulatory mechanisms affecting plasmodesmata function. We have created the freely accessible pipeline PIP1 as a resource for the screening of experimental proteomes and for the in silico prediction of PD proteins in diverse plant species.

Phloem Loading and Unloading of Sucrose: What a Long, Strange Trip from Source to Sink

Sucrose is transported from sources (mature leaves) to sinks (importing tissues such as roots, stems, fruits, and seeds) through the phloem tissues in veins. In many herbaceous crop species, sucrose must first be effluxed to the cell wall by a sugar transporter of the SWEET family prior to being taken up into phloem companion cells or sieve elements by a different sugar transporter, called SUT or SUC. The import of sucrose into these cells is termed apoplasmic phloem loading. In sinks, sucrose can similarly exit the phloem apoplasmically or, alternatively, symplasmically through plasmodesmata into connecting parenchyma storage cells. Recent advances describing the regulation and manipulation of sugar transporter expression and activities provide stimulating new insights into sucrose phloem loading in sources and unloading processes in sink tissues. Additionally, new breakthroughs have revealed distinct subpopulations of cells in leaves with different functions pertaining to phloem loading. These and other discoveries in sucrose transport are discussed.

Sphingolipids at Plasmodesmata: Structural Components and Functional Modulators

Plasmodesmata (PD) are plant-specific channels connecting adjacent cells to mediate intercellular communication of molecules essential for plant development and defense. The typical PD are organized by the close apposition of the plasma membrane (PM), the desmotubule derived from the endoplasmic reticulum (ER), and spoke-like elements linking the two membranes. The plasmodesmal PM (PD-PM) is characterized by the formation of unique microdomains enriched with sphingolipids, sterols, and specific proteins, identified by lipidomics and proteomics. These components modulate PD to adapt to the dynamic changes of developmental processes and environmental stimuli. In this review, we focus on highlighting the functions of sphingolipid species in plasmodesmata, including membrane microdomain organization, architecture transformation, callose deposition and permeability control, and signaling regulation. We also briefly discuss the difference between sphingolipids and sterols, and we propose potential unresolved questions that are of help for further understanding the correspondence between plasmodesmal structure and function.

Spatial control of potato tuberization by the TCP transcription factor BRANCHED1b

The control of carbon allocation, storage and usage is critical for plant growth and development and is exploited for both crop food production and CO₂ capture. Potato tubers are natural carbon reserves in the form of starch that have evolved to allow propagation and survival over winter. They form from stolons, below ground, where they are protected from adverse environmental conditions and animal foraging. We show that BRANCHED1b (BRC1b) acts as a tuberization repressor in aerial axillary buds, which prevents buds from competing in sink strength with stolons. BRC1b loss of function leads to ectopic production of aerial tubers and reduced underground tuberization. In aerial axillary buds, BRC1b promotes dormancy, abscisic acid responses and a reduced number of plasmodesmata. This limits sucrose accumulation and access of the tuberigen protein SP6A. BRC1b also directly interacts with SP6A and blocks its tuber-inducing activity in aerial nodes. Altogether, these actions help promote tuberization underground.

Global Identification and Characterization of C2 Domain-Containing Proteins Associated with Abiotic Stress Response in Rice (Oryza sativa L.)

C2 domain-containing proteins (C2DPs) have been identified in different genomes that contain single or multiple C2 domains in their C- or N-terminal. It possesses higher functional activity in the transmembrane regions. The identification of C2 domains were reported in a previous study, such as multiple C2 domains and transmembrane-region proteins (MCTPs) and N-terminal-TM-C2 domain proteins (NTMC2s) of rice, Arabidopsis thaliana, and cotton, whereas the C2DP gene family in rice has not been comprehensively studied, and the role of the C2DP gene in rice in response to abiotic stress is not yet fully understood. In this study, we identified 82 C2DPs in the rice genome and divided them into seven groups through phylogenetic analysis. The synteny analysis revealed that duplication events were either exhibited within the genome of rice or between the genomes of rice and other species. Through the analysis of cis-acting elements in promoters, expression profiles, and qRT-PCR results, the functions of OsC2DPs were found to be widely distributed in diverse tissues and were extensively involved in phytohormones-related and abiotic stresses response in rice. The prediction of the microRNA (miRNA) targets of OsC2DPs revealed the possibility of regulation by consistent miRNAs. Notably, OsC2DP50/51/52 as a co-tandem duplication exhibited similar expression variations and involved the coincident miRNA-regulation pathway. Moreover, the results of the genotypic variation and haplotype analysis revealed that OsC2DP17, OsC2DP29, and OsC2DP49 were associated with cold stress responses. These findings provided comprehensive insights for characterizations of OsC2DPs in rice as well as for their roles for abiotic stress.

Plasmodesmata Structural Components and Their Role in Signaling and Plant Development

Plasmodesmata are plant intercellular channels that mediate the transport of small and large molecules including RNAs and transcription factors (TFs) that regulate plant development. In this review, we present current research on plasmodesmata form and function and discuss the main regulatory pathways. We show the progress made in the development of approaches and tools to dissect the plasmodesmata proteome in diverse plant species and discuss future perspectives and challenges in this field of research.

Using Steady-State Fluorescence Anisotropy to Study Protein Clustering

Signaling pathways rely on the precise control of protein-protein interactions. Therefore, it is essential to be able to investigate such interactions with spatiotemporal resolution and in live cells. Here we describe a microscope-based fluorescence spectrometry technique to investigate homotypic interactions between GFP-labeled fusion proteins in a rapid and reproducible fashion using fluorescence anisotropy. This method is of great value for the study of protein complexes in live tissue with subcellular resolution.

Function of Plasmodesmata in the Interaction of Plants with Microbes and Viruses

Plasmodesmata (PD) are gated plant cell wall channels that allow the trafficking of molecules between cells and play important roles during plant development and in the orchestration of cellular and systemic signaling responses during interactions of plants with the biotic and abiotic environment. To allow gating, PD are equipped with signaling platforms and enzymes that regulate the size exclusion limit (SEL) of the pore. Plant-interacting microbes and viruses target PD with specific effectors to enhance their virulence and are useful probes to study PD functions.

