A wound-inducible organelle derived from endoplasmic reticulum: a plant strategy against environmental stresses?

Quantitative proteomics analysis identified new interacting proteins of JAL30 in Arabidopsis

Jacalin-related lectins (JALs) are a unique group of plant lectins derived from the jacalin protein family, which play important roles in plant defense responses. JAL30/PBP1 (PYK10 binding protein 1) interacts with inactive PYK10, exerting negative regulatory control over the size of the PYK10 complex, which is formed and activated upon insect or pathogen invasion. However, the precise interplay between JAL30 and other components remains elusive. In this study, we found JAL30 as a nucleocytoplasmic protein, but no obvious phenotype was observed in jal30-1 single mutant. Through immunoprecipitation (IP) enrichment combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS), dozens of new JAL30 interacting proteins were found in addition to several reported ones. Gene Ontology (GO) analysis revealed that these interacting proteins were highly related to the wounding and bacterial stimuli, suggesting their potential involvement in the jasmonate (JA) response. Importantly, the expression of JAL30 was induced by MeJA treatment, further highlighting its relevance in plant defense mechanisms. A novel JAL30 interacting protein, ESM1, was identified and its interaction with JAL30 was confirmed by Co-immunoprecipitation. Moreover, ESM1 was found as an O-GlcNAcylated protein, suggesting that JAL30 may possess glycosylated protein binding ability, particularly in O-GlcNAcylated protein and peptide recognition. Overall, our study provides valuable insights into the interacting protein network and biological function of JAL30, demonstrates the interaction between JAL30 and ESM1, and uncovers the potential significance of JAL30 in plant defense system, potentially through its association with PYK10 complex or JA response. SIGNIFICANCE: The biological functions of lectin proteins, including defense responses, immunity responses, signal transduction, have been well studied. Lectin proteins were also utilized to enrich glycosylated proteins for their specific carbohydrates binding capability. Jacalin-related lectins (JALs) were found to involve in plant defense mechanism. However, it is not yet clear whether JALs could use for enrichment of glycosylated proteins. In this study, we used label-free quantification method to identify interacting proteins of JAL30. A novel interacting protein, ESM1, as an O-GlcNAcylated protein was found. ESM1 has been reported to take part in defense against insect herbivory. Therefore, our findings provided experimental evidence to confirm that JALs have potential to be developed as the bio-tools to enrich glycosylated proteins. Finally, our data not only illustrated the vital biological role of JALs in plants, but also verified unique function of JAL30 in recognizing O-GlcNAcylated proteins.

ER body-resident myrosinases and tryptophan specialized metabolism modulate root microbiota assembly

Endoplasmic reticulum (ER) bodies are ER-derived structures that contain a large amount of PYK10 myrosinase, which hydrolyzes tryptophan (Trp)-derived indole glucosinolates (IGs). Given the well-described role of IGs in root-microbe interactions, we hypothesized that ER bodies in roots are important for interaction with soil-borne microbes at the root-soil interface. We used mutants impaired in ER bodies (nai1), ER body-resident myrosinases (pyk10bglu21), IG biosynthesis (myb34/51/122), and Trp specialized metabolism (cyp79b2b3) to profile their root microbiota community in natural soil, evaluate the impact of axenically collected root exudates on soil or synthetic microbial communities, and test their response to fungal endophytes in a mono-association setup. Tested mutants exhibited altered bacterial and fungal communities in rhizoplane and endosphere, respectively. Natural soils and bacterial synthetic communities treated with mutant root exudates exhibited distinctive microbial profiles from those treated with wild-type (WT) exudates. Most tested endophytes severely restricted the growth of cyp79b2b3, a part of which also impaired the growth of pyk10bglu21. Our results suggest that root ER bodies and their resident myrosinases modulate the profile of root-secreted metabolites and thereby influence root-microbiota interactions.

Fallopia japonica and Fallopia × bohemica extracts cause ultrastructural and biochemical changes in root tips of radish seedlings

Japanese knotweed (Fallopia japonica) and Bohemian knotweed (Fallopia × bohemica) are invasive plants that use allelopathy as an additional mechanism for colonization of the new habitat. Allelochemicals affect the growth of roots of neighboring plants. In the present study, we analyze the early changes associated with the inhibited root growth of radish seedlings exposed to aqueous extracts of knotweed rhizomes for 3 days. Here, we show that cells in the root cap treated with the knotweed extracts exhibited reduced cell length and displayed several ultrastructural changes, including the increased abundance of dilated ER cisternae filled with electron-dense material (ER bodies) and the accumulation of dense inclusions. Moreover, mitochondrial damage was exhibited in the root cap and the meristem zone compared to the non-treated radish seedlings. Furthermore, malfunction of the intracellular redox balance system was detected as the increased total antioxidative capacity. We also detected increased metacaspase-like proteolytic activities and, in the case of 10% extract of F. japonica, increased caspase-like proteolytic activities. These ultrastructural and biochemical effects could be the reason for the more than 60% shorter root length of treated radish seedlings compared to controls.

Integrated omics reveal novel functions and underlying mechanisms of the receptor kinase FERONIA in Arabidopsis thaliana

The receptor kinase FERONIA (FER) is a versatile regulator of plant growth and development, biotic and abiotic stress responses, and reproduction. To gain new insights into the molecular interplay of these processes and to identify new FER functions, we carried out quantitative transcriptome, proteome, and phosphoproteome profiling of Arabidopsis (Arabidopsis thaliana) wild-type and fer-4 loss-of-function mutant plants. Gene ontology terms for phytohormone signaling, abiotic stress, and biotic stress were significantly enriched among differentially expressed transcripts, differentially abundant proteins, and/or misphosphorylated proteins, in agreement with the known roles for FER in these processes. Analysis of multiomics data and subsequent experimental evidence revealed previously unknown functions for FER in endoplasmic reticulum (ER) body formation and glucosinolate biosynthesis. FER functions through the transcription factor NAI1 to mediate ER body formation. FER also negatively regulates indole glucosinolate biosynthesis, partially through NAI1. Furthermore, we found that a group of abscisic acid (ABA)-induced transcription factors is hypophosphorylated in the fer-4 mutant and demonstrated that FER acts through the transcription factor ABA INSENSITIVE5 (ABI5) to negatively regulate the ABA response during cotyledon greening. Our integrated omics study, therefore, reveals novel functions for FER and provides new insights into the underlying mechanisms of FER function.

Root growth inhibition and ultrastructural changes in radish root tips after treatment with aqueous extracts of Fallopia japonica and F. ×bohemica rhizomes

Allelopathic compounds released by invasive alien plants can suppress the growth of plants in their vicinity. The aim of this study was to investigate changes in tissue and cell structure in roots of radish seedlings treated with 10% aqueous extracts of rhizomes from the invasive knotweeds Fallopia japonica and F. ×bohemica. After 7 days of growth without and with aqueous extracts from these rhizomes, the anatomical and ultrastructural changes in the radish seedling roots were analyzed with light and transmission electron microscopy, and hydrogen peroxide was localized with diaminobenzidine, to define oxidative stress. The roots of radish seedlings treated with the knotweed extracts were shorter and thicker, due to the shorter and wider shapes of their cortex cells, which were organized in more columns than the control roots. There were signs of cell damage and oxidative stress in the root cap cells, and to a lesser extent in the meristematic zone. As well as the irregularly shaped nuclei and plasma membrane detached from the cell wall, the most prominent ultrastructural effects in the root cap cells of these aqueous rhizome extracts were the ring-shaped form of the mitochondria and large endoplasmic reticulum bodies. Excessive vacuolization was seen for the cells of the root apical meristem.

Cesium tolerance is enhanced by a chemical which binds to BETA-GLUCOSIDASE 23 in Arabidopsis thaliana

Cesium (Cs) is found at low levels in nature but does not confer any known benefit to plants. Cs and K compete in cells due to the chemical similarity of Cs to potassium (K), and can induce K deficiency in cells. In previous studies, we identified chemicals that increase Cs tolerance in plants. Among them, a small chemical compound (C₁₇H₁₉F₃N₂O₂), named CsToAcE1, was confirmed to enhance Cs tolerance while increasing Cs accumulation in plants. Treatment of plants with CsToAcE1 resulted in greater Cs and K accumulation and also alleviated Cs-induced growth retardation in Arabidopsis. In the present study, potential target proteins of CsToAcE1 were isolated from Arabidopsis to determine the mechanism by which CsToAcE1 alleviates Cs stress, while enhancing Cs accumulation. Our analysis identified one of the interacting target proteins of CsToAcE1 to be BETA-GLUCOSIDASE 23 (AtβGLU23). Interestingly, Arabidopsis atβglu23 mutants exhibited enhanced tolerance to Cs stress but did not respond to the application of CsToAcE1. Notably, application of CsToAcE1 resulted in a reduction of Cs-induced AtβGLU23 expression in wild-type plants, while this was not observed in a high affinity transporter mutant, athak5. Our data indicate that AtβGLU23 regulates plant response to Cs stress and that CsToAcE1 enhances Cs tolerance by repressing AtβGLU23. In addition, AtHAK5 also appears to be involved in this response.

Genomic Variation Landscape of the Model Salt Cress Eutrema salsugineum

Eutrema salsugineum has long been used as the model for examining salt and other abiotic stress in plants. In addition to the forward genetics approaches widely used in the lab, natural variations undoubtedly will provide a rich genetic resource for studying molecular mechanisms underlying the stress tolerance and local adaptation of this species. We used 90 resequencing whole genomes of natural populations of this species across its Asian and North American distributions to detect the selection signals for genes involved in salt and other stresses at the species-range level and local distribution. We detected selection signals for genes involved in salt and other abiotic tolerance at the species level. In addition, several cold-induced and defense genes showed selection signals due to local adaptation in North America-NE Russia or northern China, respectively. These variations and findings provide valuable resources for further deciphering genetic mechanisms underlying the stress tolerance and local adaptations of this model species.

Characterization of rhizome transcriptome and identification of a rhizomatous ER body in the clonal plant Cardamine leucantha

The rhizome is a plant organ that develops from a shoot apical meristem but penetrates into belowground environments. To characterize the gene expression profile of rhizomes, we compared the rhizome transcriptome with those of the leaves, shoots and roots of a rhizomatous Brassicaceae plant, Cardamine leucantha. Overall, rhizome transcriptomes were characterized by the absence of genes that show rhizome-specific expression and expression profiles intermediate between those of shoots and roots. Our results suggest that both endogenous developmental factors and external environmental factors are important for controlling the rhizome transcriptome. Genes that showed relatively high expression in the rhizome compared to shoots and roots included those related to belowground defense, control of reactive oxygen species and cell elongation under dark conditions. A comparison of transcriptomes further allowed us to identify the presence of an ER body, a defense-related belowground organelle, in epidermal cells of the C. leucantha rhizome, which is the first report of ER bodies in rhizome tissue.

Interplay between the unfolded protein response and reactive oxygen species: a dynamic duo

Secretory proteins undergo modifications such as glycosylation and disulphide bond formation before proper folding, and move to their final destination via the endomembrane system. Accumulation of unfolded proteins in the endoplasmic reticulum (ER) due to suboptimal environmental conditions triggers a response called the unfolded protein response (UPR), which induces a set of genes that elevate protein folding capacity in the ER. This review aims to establish a connection among ER stress, UPR, and reactive oxygen species (ROS), which remains an unexplored topic in plants. For this, we focused on mechanisms of ROS production originating from ER stress, the interaction between ER stress and overall ROS signalling process in the cell, and the interaction of ER stress with other organellar ROS signalling pathways such as of the mitochondria and chloroplasts. The roles of the UPR during plant hormone signalling and abiotic and biotic stress responses are also discussed in connection with redox and ROS signalling.