Cell-to-Cell Connection in Plant Grafting-Molecular Insights into Symplasmic Reconstruction

Grafting is a means to connect tissues from two individual plants and grow a single chimeric plant through the establishment of both apoplasmic and symplasmic connections. Recent molecular studies using RNA-sequencing data have provided genetic information on the processes involved in tissue reunion, including wound response, cell division, cell-cell adhesion, cell differentiation and vascular formation. Thus, studies on grafting increase our understanding of various aspects of plant biology. Grafting has also been used to study systemic signaling and transport of micromolecules and macromolecules in the plant body. Given that graft viability and molecular transport across graft junctions largely depend on vascular formation, a major focus in grafting biology has been the mechanism of vascular development. In addition, it has been thought that symplasmic connections via plasmodesmata are fundamentally important to share cellular information among newly proliferated cells at the graft interface and to accomplish tissue differentiation correctly. Therefore, this review focuses on plasmodesmata formation during grafting. We take advantage of interfamily grafts for unambiguous identification of the graft interface and summarize morphological aspects of de novo formation of plasmodesmata. Important molecular events are addressed by re-examining the time-course transcriptome of interfamily grafts, from which we recently identified the cell-cell adhesion mechanism. Plasmodesmata-associated genes upregulated during graft healing that may provide a link to symplasm establishment are described. We also discuss future research directions.

Cell wall damage attenuates root hair patterning and tissue morphogenesis mediated by the receptor kinase STRUBBELIG

Cell wall remodeling is essential for the control of growth and development as well as the regulation of stress responses. However, the underlying cell wall monitoring mechanisms remain poorly understood. Regulation of root hair fate and flower development in Arabidopsis thaliana requires signaling mediated by the atypical receptor kinase STRUBBELIG (SUB). Furthermore, SUB is involved in cell wall integrity signaling and regulates the cellular response to reduced levels of cellulose, a central component of the cell wall. Here, we show that continuous exposure to sub-lethal doses of the cellulose biosynthesis inhibitor isoxaben results in altered root hair patterning and floral morphogenesis. Genetically impairing cellulose biosynthesis also results in root hair patterning defects. We further show that isoxaben exerts its developmental effects through the attenuation of SUB signaling. Our evidence indicates that downregulation of SUB is a multi-step process and involves changes in SUB complex architecture at the plasma membrane, enhanced removal of SUB from the cell surface, and downregulation of SUB transcript levels. The results provide molecular insight into how the cell wall regulates cell fate and tissue morphogenesis.

Wheat Pm4 resistance to powdery mildew is controlled by alternative splice variants encoding chimeric proteins

Crop breeding for resistance to pathogens largely relies on genes encoding receptors that confer race-specific immunity. Here, we report the identification of the wheat Pm4 race-specific resistance gene to powdery mildew. Pm4 encodes a putative chimeric protein of a serine/threonine kinase and multiple C2 domains and transmembrane regions, a unique domain architecture among known resistance proteins. Pm4 undergoes constitutive alternative splicing, generating two isoforms with different protein domain topologies that are both essential for resistance function. Both isoforms interact and localize to the endoplasmatic reticulum when co-expressed. Pm4 reveals additional diversity of immune receptor architecture to be explored for breeding and suggests an endoplasmatic reticulum-based molecular mechanism of Pm4-mediated race-specific resistance.

Family-Wide Evaluation of Multiple C2 Domain and Transmembrane Region Protein in Gossypium hirsutum

Multiple C2 domain and transmembrane region proteins (MCTPs) are a group of evolutionarily conserved proteins and show emerging roles in mediating protein trafficking and signaling transduction. Although, several studies showed that MCTPs play important roles during plant growth and development, their biological functions in cotton remain largely unknown. Here, we identify and characterize 33 GhMCTP genes from upland cotton (Gossypium hirsutum) and reveal the diverse expression patterns of GhMCTPs in various tissues. We also find that GhMCTP7, GhMCTP12, and GhMCTP17 are highly expressed in the main stem apex, suggesting their possible roles in shoot development. Through analyzing different cotton species, we discover plant heights are closely related to the expression levels of GhMCTP7, GhMCTP12, and GhMCTP17. Furthermore, we silence the expression of GhMCTP genes using virus-induced gene silencing (VIGS) system in cotton and find that GhMCTP7, GhMCTP12, and GhMCTP17 play an essential role in shoot meristem development. GhMCTPs interact with GhKNAT1 and GhKNAT2 and regulate meristem development through integrating multiple signal pathways. Taken together, our results demonstrate functional redundancy of GhMCTPs in cotton shoot meristem development and provide a valuable resource to further study various functions of GhMCTPs in plant growth and development.

The genetic framework of shoot regeneration in Arabidopsis comprises master regulators and conditional fine-tuning factors

Clonal propagation and genetic engineering of plants requires regeneration, but many species are recalcitrant and there is large variability in explant responses. Here, we perform a genome-wide association study using 190 natural Arabidopsis accessions to dissect the genetics of shoot regeneration from root explants and several related in vitro traits. Strong variation is found in the recorded phenotypes and association mapping pinpoints a myriad of quantitative trait genes, including prior candidates and potential novel regeneration determinants. As most of these genes are trait- and protocol-specific, we propose a model wherein shoot regeneration is governed by many conditional fine-tuning factors and a few universal master regulators such as WUSCHEL, whose transcript levels correlate with natural variation in regenerated shoot numbers. Potentially novel genes in this last category are AT3G09925, SUP, EDA40 and DOF4.4. We urge future research in the field to consider multiple conditions and genetic backgrounds.

Robin Lardon et al. report a genome-wide association study of shoot regeneration in Arabidopsis under 2 different in vitro incubation conditions. They find wide variation in regeneration phenotypes, attributable to allelic variants in key developmental genes, and show that genetic association patterns differ depending on environmental factors.

Intercellular trafficking via plasmodesmata: molecular layers of complexity

Plasmodesmata are intercellular pores connecting together most plant cells. These structures consist of a central constricted form of the endoplasmic reticulum, encircled by some cytoplasmic space, in turn delimited by the plasma membrane, itself ultimately surrounded by the cell wall. The presence and structure of plasmodesmata create multiple routes for intercellular trafficking of a large spectrum of molecules (encompassing RNAs, proteins, hormones and metabolites) and also enable local signalling events. Movement across plasmodesmata is finely controlled in order to balance processes requiring communication with those necessitating symplastic isolation. Here, we describe the identities and roles of the molecular components (specific sets of lipids, proteins and wall polysaccharides) that shape and define plasmodesmata structural and functional domains. We highlight the extensive and dynamic interactions that exist between the plasma/endoplasmic reticulum membranes, cytoplasm and cell wall domains, binding them together to effectively define plasmodesmata shapes and purposes.