Delineation of condition specific Cis- and Trans-acting elements in plant promoters under various Endo- and exogenous stimuli

BACKGROUND

Transcription factors (TFs) play essential roles during plant development and response to environmental stresses. However, the relationships among transcription factors, cis-acting elements and target gene expression under endo- and exogenous stimuli have not been systematically characterized.

RESULTS

Here, we developed a series of bioinformatics analysis methods to infer transcriptional regulation by using numerous gene expression data from abiotic stresses and hormones treatments. After filtering the expression profiles of TF-encoding genes, 291 condition specific transcription factors (CsTFs) were obtained. Differentially expressed genes were then classified into various co-expressed gene groups based on each CsTFs. In the case studies of heat stress and ABA treatment, several known and novel cis-acting elements were identified following our bioinformatics approach. Significantly, a palindromic sequence of heat-responsive elements is recognized, and also obtained from a 3D protein structure of heat-shock protein-DNA complex. Notably, overrepresented 3- and 4-mer motifs in an enriched 8-mer motif could be a core cis-element for a CsTF. In addition, the results suggest DNA binding preferences of the same CsTFs are different according to various conditions.

CONCLUSIONS

The overall results illustrate this study may be useful in identifying condition specific cis- and trans- regulatory elements and facilitate our understanding of the relationships among TFs, cis-acting elements and target gene expression.

Function of Hevea brasiliensis NAC1 in dehydration-induced laticifer differentiation and latex biosynthesis

MAIN CONCLUSIONS

HbNAC1 is a transcription factor in rubber plants whose expression is induced by dehydration, leading to latex biosynthesis. Laticifer is a special tissue in Hevea brasiliensis where natural rubber is biosynthesized and accumulated. In young stems of epicormic shoots, the differentiation of secondary laticifers can be induced by wounding, which can be prevented when the wounding site is wrapped. Using this system, differentially expressed genes were screened by suppression subtractive hybridization (SSH) and macroarray analyses. This led to the identification of several dehydration-related genes that could be involved in laticifer differentiation and/or latex biosynthesis, including a NAC transcription factor (termed as HbNAC1). Tissue sections confirmed that local tissue dehydration was a key signal for laticifer differentiation. HbNAC1 was localized at the nucleus and showed strong transcriptional activity in yeast, suggesting that HbNAC1 is a transcription factor. Furthermore, HbNAC1 was found to bind to the cis-element CACG in the promoter region of the gene encoding the small rubber particle protein (SRPP). Transgenic experiments also confirmed that HbNAC1 interacted with the SRPP promoter when co-expressed, and enhanced expression of the reporter gene β-glucuronidase occurred in planta. In addition, overexpression of HbNAC1 in tobacco plants conferred drought tolerance. Together, the data suggest that HbNAC1 might be involved in dehydration-induced laticifer differentiation and latex biosynthesis.

PYK10 myrosinase reveals a functional coordination between endoplasmic reticulum bodies and glucosinolates in Arabidopsis thaliana

The endoplasmic reticulum body (ER body) is an organelle derived from the ER that occurs in only three families of the order Brassicales and is suggested to be involved in plant defense. ER bodies in Arabidopsis thaliana contain large amounts of β-glucosidases, but the physiological functions of ER bodies and these enzymes remain largely unclear. Here we show that PYK10, the most abundant β-glucosidase in A. thaliana root ER bodies, hydrolyzes indole glucosinolates (IGs) in addition to the previously reported in vitro substrate scopolin. We found a striking co-expression between ER body-related genes (including PYK10), glucosinolate biosynthetic genes and the genes for so-called specifier proteins affecting the terminal products of myrosinase-mediated glucosinolate metabolism, indicating that these systems have been integrated into a common transcriptional network. Consistent with this, comparative metabolite profiling utilizing a number of A. thaliana relatives within Brassicaceae identified a clear phylogenetic co-occurrence between ER bodies and IGs, but not between ER bodies and scopolin. Collectively, our findings suggest a functional link between ER bodies and glucosinolate metabolism in planta. In addition, in silico three-dimensional modeling, combined with phylogenomic analysis, suggests that PYK10 represents a clade of 16 myrosinases that arose independently from the other well-documented class of six thioglucoside glucohydrolases. These findings provide deeper insights into how glucosinolates are metabolized in cruciferous plants and reveal variation of the myrosinase-glucosinolate system within individual plants.

The Arabidopsis PLAT domain protein1 is critically involved in abiotic stress tolerance

Despite the completion of the Arabidopsis genome sequence, for only a relatively low percentage of the encoded proteins experimental evidence concerning their function is available. Plant proteins that harbour a single PLAT (Polycystin, Lipoxygenase, Alpha-toxin and Triacylglycerol lipase) domain and belong to the PLAT-plant-stress protein family are ubiquitously present in monocot and dicots. However, the function of PLAT-plant-stress proteins is still poorly understood. Therefore, we have assessed the function of the uncharacterised Arabidopsis PLAT-plant-stress family members through a combination of functional genetic and physiological approaches. PLAT1 overexpression conferred increased abiotic stress tolerance, including cold, drought and salt stress, while loss-of-function resulted in opposite effects on abiotic stress tolerance. Strikingly, PLAT1 promoted growth under non-stressed conditions. Abiotic stress treatments induced PLAT1 expression and caused expansion of its expression domain. The ABF/ABRE transcription factors, which are positive mediators of abscisic acid signalling, activate PLAT1 promoter activity in transactivation assays and directly bind to the ABRE elements located in this promoter in electrophoretic mobility shift assays. This suggests that PLAT1 represents a novel downstream target of the abscisic acid signalling pathway. Thus, we showed that PLAT1 critically functions as positive regulator of abiotic stress tolerance, but also is involved in regulating plant growth, and thereby assigned a function to this previously uncharacterised PLAT domain protein. The functional data obtained for PLAT1 support that PLAT-plant-stress proteins in general could be promising targets for improving abiotic stress tolerance without yield penalty.

ER bodies in plants of the Brassicales order: biogenesis and association with innate immunity

The endoplasmic reticulum (ER) forms highly organized network structures composed of tubules and cisternae. Many plant species develop additional ER-derived structures, most of which are specific for certain groups of species. In particular, a rod-shaped structure designated as the ER body is produced by plants of the Brassicales order, which includes Arabidopsis thaliana. Genetic analyses and characterization of A. thaliana mutants possessing a disorganized ER morphology or lacking ER bodies have provided insights into the highly organized mechanisms responsible for the formation of these unique ER structures. The accumulation of proteins specific for the ER body within the ER plays an important role in the formation of ER bodies. However, a mutant that exhibits morphological defects of both the ER and ER bodies has not been identified. This suggests that plants in the Brassicales order have evolved novel mechanisms for the development of this unique organelle, which are distinct from those used to maintain generic ER structures. In A. thaliana, ER bodies are ubiquitous in seedlings and roots, but rare in rosette leaves. Wounding of rosette leaves induces de novo formation of ER bodies, suggesting that these structures are associated with resistance against pathogens and/or herbivores. ER bodies accumulate a large amount of β-glucosidases, which can produce substances that potentially protect against invading pests. Biochemical studies have determined that the enzymatic activities of these β-glucosidases are enhanced during cell collapse. These results suggest that ER bodies are involved in plant immunity, although there is no direct evidence of this. In this review, we provide recent perspectives of ER and ER body formation in A. thaliana, and discuss clues for the functions of ER bodies. We highlight defense strategies against biotic stress that are unique for the Brassicales order, and discuss how ER structures could contribute to these strategies.

ML3 is a NEDD8- and ubiquitin-modified protein

NEDD8 (NEURAL PRECURSOR CELL-EXPRESSED, DEVELOPMENTALLY DOWN-REGULATED PROTEIN8) is an evolutionarily conserved 8-kD protein that is closely related to ubiquitin and that can be conjugated like ubiquitin to specific lysine residues of target proteins in eukaryotes. In contrast to ubiquitin, for which a broad range of substrate proteins are known, only a very limited number of NEDD8 target proteins have been identified to date. Best understood, and also evolutionarily conserved, is the NEDD8 modification (neddylation) of cullins, core subunits of the cullin-RING-type E3 ubiquitin ligases that promote the polyubiquitylation of degradation targets in eukaryotes. Here, we show that Myeloid differentiation factor-2-related lipid-recognition domain protein ML3 is an NEDD8- as well as ubiquitin-modified protein in Arabidopsis (Arabidopsis thaliana) and examine the functional role of ML3 in the plant cell. Our analysis indicates that ML3 resides in the vacuole as well as in endoplasmic reticulum (ER) bodies. ER bodies are Brassicales-specific ER-derived organelles and, similar to other ER body proteins, ML3 orthologs can only be identified in this order of flowering plants. ML3 gene expression is promoted by wounding as well as by the phytohormone jasmonic acid and repressed by ethylene, signals that are known to induce and repress ER body formation, respectively. Furthermore, ML3 protein abundance is dependent on NAI1, a master regulator of ER body formation in Arabidopsis. The regulation of ML3 expression and the localization of ML3 in ER bodies and the vacuole is in agreement with a demonstrated importance of ML3 in the defense to herbivore attack. Here, we extend the spectrum of ML3 biological functions by demonstrating a role in the response to microbial pathogens.

The endoplasmic reticulum is a reservoir for WAVE/SCAR regulatory complex signaling in the Arabidopsis leaf

During plant cell morphogenesis, signal transduction and cytoskeletal dynamics interact to locally organize the cytoplasm and define the geometry of cell expansion. The WAVE/SCAR (for WASP family verprolin homologous/suppressor of cyclic AMP receptor) regulatory complex (W/SRC) is an evolutionarily conserved heteromeric protein complex. Within the plant kingdom W/SRC is a broadly used effector that converts Rho-of-Plants (ROP)/Rac small GTPase signals into Actin-Related Protein2/3 and actin-dependent growth responses. Although the components and biochemistry of the W/SRC pathway are well understood, a basic understanding of how cells partition W/SRC into active and inactive pools is lacking. In this paper, we report that the endoplasmic reticulum (ER) is an important organelle for W/SRC regulation. We determined that a large intracellular pool of the core W/SRC subunit NAP1, like the known positive regulator of W/SRC, the DOCK family guanine nucleotide-exchange factor SPIKE1 (SPK1), localizes to the surface of the ER. The ER-associated NAP1 is inactive because it displays little colocalization with the actin network, and ER localization requires neither activating signals from SPK1 nor a physical association with its W/SRC-binding partner, SRA1. Our results indicate that in Arabidopsis (Arabidopsis thaliana) leaf pavement cells and trichomes, the ER is a reservoir for W/SRC signaling and may have a key role in the early steps of W/SRC assembly and/or activation.

Identification of two novel endoplasmic reticulum body-specific integral membrane proteins

The endoplasmic reticulum (ER) body, a large compartment specific to the Brassicales, accumulates β-glucosidase and possibly plays a role in the defense against pathogens and herbivores. Although the ER body is a subdomain of the ER, it is unclear whether any ER body-specific membrane protein exists. In this study, we identified two integral membrane proteins of the ER body in Arabidopsis (Arabidopsis thaliana) and termed them MEMBRANE PROTEIN OF ENDOPLASMIC RETICULUM BODY1 (MEB1) and MEB2. In Arabidopsis, a basic helix-loop-helix transcription factor, NAI1, and an ER body component, NAI2, regulate ER body formation. The expression profiles of MEB1 and MEB2 are similar to those of NAI1, NAI2, and ER body β-glucosidase PYK10 in Arabidopsis. The expression of MEB1 and MEB2 was reduced in the nai1 mutant, indicating that NAI1 regulates the expression of MEB1 and MEB2 genes. MEB1 and MEB2 proteins localize to the ER body membrane but not to the ER network, suggesting that these proteins are specifically recruited to the ER body membrane. MEB1 and MEB2 physically interacted with ER body component NAI2, and they were diffused throughout the ER network in the nai2 mutant, which has no ER body. Heterologous expression of MEB1 and MEB2 in yeast (Saccharomyces cerevisiae) suppresses iron and manganese toxicity, suggesting that MEB1 and MEB2 are metal transporters. These results indicate that the membrane of ER bodies has specific membrane proteins and suggest that the ER body is involved in defense against metal stress as well as pathogens and herbivores.