Genome-wide identification and characterization of multiple C2 domains and transmembrane region proteins in Gossypium hirsutum

Background

Multiple C2 domains and transmembrane region proteins (MCTPs) may act as transport mediators of other regulators. Although increased number of MCTPs in higher plants implies their diverse and specific functions in plant growth and development, only a few plant MCTPs have been studied and no study on the MCTPs in cotton has been reported.

Results

In this study, we identified 31 MCTPs in G. hirsutum, which were classified into five subfamilies according to the phylogenetic analysis. GhMCTPs from subfamily V exhibited isoelectric points (pIs) less than 7, whereas GhMCTPs from subfamily I, II, III and IV exhibited pIs more than 7.5, implying their distinct biological functions. In addition, GhMCTPs within subfamily III, IV and V exhibited more diverse physicochemical properties, domain architectures and expression patterns than GhMCTPs within subfamily I and II, suggesting that GhMCTPs within subfamily III, IV and V diverged to perform more diverse and specific functions. Analyses of conserved motifs and pIs indicated that the N-terminus was more divergent than the C-terminus and GhMCTPs’ functional divergence might be mainly contributed by the N-terminus. Furthermore, yeast two-hybrid assay indicated that the N-terminus was responsible to interact with target proteins. Phylogenetic analysis classified multiple N-terminal C2 domains into four subclades, suggesting that these C2 domains performed different molecular functions in mediating the transport of target proteins.

Conclusions

Our systematic characterization of MCTPs in G. hirsutum will provide helpful information to further research GhMCTPs’ molecular roles in mediating other regulators’ transport to coordinate growth and development of various cotton tissues.

Arabidopsis Transmembrane Receptor-Like Kinases (RLKs): A Bridge between Extracellular Signal and Intracellular Regulatory Machinery

Receptors form the crux for any biochemical signaling. Receptor-like kinases (RLKs) are conserved protein kinases in eukaryotes that establish signaling circuits to transduce information from outer plant cell membrane to the nucleus of plant cells, eventually activating processes directing growth, development, stress responses, and disease resistance. Plant RLKs share considerable homology with the receptor tyrosine kinases (RTKs) of the animal system, differing at the site of phosphorylation. Typically, RLKs have a membrane-localization signal in the amino-terminal, followed by an extracellular ligand-binding domain, a solitary membrane-spanning domain, and a cytoplasmic kinase domain. The functional characterization of ligand-binding domains of the various RLKs has demonstrated their essential role in the perception of extracellular stimuli, while its cytosolic kinase domain is usually confined to the phosphorylation of their substrates to control downstream regulatory machinery. Identification of the several ligands of RLKs, as well as a few of its immediate substrates have predominantly contributed to a better understanding of the fundamental signaling mechanisms. In the model plant Arabidopsis, several studies have indicated that multiple RLKs are involved in modulating various types of physiological roles via diverse signaling routes. Here, we summarize recent advances and provide an updated overview of transmembrane RLKs in Arabidopsis.

Mass-spectrometry-based draft of the Arabidopsis proteome

Plants are essential for life and are extremely diverse organisms with unique molecular capabilities¹. Here we present a quantitative atlas of the transcriptomes, proteomes and phosphoproteomes of 30 tissues of the model plant Arabidopsis thaliana. Our analysis provides initial answers to how many genes exist as proteins (more than 18,000), where they are expressed, in which approximate quantities (a dynamic range of more than six orders of magnitude) and to what extent they are phosphorylated (over 43,000 sites). We present examples of how the data may be used, such as to discover proteins that are translated from short open-reading frames, to uncover sequence motifs that are involved in the regulation of protein production, and to identify tissue-specific protein complexes or phosphorylation-mediated signalling events. Interactive access to this resource for the plant community is provided by the ProteomicsDB and ATHENA databases, which include powerful bioinformatics tools to explore and characterize Arabidopsis proteins, their modifications and interactions.

Genome-wide identification and phylogenetic analysis of rice FTIP gene family

FT-INTERACTING PROTEIN (FTIP) gene family in rice are the members of multiple C2 domain and transmembrane region proteins (MCTPs). There are many homologs of OsFTIPs in plants; however, the bioinformatics of them remains unclear. In the studies, 13 OsFTIP genes are identified in rice. OsFTIPs are unevenly located in 12 chromosomes. The OsFTIPs are phylogenetically divided into three clades. Cis-elements respond to abiotic stress, light, and hormones are found in the promoter region of OsFTIPs which are induced by the stimuli. All OsFTIPs are expressed with different profiles. Syntenic analysis of 128 OsFTIPs and FTIP-like homologs reveals that various number of gene pairs are identified between rice and other species. The 128 FTIP-like homologs are divided into six groups which fall into three classes. Ten motifs are shared by most OsFTIPs and their homologs. The studies provide a theoretical basis for further elucidating the functions of OsFTIP gene family.

The Role of Plasmodesmata-Associated Receptor in Plant Development and Environmental Response

Over the last decade, plasmodesmata (PD) symplasmic nano-channels were reported to be involved in various cell biology activities to prop up within plant growth and development as well as environmental stresses. Indeed, this is highly influenced by their native structure, which is lined with the plasma membrane (PM), conferring a suitable biological landscape for numerous plant receptors that correspond to signaling pathways. However, there are more than six hundred members of Arabidopsis thaliana membrane-localized receptors and over one thousand receptors in rice have been identified, many of which are likely to respond to the external stimuli. This review focuses on the class of plasmodesmal-receptor like proteins (PD-RLPs)/plasmodesmal-receptor-like kinases (PD-RLKs) found in planta. We summarize and discuss the current knowledge regarding RLPs/RLKs that reside at PD-PM channels in response to plant growth, development, and stress adaptation.