ERMO3/MVP1/GOLD36 is involved in a cell type-specific mechanism for maintaining ER morphology in Arabidopsis thaliana

The endoplasmic reticulum (ER) has a unique, network-like morphology. The ER structures are composed of tubules, cisternae, and three-way junctions. This morphology is highly conserved among eukaryotes, but the molecular mechanism that maintains ER morphology has not yet been elucidated. In addition, certain Brassicaceae plants develop a unique ER-derived organelle called the ER body. This organelle accumulates large amounts of PYK10, a β-glucosidase, but its physiological functions are still obscure. We aimed to identify a novel factor required for maintaining the morphology of the ER, including ER bodies, and employed a forward-genetic approach using transgenic Arabidopsis thaliana (GFP-h) with fluorescently-labeled ER. We isolated and investigated a mutant (designated endoplasmic reticulum morphology3, ermo3) with huge aggregates and abnormal punctate structures of ER. ERMO3 encodes a GDSL-lipase/esterase family protein, also known as MVP1. Here, we showed that, although ERMO3/MVP1/GOLD36 was expressed ubiquitously, the morphological defects of ermo3 were specifically seen in a certain type of cells where ER bodies developed. Coimmunoprecipitation analysis combined with mass spectrometry revealed that ERMO3/MVP1/GOLD36 interacts with the PYK10 complex, a huge protein complex that is thought to be important for ER body-related defense systems. We also found that the depletion of transcription factor NAI1, a master regulator for ER body formation, suppressed the formation of ER-aggregates in ermo3 cells, suggesting that NAI1 expression plays an important role in the abnormal aggregation of ER. Our results suggest that ERMO3/MVP1/GOLD36 is required for preventing ER and other organelles from abnormal aggregation and for maintaining proper ER morphology in a coordinated manner with NAI1.

Unique defense strategy by the endoplasmic reticulum body in plants

The endoplasmic reticulum (ER) is a site for the production of secretory proteins. Plants have developed ER subdomains for protein storage. The ER body is one such structure, which is observed in Brassicaceae plants. ER bodies accumulate in seedlings and roots or in wounded leaves in Arabidopsis. ER bodies contain high amounts of the β-glucosidases PYK10/BGLU23 in seedlings and roots or BGLU18 in wounded tissues. These results suggest that ER bodies are involved in the metabolism of glycoside molecules, presumably to produce repellents against pests and fungi. When Arabidopsis roots are homogenized, PYK10 formed large protein aggregates that include other β-glucosidases (BGLU21 and BGLU22), GDSL lipase-like proteins (GLL22) and cytosolic jacalin-related lectins (PBP1/JAL30, JAL31, JAL33, JAL34 and JAL35). Glucosidase activity increases by the aggregate formation. NAI1, a basic helix-loop-helix transcription factor, regulates the expression of the ER body proteins PYK10 and NAI2. Reduced expression of NAI2, PYK10 and BGLU21 resulted in abnormal ER body formation, indicating that these components regulate ER body formation. PYK10, BGLU21 and BGLU22 possess hydrolytic activity for scopolin, a coumaroyl glucoside that accumulates in the roots of Arabidopsis, and nai1 and pyk10 mutants are more susceptible to the symbiotic fungus Piriformospora indica. Therefore, it appears that the ER body is a unique organelle of Brassicaceae plants that is important for defense against pests and fungi.

ABA-dependent and -independent G-protein signaling in Arabidopsis roots revealed through an iTRAQ proteomics approach

Heterotrimeric G-proteins are important signal transducers in all eukaryotes. The plant hormone abscisic acid (ABA) has emerged as a key regulator of G-protein-mediated signaling pathways in plants. ABA-regulation of G-protein signaling involves both conventional and novel mechanisms. We have utilized the null mutant of the Arabidopsis G-protein α subunit gpa1 to evaluate to what extent ABA-dependent changes in the proteome are regulated by G-proteins. We used Arabidopsis root tissue as both ABA and G-proteins, individually and in combination, affect root growth and development. We identified 720 proteins, of which 42 showed GPA1-dependent and 74 showed ABA-dependent abundance changes. A majority of ABA-regulated proteins were also GPA1-dependent. Our data provide insight into how tissue specificity might be achieved in ABA-regulated G-protein signaling. A number of proteins related to ER body formation and intracellular trafficking were altered in gpa1 mutant, suggesting a novel role for GPA1 in these pathways. A potential link between ABA metabolism and ABA signaling was also revealed. The comparison of protein abundance changes in the absence of ABA offers clues to the role of GPA1 in ABA-independent signaling pathways, for example, regulation of cell division. These findings substantially contribute to our knowledge of G-protein signaling mechanisms in plants.

β-Glucosidases

β-Glucosidases (3.2.1.21) are found in all domains of living organisms, where they play essential roles in the removal of nonreducing terminal glucosyl residues from saccharides and glycosides. β-Glucosidases function in glycolipid and exogenous glycoside metabolism in animals, defense, cell wall lignification, cell wall β-glucan turnover, phytohormone activation, and release of aromatic compounds in plants, and biomass conversion in microorganisms. These functions lead to many agricultural and industrial applications. β-Glucosidases have been classified into glycoside hydrolase (GH) families GH1, GH3, GH5, GH9, and GH30, based on their amino acid sequences, while other β-glucosidases remain to be classified. The GH1, GH5, and GH30 β-glucosidases fall in GH Clan A, which consists of proteins with (β/α)(8)-barrel structures. In contrast, the active site of GH3 enzymes comprises two domains, while GH9 enzymes have (α/α)(6) barrel structures. The mechanism by which GH1 enzymes recognize and hydrolyze substrates with different specificities remains an area of intense study.

Scopolin-hydrolyzing beta-glucosidases in roots of Arabidopsis

Three beta-glucosidases (At1g66270-BGLU21, At1g66280-BGLU22, and At3g09260-BGLU23) were purified from the roots of Arabidopsis and their cDNAs were expressed in insect cells. In addition, two beta-glucosidase binding protein cDNAs (At3g16420; PBPI and At3g16430; PBPII) were expressed in Escherichia coli and their protein products purified. These binding proteins interact with beta-glucosidases and activate them. BGLU21, 22 and 23 hydrolyzed the natural substrate scopolin specifically and also hydrolyzed to some extent substrates whose aglycone moiety is similar to scopolin (e.g. esculin and 4-MU-glucoside). In contrast, they hydrolyzed poorly DIMBOA-glucoside and did not hydrolyze pNP- and oNP-glucosides. We determined the physicochemical properties of native and recombinant BGLUs, and found no differences between them. They were stable in a narrow pH range (5-7.5) and had temperature and pH optima for activity at 35 degrees C and pH 5.5, respectively. As for thermostability, >95% of their activity was retained at 40 degrees C but dramatically decreased at >50 degrees C. The apparent K(m) of native and recombinant enzymes for scopolin was 0.73 and 0.81 mM, respectively, and it was 5.8 and 9.7 mM, respectively, for esculin. Western blot analysis showed that all three enzymes were exclusively expressed in roots of seedlings but not in any other plant part or organ under normal conditions. Furthermore, spatial expression patterns of all eight genes belonging to subfamily 3 were investigated at the transcription level by RT-PCR.

The ER body, a new organelle in Arabidopsis thaliana, requires NAI2 for its formation and accumulates specific beta-glucosidases

Plants develop various ER-derived structures with specific functions. The ER body found in Arabidopsis thaliana is a spindle-shaped structure. ER bodies accumulate in epidermal cells in seedlings or are induced by wounding. The molecular mechanisms underlying the formation of the ER body remained obscure. We isolated an ER body-deficient mutant in Arabidopsis seedlings, which we termed nai2. The NAI2 gene encodes a member of a unique protein family. NAI2 localizes to the ER body and the downregulation of NAI2 elongates ER bodies and reduces their number. ER bodies specifically accumulate high levels of PYK10/BGLU23, which is a beta-glucosidase that bears an ER retention signal. Additionally, in the nai2 mutant, PYK10 protein is diffuse throughout the ER and the PYK10 protein level is reduced. These observations indicate that NAI2 is a key factor for the formation of ER bodies and for the accumulation of PYK10 in the ER bodies of Arabidopsis. We also found that BGLU18, which encodes another beta-glucosidase with an ER retention signal, is induced at the site of wounding. Immunocytochemical analysis revealed that the BGLU18 protein is exclusively localized in ER bodies formed directly at the wounding site of cotyledons. These results suggest that BGLU18 is a component of the ER body in wounded leaves of Arabidopsis.

NAI2 is an endoplasmic reticulum body component that enables ER body formation in Arabidopsis thaliana

Plants develop various endoplasmic reticulum (ER)-derived structures, each of which has specific functions. The ER body found in Arabidopsis thaliana is a spindle-shaped structure that specifically accumulates high levels of PYK10/BGLU23, a beta-glucosidase that bears an ER-retention signal. The molecular mechanisms underlying the formation of the ER body remain obscure. We isolated an ER body-deficient mutant in Arabidopsis seedlings that we termed nai2. The NAI2 gene (At3g15950) encodes a member of a unique protein family that is only found in the Brassicaceae. NAI2 localizes to the ER body, and a reduction in NAI2 gene expression elongates ER bodies and reduces their numbers. NAI2 deficiency does not affect PYK10 mRNA levels but reduces the level of PYK10 protein, which becomes uniformly diffused throughout the ER. NAI1, a transcription factor responsible for ER body formation, regulates NAI2 gene expression. These observations indicate that NAI2 is a key factor that enables ER body formation and the accumulation of PYK10 in ER bodies of Arabidopsis. Interestingly, ER body-like structures are also restricted to the Brassicales, including the Brassicaceae. NAI2 homologs may have evolved specifically in Brassicales for the purpose of producing ER body-like structures.

Antagonistic jacalin-related lectins regulate the size of ER body-type beta-glucosidase complexes in Arabidopsis thaliana

PYK10/BGLU23 is a beta-glucosidase that is a major protein of ER bodies, which are endoplasmic reticulum (ER)-derived organelles that may be involved in defense systems. PYK10 has active and inactive forms. Active PYK10 molecules form large complexes with diameters ranging from 0.65 microm to > 70 microm. We identified three beta-glucosidases (PYK10, BGLU21 and BGLU22), five jacalin-related lectins (JALs) and a GDSL lipase-like protein (GLL) in the purified PYK10 complex. Expression levels of JALs and GLLs were lower in the nai1-1 mutant, which has no ER bodies, than in Col-0. The subcellular localization of PYK10 is predicted to be different from the localizations of JALs and GLLs. This suggests that PYK10 interacts with its partners (JALs and GLLs) when the subcellular structure is destroyed by pathogens. The PYK10 complex was found to be larger in the pbp1-1 and jal22-1 mutants than in Col-0, while it was smaller in the jal23-1, jal31-1 and jal31-2 mutants than in Col-0. These results show that two types of JALs having opposite roles regulate the size of the PYK10 complex antagonistically. We define the two types of lectins as a 'polymerizer-type lectin' and an 'inhibitor-type lectin'. Interestingly, the closest homologs of polymerizer-type lectins (JAL31 and JAL23) were inhibitor-type lectins (PBP1/JAL30 and JAL22). The pairs of polymerizer-type and inhibitor-type lectins reported here are good examples of genes that have evolved new functions after gene duplication (neofunctionalization).