Dare to change, the dynamics behind plasmodesmata-mediated cell-to-cell communication

Plasmodesmata pores control the entry and exit of molecules at cell-to-cell boundaries. Hundreds of pores perforate the plant cell wall, connecting cells together and establishing direct cytosolic and membrane continuity. This ability to connect cells in such a way is a hallmark of plant physiology and is thought to have allowed sessile multicellularity in Plantae kingdom. Indeed, plasmodesmata-mediated cell-to-cell signalling is fundamental to many plant-related processes. In fact, there are so many facets of plant biology under the control of plasmodesmata that it is hard to conceive how such tiny structures can do so much. While they provide 'open doors' between cells, they also need to guarantee cellular identities and territories by selectively transporting molecules. Although plasmodesmata operating mode remains difficult to grasp, little by little plant scientists are divulging their secrets. In this review, we highlight novel functions of cell-to-cell signalling and share recent insights into how plasmodesmata structural and molecular signatures confer functional specificity and plasticity to these unique cellular machines.

The Arabidopsis receptor kinase STRUBBELIG regulates the response to cellulose deficiency

Plant cells are encased in a semi-rigid cell wall of complex build. As a consequence, cell wall remodeling is essential for the control of growth and development as well as the regulation of abiotic and biotic stress responses. Plant cells actively sense physico-chemical changes in the cell wall and initiate corresponding cellular responses. However, the underlying cell wall monitoring mechanisms remain poorly understood. In Arabidopsis the atypical receptor kinase STRUBBELIG (SUB) mediates tissue morphogenesis. Here, we show that SUB-mediated signal transduction also regulates the cellular response to a reduction in the biosynthesis of cellulose, a central carbohydrate component of the cell wall. SUB signaling affects early increase of intracellular reactive oxygen species, stress gene induction as well as ectopic lignin and callose accumulation upon exogenous application of the cellulose biosynthesis inhibitor isoxaben. Moreover, our data reveal that SUB signaling is required for maintaining cell size and shape of root epidermal cells and the recovery of root growth after transient exposure to isoxaben. SUB is also required for root growth arrest in mutants with defective cellulose biosynthesis. Genetic data further indicate that SUB controls the isoxaben-induced cell wall stress response independently from other known receptor kinase genes mediating this response, such as THESEUS1 or MIK2. We propose that SUB functions in a least two distinct biological processes: the control of tissue morphogenesis and the response to cell wall damage. Taken together, our results reveal a novel signal transduction pathway that contributes to the molecular framework underlying cell wall integrity signaling.

Plant cells are encapsulated by a semi-rigid and biochemically complex cell wall. This particular feature has consequences for multiple biologically important processes, such as cell and organ growth or various stress responses. For a plant cell to grow the cell wall has to be modified to allow cell expansion, which is driven by outward-directed turgor pressure generated inside the cell. In return, changes in cell wall architecture need to be monitored by individual cells, and to be coordinated across cells in a growing tissue, for an organ to attain its regular size and shape. Cell wall surveillance also comes into play in the reaction against certain stresses, including for example infection by plant pathogens, many of which break through the cell wall during infection, thereby generating wall-derived factors that can induce defense responses. There is only limited knowledge regarding the molecular system that monitors the composition and status of the cell wall. Here we provide further insight into the mechanism. We show that the cell surface receptor STRUBBELIG, previously known to control organ development in Arabidopsis, also promotes the cell’s response to reduced amounts of cellulose, a main component of the cell wall.

Just passing through: The auxin gradient of the root meristem

The root meristem-one of the plant's centers of continuous growth-is a conveyer belt in which cells of different identities are pushed through gradients along the root's longitudinal axis. An auxin gradient has long been implicated in controlling the progression of cell states in the root meristem. Recent work has shown that a PLETHORA (PLT) protein transcription factor gradient, which is under a delayed auxin response, has a dose-dependent effect on the differentiation state of cells. The direct effect of auxin concentration on differential transcriptional outputs remains unclear. Genomic and other analyses of regulatory sequences show that auxin responses are likely controlled by combinatorial inputs from transcription factors outside the core auxin signaling pathway. The passage through the meristem exposes cells to varying positional signals that could help them interpret auxin inputs independent of gradient effects. One open question is whether cells process information from the changes in the gradient over time as they move through the auxin gradient.

Creating Contacts Between Replication and Movement at Plasmodesmata - A Role for Membrane Contact Sites in Plant Virus Infections?

To infect their hosts and cause disease, plant viruses must replicate within cells and move throughout the plant both locally and systemically. RNA virus replication occurs on the surface of various cellular membranes, whose shape and composition become extensively modified in the process. Membrane contact sites (MCS) can mediate non-vesicular lipid-shuttling between different membranes and viruses co-opt components of these structures to make their membrane environment suitable for replication. Whereas animal viruses exit and enter cells when moving throughout their host, the rigid wall of plant cells obstructs this pathway and plant viruses therefore move between cells symplastically through plasmodesmata (PD). PD are membranous channels connecting nearly all plant cells and are now viewed to constitute a specialized type of endoplasmic reticulum (ER)-plasma membrane (PM) MCS themselves. Thus, both replication and movement of plant viruses rely on MCS. However, recent work also suggests that for some viruses, replication and movement are closely coupled at ER-PM MCS at the entrances of PD. Movement-coupled replication at PD may be distinct from the main bulk of replication and virus accumulation, which produces progeny virions for plant-to-plant transmission. Thus, MCS play a central role in plant virus infections, and may provide a link between two essential steps in the viral life cycle, replication and movement. Here, we provide an overview of plant virus-MCS interactions identified to date, and place these in the context of the connection between viral replication and cell-to-cell movement.

Investigations into a putative role for the novel BRASSIKIN pseudokinases in compatible pollen-stigma interactions in Arabidopsis thaliana

BACKGROUND

In the Brassicaceae, the early stages of compatible pollen-stigma interactions are tightly controlled with early checkpoints regulating pollen adhesion, hydration and germination, and pollen tube entry into the stigmatic surface. However, the early signalling events in the stigma which trigger these compatible interactions remain unknown.

RESULTS

A set of stigma-expressed pseudokinase genes, termed BRASSIKINs (BKNs), were identified and found to be present in only core Brassicaceae genomes. In Arabidopsis thaliana Col-0, BKN1 displayed stigma-specific expression while the BKN2 gene was expressed in other tissues as well. CRISPR deletion mutations were generated for the two tandemly linked BKNs, and very mild hydration defects were observed for wild-type Col-0 pollen when placed on the bkn1/2 mutant stigmas. In further analyses, the predominant transcript for the stigma-specific BKN1 was found to have a premature stop codon in the Col-0 ecotype, but a survey of the 1001 Arabidopsis genomes uncovered three ecotypes that encoded a full-length BKN1 protein. Furthermore, phylogenetic analyses identified intact BKN1 orthologues in the closely related outcrossing Arabidopsis species, A. lyrata and A. halleri. Finally, the BKN pseudokinases were found to be plasma-membrane localized through the dual lipid modification of myristoylation and palmitoylation, and this localization would be consistent with a role in signaling complexes.

CONCLUSION

In this study, we have characterized the novel Brassicaceae-specific family of BKN pseudokinase genes, and examined the function of BKN1 and BKN2 in the context of pollen-stigma interactions in A. thaliana Col-0. Additionally, premature stop codons were identified in the predicted stigma specific BKN1 gene in a number of the 1001 A. thaliana ecotype genomes, and this was in contrast to the out-crossing Arabidopsis species which carried intact copies of BKN1. Thus, understanding the function of BKN1 in other Brassicaceae species will be a key direction for future studies.

Maize Carbohydrate Partitioning Defective33 Encodes an MCTP Protein and Functions in Sucrose Export from Leaves

To sustain plant growth, development, and crop yield, sucrose must be transported from leaves to distant parts of the plant, such as seeds and roots. To identify genes that regulate sucrose accumulation and transport in maize (Zea mays), we isolated carbohydrate partitioning defective33 (cpd33), a recessive mutant that accumulated excess starch and soluble sugars in mature leaves. The cpd33 mutants also exhibited chlorosis in the leaf blades, greatly diminished plant growth, and reduced fertility. Cpd33 encodes a protein containing multiple C2 domains and transmembrane regions. Subcellular localization experiments showed the CPD33 protein localized to plasmodesmata (PD), the plasma membrane, and the endoplasmic reticulum. We also found that a loss-of-function mutant of the CPD33 homolog in Arabidopsis, QUIRKY, had a similar carbohydrate hyperaccumulation phenotype. Radioactively labeled sucrose transport assays showed that sucrose export was significantly lower in cpd33 mutant leaves relative to wild-type leaves. However, PD transport in the adaxial-abaxial direction was unaffected in cpd33 mutant leaves. Intriguingly, transmission electron microscopy revealed fewer PD at the companion cell-sieve element interface in mutant phloem tissue, providing a possible explanation for the reduced sucrose export in mutant leaves. Collectively, our results suggest that CPD33 functions to promote symplastic transport into sieve elements.

The Arabidopsis receptor kinase STRUBBELIG undergoes clathrin-dependent endocytosis

Signaling mediated by cell surface receptor kinases is central to the coordination of growth patterns during organogenesis. Receptor kinase signaling is in part controlled through endocytosis and subcellular distribution of the respective receptor kinase. For the majority of plant cell surface receptors, the underlying trafficking mechanisms are not characterized. In Arabidopsis, tissue morphogenesis requires the atypical receptor kinase STRUBBELIG (SUB). Here, we studied the endocytic mechanism of SUB. Our data revealed that a functional SUB-enhanced green fluorescent protein (EGFP) fusion is ubiquitinated in vivo. We further showed that plasma membrane-bound SUB:EGFP becomes internalized in a clathrin-dependent fashion. We also found that SUB:EGFP associates with the trans-Golgi network and accumulates in multivesicular bodies and the vacuole. Co-immunoprecipitation experiments revealed that SUB:EGFP and clathrin are present within the same protein complex. Our genetic analysis showed that SUB and CLATHRIN HEAVY CHAIN (CHC) 2 regulate root hair patterning. By contrast, genetic reduction of CHC activity ameliorates the floral defects of sub mutants. Taken together, the data indicate that SUB undergoes clathrin-mediated endocytosis, that this process does not rely on stimulation of SUB signaling by an exogenous agent, and that SUB genetically interacts with clathrin-dependent pathways in a tissue-specific manner.

Multiple C2 domains and transmembrane region proteins (MCTPs) tether membranes at plasmodesmata

In eukaryotes, membrane contact sites (MCS) allow direct communication between organelles. Plants have evolved a unique type of MCS, inside intercellular pores, the plasmodesmata, where endoplasmic reticulum (ER)-plasma membrane (PM) contacts coincide with regulation of cell-to-cell signalling. The molecular mechanism and function of membrane tethering within plasmodesmata remain unknown. Here, we show that the multiple C2 domains and transmembrane region protein (MCTP) family, key regulators of cell-to-cell signalling in plants, act as ER-PM tethers specifically at plasmodesmata. We report that MCTPs are plasmodesmata proteins that insert into the ER via their transmembrane region while their C2 domains dock to the PM through interaction with anionic phospholipids. A Atmctp3/Atmctp4 loss of function mutant induces plant developmental defects, impaired plasmodesmata function and composition, while MCTP4 expression in a yeast Δtether mutant partially restores ER-PM tethering. Our data suggest that MCTPs are unique membrane tethers controlling both ER-PM contacts and cell-to-cell signalling.

Asymmetric Redundancy of ZERZAUST and ZERZAUST HOMOLOG in Different Accessions of Arabidopsis thaliana

Divergence among duplicate genes is one of the important sources of evolutionary innovation. But, the contribution of duplicate divergence to variation in Arabidopsis accessions is sparsely known. Recently, we studied the role of a cell wall localized protein, ZERZAUST (ZET), in Landsberg erecta (Ler) accession, lack of which results in aberrant plant morphology. Here, we present the study of ZET in Columbia (Col) accession, which not only showed differential expression patterns in comparison to Ler, but also revealed its close homolog, ZERZAUST HOMOLOG (ZETH). Although, genetic analysis implied redundancy, expression analysis revealed divergence, with ZETH showing minimal expression in both Col and Ler. In addition, ZETH shows relatively higher expression levels in Col compared to Ler. Our data also reveal compensatory up-regulation of ZETH in Col, but not in Ler, implying it is perhaps dispensable in Ler. However, a novel CRISPR/Cas9-induced zeth allele confirmed that ZETH has residual activity in Ler. Finally, the synergistic interaction of the receptor-like kinase gene, ERECTA with ZET in ameliorating morphological defects suggests crucial role of modifiers on plant phenotype. The results provide genetic evidence for accession-specific differences in compensation mechanism and asymmetric gene contribution. Thus, our work reveals a novel example for how weakly expressed homologs contribute to diversity among accessions.