Transcription factor MYC2 is involved in priming for enhanced defense during rhizobacteria-induced systemic resistance in Arabidopsis thaliana

Upon appropriate stimulation, plants can develop an enhanced capacity to express infection-induced cellular defense responses, a phenomenon known as the primed state. Colonization of the roots of Arabidopsis thaliana by the beneficial rhizobacterial strain Pseudomonas fluorescens WCS417r primes the leaf tissue for enhanced pathogen- and insect-induced expression of jasmonate (JA)-responsive genes, resulting in an induced systemic resistance (ISR) that is effective against different types of pathogens and insect herbivores. Here the molecular mechanism of this rhizobacteria-induced priming response was investigated using a whole-genome transcript profiling approach. Out of the 1879 putative methyl jasmonate (MeJA)-responsive genes, 442 genes displayed a primed expression pattern in ISR-expressing plants. Promoter analysis of ISR-primed, MeJA-responsive genes and ISR-primed, Pseudomonas syringae pv. tomato DC3000 (Pst DC3000)-responsive genes revealed over-representation of the G-box-like motif 5'-CACATG-3'. This motif is a binding site for the transcription factor MYC2, which plays a central role in JA- and abscisic acid-regulated signaling. MYC2 expression was consistently up-regulated in ISR-expressing plants. Moreover, mutants impaired in the JASMONATE-INSENSITIVE1/MYC2 gene (jin1-1 and jin1-2) were unable to mount WCS417r-ISR against Pst DC3000 and the downy mildew pathogen Hyaloperonospora parasitica. Together, these results pinpoint MYC2 as a potential regulator in priming for enhanced JA-responsive gene expression during rhizobacteria-mediated ISR.

A serine involved in actin-dependent subcellular localization of a stress-induced tobacco BY-2 hydroxymethylglutaryl-CoA reductase isoform

3-Hydroxy-3-methylglutaryl-CoA reductase (HMGR) is unique in the first part of the cytoplasmic isoprenoid pathway, as it contains a membrane domain that includes ER-specific retention motifs. When fused to GFP, this domain targets two tobacco BY-2 HMGR isoforms differentially. While the first isoform is ER-localized, a second stress-induced one forms globular structures connected by tubular structures. A serine positioned upstream of the ER retention motif seems to be implicated in this specific subcellular localization. Surprisingly, these structures are closely connected to F-actin, and their intactness is dependent upon the integrity of the filaments or the action of a calmodulin antagonist.

GER1, a GDSL motif-encoding gene from rice is a novel early light- and jasmonate-induced gene

The reaction of the rice mutant HEBIBA differs from that of wild-type rice in that the mutant responds inversely to red light and is defective in the light-triggered biosynthesis of jasmonic acid (JA). Using the wild type and the HEBIBA mutant of rice in a differential display screen, we attempted to identify genes that act in or near the convergence point of light and JA signalling. We isolated specifically regulated DNA fragments from approximately 10 000 displayed bands, and identified a new early light- and JA-induced gene. This gene encodes an enzyme containing a GDSL motif, showing 38 % identity at the amino acid level to lipase Arab-1 in Arabidopsis thaliana. The GDSL CONTAINING ENZYME RICE 1 gene (GER1) is rapidly induced by both red (R) and far-red (FR) light and by JA. The results are discussed with respect to a possible role for GER1 as a negative regulator of coleoptile elongation in the context of recent findings on the impact of JA on light signalling.

The role of ethylene in host-pathogen interactions

The phytohormone ethylene is a principal modulator in many aspects of plant life, including various mechanisms by which plants react to pathogen attack. Induced ethylene biosynthesis and subsequent intracellular signaling through a single conserved pathway have been well characterized. This leads to a cascade of transcription factors consisting of primary EIN3-like regulators and downstream ERF-like transcription factors. The latter control the expression of various effector genes involved in various aspects of systemic induced defense responses. Moreover, at this level significant cross-talk occurs with other defense response pathways controlled by salicylic acid and jasmonate, eventually resulting in a differentiated disease response.

Activation of an ER-body-localized beta-glucosidase via a cytosolic binding partner in damaged tissues of Arabidopsis thaliana

The ER body is an endoplasmic reticulum (ER)-derived organelle. Because ER bodies are induced by wounding and methyl jasmonate (MeJA) treatment in rosette leaves, they might be responsible for defense systems. Recently, we isolated nai1 mutants that have no ER body and showed that the levels of PYK10 and PBP1 (PYK10-binding protein 1: At3g16420) were decreased in nai1 mutants. PYK10 is a beta-glucosidase that is localized in ER bodies. PBP1 consists of two repeated regions, each of which is highly homologous to the alpha-chain of jacalin, a carbohydrate-binding protein (lectin) of Artocarpus integriforia. We show in this study that PYK10 has two forms, an active form and an inactive form. The amount of active form increased during incubation of root homogenate. On the other hand, PYK10 separated into soluble and insoluble forms. Active PYK10 molecules mainly occurred as the insoluble form and inactive PYK10 molecules remain soluble. This suggests that the activation of PYK10 needs polymerization. In homogenates of both a pbp1 mutant and the wild type, PYK10 becomes insoluble, while PYK10 activity in pbp1 is only half of that in the wild type. PBP1 has an ability to interact with PYK10. Nonetheless, PBP1 does not bind active PYK10. These results suggest that PBP1 has some effect on the activation of PYK10. In addition, PBP1 was found to have a different subcellular distribution from PYK10. PBP1 may act like a molecular chaperone that facilitates the correct polymerization of PYK10, when tissues are damaged and subcellular structures are destroyed by pests.

Ethylene signal transduction

BACKGROUND

The phytohormone ethylene is a key regulator of plant growth and development. Components of the pathway for ethylene signal transduction were identified by genetic approaches in Arabidopsis and have now been shown to function in agronomically important plants as well.

SCOPE

This review focuses on recent advances in our knowledge on ethylene signal transduction, in particular on recently proposed components of the pathway, on the interaction between the pathway components and on the roles of transcriptional and post-transcriptional regulation in ethylene signalling.

CONCLUSIONS

Data indicate that the site of ethylene perception is at the endoplasmic reticulum and point to the importance of protein complexes in mediating the initial steps in ethylene signal transduction. The expression level of pathway components is regulated by both transcriptional and post-transcriptional mechanisms, degradation of the transcription factor EIN3 being a primary means by which the sensitivity of plants to ethylene is regulated. EIN3 also represents a control point for cross-talk with other signalling pathways, as exemplified by the effects of glucose upon its expression level. Amplification of the initial ethylene signal is likely to play a significant role in signal transduction and several mechanisms exist by which this may occur based on properties of known pathway components. Signal output from the pathway is mediated in part by carefully orchestrated changes in gene expression, the breadth of these changes now becoming clear through expression analysis using microarrays.

Keeping the Leaves Green Above Us

The plant immune system relies to a great extent on the highly regulated expression of hundreds of defense genes encoding antimicrobial proteins, such as defensins, and antiherbivore proteins, such as lectins. The expression of many of these genes is controlled by a family of mediators known as jasmonates; these cyclic oxygenated fatty acid derivatives are reminiscent of prostaglandins. The roles of jasmonates also extend to the control of reproductive development. How are these complex events regulated? Nearly 20 members of the jasmonate family have been characterized. Some, like jasmonic acid, exist in unmodified forms, whereas others are conjugated to other lipids or to hydrophobic amino acids. Why do so many chemically different forms of these mediators exist, and do individual jasmonates have unique signaling properties or are they made to facilitate transport within and between cells? Key features of the jasmonate signal pathway have been identified and include the specific activation of E3-type ubiquitin ligases thought to target as-yet-undescribed transcriptional repressors for modification or destruction. Several classes of transcription factor are known to function in the jasmonate pathway, and, in some cases, these proteins provide nodes that integrate this network with other important defensive and developmental pathways. Progress in jasmonate research is now rapid, but large gaps in our knowledge exist. Aimed to keep pace with progress, the ensemble of jasmonate Connections Maps at the Signal Transduction Knowledge Environment describe (i) the canonical signaling pathway, (ii) the Arabidopsis signaling pathway, and (iii) the biogenesis and structures of the jasmonates themselves.

The plant proteolytic machinery and its role in defence

The diverse roles of plant proteases in defence responses that are triggered by pathogens or pests are becoming clearer. Some proteases, such as papain in latex, execute the attack on the invading organism. Other proteases seem to be part of a signalling cascade, as indicated by protease inhibitor studies. Such a role has also been suggested for the recently discovered metacaspases and CDR1. Some proteases, such as RCR3, even act in perceiving the invader. These exciting recent reports are probably just the first examples of what lies beneath. More roles for plant proteases in defence, as well as the regulation and substrates of these enzymes, are waiting to be discovered.

Comparative genomics in salt tolerance between Arabidopsis and aRabidopsis-related halophyte salt cress using Arabidopsis microarray

Salt cress (Thellungiella halophila), a halophyte, is a genetic model system with a small plant size, short life cycle, copious seed production, small genome size, and an efficient transformation. Its genes have a high sequence identity (90%-95% at cDNA level) to genes of its close relative, Arabidopsis. These qualities are advantageous not only in genetics but also in genomics, such as gene expression profiling using Arabidopsis cDNA microarrays. Although salt cress plants are salt tolerant and can grow in 500 mm NaCl medium, they do not have salt glands or other morphological alterations either before or after salt adaptation. This suggests that the salt tolerance in salt cress results from mechanisms that are similar to those operating in glycophytes. To elucidate the differences in the regulation of salt tolerance between salt cress and Arabidopsis, we analyzed the gene expression profiles in salt cress by using a full-length Arabidopsis cDNA microarray. In salt cress, only a few genes were induced by 250 mm NaCl stress in contrast to Arabidopsis. Notably a large number of known abiotic- and biotic-stress inducible genes, including Fe-SOD, P5CS, PDF1.2, AtNCED, P-protein, beta-glucosidase, and SOS1, were expressed in salt cress at high levels even in the absence of stress. Under normal growing conditions, salt cress accumulated Pro at much higher levels than did Arabidopsis, and this corresponded to a higher expression of AtP5CS in salt cress, a key enzyme of Pro biosynthesis. Furthermore, salt cress was more tolerant to oxidative stress than Arabidopsis. Stress tolerance of salt cress may be due to constitutive overexpression of many genes that function in stress tolerance and that are stress inducible in Arabidopsis.

Activity profiling of papain-like cysteine proteases in plants

Transcriptomic and proteomic technologies are generating a wealth of data that are frequently used by scientists to predict the function of proteins based on their expression or presence. However, activity of many proteins, such as transcription factors, kinases, and proteases, depends on posttranslational modifications that frequently are not detected by these technologies. Therefore, to monitor activity of proteases rather than their abundance, we introduce protease activity profiling in plants. This technology is based on the use of biotinylated, irreversible protease inhibitors that react with active proteases in a mechanism-based manner. Using a biotinylated derivative of the Cys protease inhibitor E-64, we display simultaneous activities of many papain-like Cys proteases in extracts from various tissues and from different plant species. Labeling is pH dependent, stimulated with reducing agents, and inhibited specifically by Cys protease inhibitors but not by inhibitors of other protease classes. Using one-step affinity capture of biotinylated proteases followed by sequencing mass spectrometry, we identified proteases that include xylem-specific XCP2, desiccation-induced RD21, and cathepsin B- and aleurain-like proteases. Together, these results demonstrate that this technology can identify differentially activated proteases and/or characterize the activity of a particular protease within complex mixtures.