QUIRKY regulates root epidermal cell patterning through stabilizing SCRAMBLED to control CAPRICE movement in Arabidopsis

SCM, a leucine-rich repeat receptor-like kinase, is required for root epidermal cells to appropriately interpret their location and generate the proper cell-type pattern during Arabidopsis root development. Here, via a screen for scm-like mutants we describe a new allele of the QKY gene. We find that QKY is required for the appropriate spatial expression of several epidermal cell fate regulators in a similar manner as SCM in roots, and that QKY and SCM are necessary for the efficient movement of CPC between epidermal cells. We also show that turnover of SCM is mediated by a vacuolar degradation pathway triggered by ubiquitination, and that QKY prevents this SCM ubiquitination through their physical interaction. These results suggest that QKY stabilizes SCM through interaction, and this complex facilitates CPC movement between the epidermal cells to help establish the cell-type pattern in the Arabidopsis root epidermis.

SCM is a receptor-like kinase that ensures proper root patterning. Here, Song et al. find that SCM promotes the movement of CPC from non-hair cells to neighboring root epidermal cells and identify QKY as an additional facilitator of CPC mobility that acts by preventing vacuolar degradation of SCM.

Mechanical Conflicts in Twisting Growth Revealed by Cell-Cell Adhesion Defects

Many plants grow organs and tissues with twisted shapes. Arabidopsis mutants with impaired microtubule dynamics exhibit such a phenotype constitutively. Although the activity of the corresponding microtubule regulators is better understood at the molecular level, how large-scale twisting can emerge in the mutants remains largely unknown. Classically, oblique cortical microtubules would constrain the deposition of cellulose microfibrils in cells, and such conflicts at the cell level would be relaxed at the tissue scale by supracellular torsion. This model implicitly assumes that cell-cell adhesion is a key step to transpose local mechanical conflicts into a macroscopic twisting phenotype. Here we tested this prediction using the quasimodo1 mutant, which displays cell-cell adhesion defects. Using the spriral2/tortifolia1 mutant with hypocotyl helical growth, we found that qua1-induced cell-cell adhesion defects restore straight growth in qua1-1 spr2-2. Detached cells in qua1-1 spr2-2 displayed helical growth, confirming that straight growth results from the lack of mechanical coupling between cells rather than a restoration of SPR2 activity in the qua1 mutant. Because adhesion defects in qua1 depend on tension in the outer wall, we also showed that hypocotyl twisting in qua1-1 spr2-2 could be restored when decreasing the matrix potential of the growth medium, i.e., by reducing the magnitude of the pulling force between adjacent cells, in the double mutant. Interestingly, the induction of straight growth in qua1-1 spr2-2 could be achieved beyond hypocotyls, as leaves also displayed a flat phenotype in the double mutant. Altogether, these results provide formal experimental support for a scenario in which twisted growth in spr2 mutant would result from the relaxation of local mechanical conflicts between adjacent cells via global organ torsion.

The AGC protein kinase UNICORN controls planar growth by attenuating PDK1 in Arabidopsis thaliana

Tissue morphogenesis critically depends on the coordination of cellular growth patterns. In plants, many organs consist of clonally distinct cell layers, such as the epidermis, whose cells undergo divisions that are oriented along the plane of the layer. The developmental control of such planar growth is poorly understood. We have previously identified the Arabidopsis AGCVIII-class protein kinase UNICORN (UCN) as a central regulator of this process. Plants lacking UCN activity show spontaneous formation of ectopic multicellular protrusions in integuments and malformed petals indicating that UCN suppresses uncontrolled growth in those tissues. In the current model UCN regulates planar growth of integuments in part by directly repressing the putative transcription factor ABERRANT TESTA SHAPE (ATS). Here we report on the identification of 3-PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE 1 (PDK1) as a novel factor involved in UCN-mediated growth control. PDK1 constitutes a basic component of signaling mediated by AGC protein kinases throughout eukaryotes. Arabidopsis PDK1 is implied in stress responses and growth promotion. Here we show that loss-of-function mutations in PDK1 suppress aberrant growth in integuments and petals of ucn mutants. Additional genetic, in vitro, and cell biological data support the view that UCN functions by repressing PDK1. Furthermore, our data indicate that PDK1 is indirectly required for deregulated growth caused by ATS overexpression. Our findings support a model proposing that UCN suppresses ectopic growth in integuments through two independent processes: the attenuation of the protein kinase PDK1 in the cytoplasm and the repression of the transcription factor ATS in the nucleus.

Seed coat thickness in the evolution of angiosperms

The seed habit represents a remarkable evolutionary advance in plant sexual reproduction. Since the Paleozoic, seeds carry a seed coat that protects, nourishes and facilitates the dispersal of the fertilization product(s). The seed coat architecture evolved to adapt to different environments and reproductive strategies in part by modifying its thickness. Here, we review the great natural diversity observed in seed coat thickness among angiosperms and its molecular regulation in Arabidopsis.

Plasmodesmata at a glance

Plasmodesmata are cytoplasmic communication channels that are vital for the physiology and development of all plants. They facilitate the intercellular movement of various cargos - ranging from small molecules, such as sugars, ions and other essential nutrients and chemicals, to large complex molecules, such as proteins and different types of RNA species - by bridging neighboring cells across their cell walls. Structurally, an individual channel consists of the cytoplasmic sleeve that is formed between the endoplasmic reticulum and the plasma membrane leaflets. Plasmodesmata are highly versatile channels; they vary in number and structure, and undergo constant adjustments to their permeability in response to many internal and external cues. In this Cell Science at a Glance article and accompanying poster, we provide an overview of plasmodesmata form and function, with highlights on their development and variation, associated components and mobile factors. In addition, we present methodologies that are currently used to study plasmodesmata-mediated intercellular communication.

Symplasmic Intercellular Communication through Plasmodesmata

Communication between cells is an essential process for developing and maintaining multicellular collaboration during plant development and physiological adaptation in response to environmental stimuli. The intercellular movement of proteins and RNAs in addition to the movement of small nutrients or signaling molecules such as sugars and phytohormones has emerged as a novel mechanism of cell-to-cell signaling in plants. As a strategy for efficient intercellular communication and long-distance molecule movement, plants have evolved plant-specific symplasmic communication networks via plasmodesmata (PDs) and the phloem.

Proteomic Analysis of Plasmodesmata From Populus Cell Suspension Cultures in Relation With Callose Biosynthesis

Plasmodesmata are channels that link adjacent cells in plant tissues through which molecular exchanges take place. They are involved in multiple processes vital to plant cells, such as responses to hormonal signaling or environmental challenges including osmotic stress, wounding and pathogen attack. Despite the importance of plasmodesmata, their proteome is not well-defined. Here, we have isolated fractions enriched in plasmodesmata from cell suspension cultures of Populus trichocarpa and identified 201 proteins that are enriched in these fractions, thereby providing further insight on the multiple functions of plasmodesmata. Proteomics analysis revealed an enrichment of proteins specifically involved in responses to stress, transport, metabolism and signal transduction. Consistent with the role of callose deposition and turnover in the closure and aperture of the plasmodesmata and our proteomic analysis, we demonstrate the enrichment of callose synthase activity in the plasmodesmata represented by several gene products. A new form of calcium-independent callose synthase activity was detected, in addition to the typical calcium-dependent enzyme activity, suggesting a role of calcium in the regulation of plasmodesmata through two forms of callose synthase activities. Our report provides the first proteomic investigation of the plasmodesmata from a tree species and the direct biochemical evidence for the occurrence of several forms of active callose synthases in these structures. Data are available via ProteomeXchange with identifier PXD010692.

Shaping intercellular channels of plasmodesmata: the structure-to-function missing link

Plasmodesmata (PD) are a hallmark of the plant kingdom and a cornerstone of plant biology and physiology, forming the conduits for the cell-to-cell transfer of proteins, RNA and various metabolites, including hormones. They connect the cytosols and endomembranes of cells, which allows enhanced cell-to-cell communication and synchronization. Because of their unique position as intercellular gateways, they are at the frontline of plant defence and signalling and constitute the battleground for virus replication and spreading. The membranous organization of PD is remarkable, where a tightly furled strand of endoplasmic reticulum comes into close apposition with the plasma membrane, the two connected by spoke-like elements. The role of these structural features is, to date, still not completely understood. Recent data on PD seem to point in an unexpected direction, establishing a close parallel between PD and membrane contact sites and defining plasmodesmal membranes as microdomains. However, the implications of this new viewpoint are not fully understood. Aided by available phylogenetic data, this review attempts to reassess the function of the different elements comprising the PD and the relevance of membrane lipid composition and biophysics in defining specialized microdomains of PD, critical for their function.

Comparative proteomic profiling of the choline transporter-like1 (CHER1) mutant provides insights into plasmodesmata composition of fully developed Arabidopsis thaliana leaves

In plants, intercellular communication and exchange are highly dependent on cell wall bridging structures between adhering cells, so-called plasmodesmata (PD). In our previous genetic screen for PD-deficient Arabidopsis mutants, we described choline transporter-like 1 (CHER1) being important for PD genesis and maturation. Leaves of cher1 mutant plants have up to 10 times less PD, which do not develop to complex structures. Here we utilize the T-DNA insertion mutant cher1-4 and report a deep comparative proteomic workflow for the identification of cell-wall-embedded PD-associated proteins. Analyzing triplicates of cell-wall-enriched fractions in depth by fractionation and quantitative high-resolution mass spectrometry, we compared > 5000 proteins obtained from fully developed leaves. Comparative data analysis and subsequent filtering generated a list of 61 proteins being significantly more abundant in Col-0. This list was enriched for previously described PD-associated proteins. To validate PD association of so far uncharacterized proteins, subcellular localization analyses were carried out by confocal laser-scanning microscopy. This study confirmed the association of PD for three out of four selected candidates, indicating that the comparative approach indeed allowed identification of so far undescribed PD-associated proteins. Performing comparative cell wall proteomics of Nicotiana benthamiana tissue, we observed an increase in abundance of these three selected candidates during sink to source transition. Taken together, our comparative proteomic approach revealed a valuable data set of potential PD-associated proteins, which can be used as a resource to unravel the molecular composition of complex PD and to investigate their function in cell-to-cell communication.

A calmodulin-like protein regulates plasmodesmal closure during bacterial immune responses

Plants sense microbial signatures via activation of pattern recognition receptors (PPRs), which trigger a range of cellular defences. One response is the closure of plasmodesmata, which reduces symplastic connectivity and the capacity for direct molecular exchange between host cells. Plasmodesmal flux is regulated by a variety of environmental cues but the downstream signalling pathways are poorly defined, especially the way in which calcium regulates plasmodesmal closure. Here, we identify that closure of plasmodesmata in response to bacterial flagellin, but not fungal chitin, is mediated by a plasmodesmal-localized Ca²⁺ -binding protein Calmodulin-like 41 (CML41). CML41 is transcriptionally upregulated by flg22 and facilitates rapid callose deposition at plasmodesmata following flg22 treatment. CML41 acts independently of other defence responses triggered by flg22 perception and reduces bacterial infection. We propose that CML41 enables Ca²⁺ -signalling specificity during bacterial pathogen attack and is required for a complete defence response against Pseudomonas syringae.

Architecture and permeability of post-cytokinesis plasmodesmata lacking cytoplasmic sleeves

Plasmodesmata are remarkable cellular machines responsible for the controlled exchange of proteins, small RNAs and signalling molecules between cells. They are lined by the plasma membrane (PM), contain a strand of tubular endoplasmic reticulum (ER), and the space between these two membranes is thought to control plasmodesmata permeability. Here, we have reconstructed plasmodesmata three-dimensional (3D) ultrastructure with an unprecedented level of 3D information using electron tomography. We show that within plasmodesmata, ER-PM contact sites undergo substantial remodelling events during cell differentiation. Instead of being open pores, post-cytokinesis plasmodesmata present such intimate ER-PM contact along the entire length of the pores that no intermembrane gap is visible. Later on, during cell expansion, the plasmodesmata pore widens and the two membranes separate, leaving a cytosolic sleeve spanned by tethers whose presence correlates with the appearance of the intermembrane gap. Surprisingly, the post-cytokinesis plasmodesmata allow diffusion of macromolecules despite the apparent lack of an open cytoplasmic sleeve, forcing the reassessment of the mechanisms that control plant cell-cell communication.

The cell wall-localized atypical β-1,3 glucanase ZERZAUST controls tissue morphogenesis in Arabidopsis thaliana

Orchestration of cellular behavior in plant organogenesis requires integration of intercellular communication and cell wall dynamics. The underlying signaling mechanisms are poorly understood. Tissue morphogenesis in Arabidopsis depends on the receptor-like kinase STRUBBELIG. Mutations in ZERZAUST were previously shown to result in a strubbelig-like mutant phenotype. Here, we report on the molecular identification and functional characterization of ZERZAUST We show that ZERZAUST encodes a putative GPI-anchored β-1,3 glucanase suggested to degrade the cell wall polymer callose. However, a combination of in vitro, cell biological and genetic experiments indicate that ZERZAUST is not involved in the regulation of callose accumulation. Nonetheless, Fourier-transformed infrared-spectroscopy revealed that zerzaust mutants show defects in cell wall composition. Furthermore, the results indicate that ZERZAUST represents a mobile apoplastic protein, and that its carbohydrate-binding module family 43 domain is required for proper subcellular localization and function whereas its GPI anchor is dispensable. Our collective data reveal that the atypical β-1,3 glucanase ZERZAUST acts in a non-cell-autonomous manner and is required for cell wall organization during tissue morphogenesis.

De novo Transcriptome Profiling of Flowers, Flower Pedicels and Pods of Lupinus luteus (Yellow Lupine) Reveals Complex Expression Changes during Organ Abscission

Yellow lupine (Lupinus luteus L., Taper c.), a member of the legume family (Fabaceae L.), has an enormous practical importance. Its excessive flower and pod abscission represents an economic drawback, as proper flower and seed formation and development is crucial for the plant's productivity. Generative organ detachment takes place at the basis of the pedicels, within a specialized group of cells collectively known as the abscission zone (AZ). During plant growth these cells become competent to respond to specific signals that trigger separation and lead to the abolition of cell wall adhesion. Little is known about the molecular network controlling the yellow lupine organ abscission. The aim of our study was to establish the divergences and similarities in transcriptional networks in the pods, flowers and flower pedicels abscised or maintained on the plant, and to identify genes playing key roles in generative organ abscission in yellow lupine. Based on de novo transcriptome assembly, we identified 166,473 unigenes representing 219,514 assembled unique transcripts from flowers, flower pedicels and pods undergoing abscission and from control organs. Comparison of the cDNA libraries from dropped and control organs helped in identifying 1,343, 2,933 and 1,491 differentially expressed genes (DEGs) in the flowers, flower pedicels and pods, respectively. In DEG analyses, we focused on genes involved in phytohormonal regulation, cell wall functioning and metabolic pathways. Our results indicate that auxin, ethylene and gibberellins are some of the main factors engaged in generative organ abscission. Identified 28 DEGs common for all library comparisons are involved in cell wall functioning, protein metabolism, water homeostasis and stress response. Interestingly, among the common DEGs we also found an miR169 precursor, which is the first evidence of micro RNA engaged in abscission. A KEGG pathway enrichment analysis revealed that the identified DEGs were predominantly involved in carbohydrate and amino acid metabolism, but some other pathways were also targeted. This study represents the first comprehensive transcriptome-based characterization of organ abscission in L. luteus and provides a valuable data source not only for understanding the abscission signaling pathway in yellow lupine, but also for further research aimed at improving crop yields.

Plasmodesmata-Mediated Cell-to-Cell Communication in the Shoot Apical Meristem: How Stem Cells Talk

Positional information is crucial for the determination of plant cell fates, and it is established based on coordinated cell-to-cell communication, which in turn is essential for plant growth and development. Plants have evolved a unique communication pathway, with tiny channels called plasmodesmata (PD) spanning the cell wall. PD interconnect most cells in the plant and generate a cytoplasmic continuum, to mediate short- and long-distance trafficking of various molecules. Cell-to-cell communication through PD plays a role in transmitting positional signals, however, the regulatory mechanisms of PD-mediated trafficking are still largely unknown. The induction and maintenance of stem cells in the shoot apical meristem (SAM) depends on PDmediated cell-to-cell communication, hence, it is an optimal model for dissecting the regulatory mechanisms of PD-mediated cell-to-cell communication and its function in specifying cell fates. In this review, we summarize recent knowledge of PD-mediated cell-to-cell communication in the SAM, and discuss mechanisms underlying molecular trafficking through PD and its role in plant development.

Using fluorescence lifetime microscopy to study the subcellular localization of anthocyanins

Anthocyanins are flavonoid pigments that accumulate in most seed plants. They are synthesized in the cytoplasm but accumulate inside the vacuoles. Anthocyanins are pigmented at the lower vacuolar pH, but in the cytoplasm they can be visualized based on their fluorescence properties. Thus, anthocyanins provide an ideal system for the development of new methods to investigate cytoplasmic pools and association with other molecular components. We have analyzed the fluorescence decay of anthocyanins by fluorescence lifetime imaging microscopy (FLIM), in both in vitro and in vivo conditions, using wild-type and mutant Arabidopsis thaliana seedlings. Within plant cells, the amplitude-weighted mean fluorescence lifetime (τ_m ) correlated with distinct subcellular localizations of anthocyanins. The vacuolar pool of anthocyanins exhibited shorter τ_m than the cytoplasmic pool. Consistently, lowering the pH of anthocyanins in solution shortened their fluorescence decay. We propose that FLIM is a useful tool for understanding the trafficking of anthocyanins and, potentially, for estimating vacuolar pH inside intact plant cells.

Receptor Complex Mediated Regulation of Symplastic Traffic

Plant receptor kinases (RKs) and receptor proteins (RPs) are involved in a plethora of cellular processes, including developmental decisions and immune responses. There is increasing evidence that plasmodesmata (PD)-localized RKs and RPs act as nexuses that perceive extracellular signals and convey them into intra- and intercellular responses by regulating the exchange of molecules through PD. How RK/RP complexes regulate the specific and nonspecific traffic of molecules through PD, and how these receptors are specifically targeted to PD, have been elusive but underpin comprehensive understanding of the function and regulation of the symplast. In this review we gather the current knowledge of RK/RP complex function at PD and how they might regulate intercellular traffic.