Arabidopsis protein disulfide isomerase-5 inhibits cysteine proteases during trafficking to vacuoles before programmed cell death of the endothelium in developing seeds

Targeting a cysteine proteinase inhibitor and a defensin-like protein in Litchi chinensis seed development leveraging endosperm single-nucleus transcriptome

Seed development is one of the most important agricultural traits, determining both the crop yield and quality of fleshy fruits. A typically abortive litchi cultivar, Guiwei, exhibits heterogeneity in seed size across production areas, years, and individual trees. Previous studies have shown that 'Guiwei' seed development failure is associated with endosperm arrest and chilling conditions. Herein, we identified a cysteine proteinase inhibitor (LcCPI5) and defensin-like protein (LcDEFL) as key genes in determining 'Guiwei' seed development through combined analysis of 'Guiwei' and 'Huaizhi' endosperm single-nucleus RNA-sequence and transcriptome data of 'Guiwei' seed subjected to different temperature treatments. LcCPI5 was exclusively expressed in the endosperm sample of 'Guiwei' at 25 days post-anthesis, and its expression decreased in response to chilling. The silencing of LcCPI5 led to significantly larger seeds, whereas employing the cysteine proteinase inhibitor E-64 resulted in smaller seeds in the cultivar 'Guiwei'. Unlike LcCPI5, LcDEFL promotes litchi seed development. The large seed cultivar 'Huaizhi' had substantially higher expression of LcDEFL than the partly abortive cultivar 'Guiwei'. LcDEFL silencing led to a notable reduction in the size of litchi seeds. These findings point to the post-translational modulation of cysteine proteinase and the critical role of cysteine-rich proteins in litchi seed development.

Triticain alpha represents the major active papain-like cysteine protease in naturally senescing and ozone-treated leaves of wheat

Current background tropospheric ozone (O3) concentrations have significant adverse effects on wheat. O3 generally induces oxidative damages and premature leaf senescence leading to important yield losses. As leaf protein degradation and recycling is involved in both maintaining cell longevity during abiotic stresses and performing efficient nitrogen remobilization during senescence, we aimed to identify proteases involved in acidic endoproteolytic activities during natural and O3-induced leaf senescence in wheat. Field-grown plants of two winter wheat cultivars were exposed to ambient and semi-controlled chronic O3 concentrations, from pre-anthesis to grain harvest. Yield parameters were impacted by the most elevated O3 exposure for both cultivars. At the cellular level, our analysis revealed that both natural leaf senescence and O3 treatments induced a stimulation of acidic (pH 5.5) endoproteolytic activities, mostly due to papain-like cysteine proteases (PLCPs). Identification of active PLCPs using activity-based protein profiling (ABPP) revealed that Triticain α was the major active PLCP in senescing flag leaves and the only PLCP whose abundance increased with O3 stress, a result of positive transcriptional regulation. Our study provides novel insight into the implication of PLCP-mediated proteolysis in O3 sensitivity in a major crop.

Pull the fuzes: Processing protein precursors to generate apoplastic danger signals for triggering plant immunity

The apoplast is one of the first cellular compartments outside the plasma membrane encountered by phytopathogenic microbes in the early stages of plant tissue invasion. Plants have developed sophisticated surveillance mechanisms to sense danger events at the cell surface and promptly activate immunity. However, a fine tuning of the activation of immune pathways is necessary to mount a robust and effective defense response. Several endogenous proteins and enzymes are synthesized as inactive precursors, and their post-translational processing has emerged as a critical mechanism for triggering alarms in the apoplast. In this review, we focus on the precursors of phytocytokines, cell wall remodeling enzymes, and proteases. The physiological events that convert inactive precursors into immunomodulatory active peptides or enzymes are described. This review also explores the functional synergies among phytocytokines, cell wall damage-associated molecular patterns, and remodeling, highlighting their roles in boosting extracellular immunity and reinforcing defenses against pests.

WRKY47 transcription factor modulates leaf senescence through regulating PCD-associated genes in Arabidopsis

Transcription factors play crucial roles in almost all physiological processes including leaf senescence. Cell death is a typical symptom appearing in senescing leaves, which is also classified as developmental programmed cell death (PCD). However, the link between PCD and leaf senescence still remains unclear. Here, we found a WRKY transcription factor WRKY47 positively modulates age-dependent leaf senescence in Arabidopsis (Arabidopsis thaliana). WRKY47 was expressed preferentially in senescing leaves. A subcellular localization assay indicated that WRKY47 was exclusively localized in nuclei. Overexpression of WRKY47 showed precocious leaf senescence, with less chlorophyll content and higher electrolyte leakage, but loss-of-function mutants of WRKY47 delayed this biological process. Through qRT-PCR and dual luciferase reporter assays, we found that WRKY47 could activate the expression of senescence-associated genes (SAGs) and PCD-associated genes to regulate leaf senescence. Furthermore, through electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation (ChIP)-qPCR, WRKY47 was found to bind to W-box fragments in promoter regions of BFN1 (Bifunctional Nuclease 1) and MC6 (Metacaspase 6) directly. In general, our research revealed that WRKY47 regulates age-dependent leaf senescence by activating the transcription of two PCD-associated genes.

Protein disulfide isomerase-9 interacts with the lumenal region of the transmembrane endoplasmic reticulum stress sensor kinase, IRE1, to modulate the unfolded protein response in Arabidopsis

Environmental stressors disrupt secretory protein folding and proteostasis in the endoplasmic reticulum (ER), leading to ER stress. The unfolded protein response (UPR) senses ER stress and restores proteostasis by increasing the expression of ER-resident protein folding chaperones, such as protein disulfide isomerases (PDIs). In plants, the transmembrane ER stress sensor kinase, IRE1, activates the UPR by unconventionally splicing the mRNA encoding the bZIP60 transcription factor, triggering UPR gene transcription. The induced PDIs catalyze disulfide-based polypeptide folding to restore the folding capacity in the ER; however, the substrates with which PDIs interact are largely unknown. Here, we demonstrate that the Arabidopsis PDI-M subfamily member, PDI9, modulates the UPR through interaction with IRE1. This PDI9-IRE1 interaction was largely dependent on Cys63 in the first dithiol redox active domain of PDI9, and Cys233 and Cys107 in the ER lumenal domain of IRE1A and IRE1B, respectively. In vitro and in vivo, PDI9 coimmunoprecipitated with IRE1A and IRE1B. Moreover, the PDI9:RFP and Green Fluorescence Protein (GFP):IRE1 fusions exhibited strong interactions as measured by fluorescence lifetime imaging microscopy-fluorescence resonance energy transfer (FLIM-FRET) when coexpressed in mesophyll protoplasts. The UPR-responsive PDI9 promoter:mCherry reporter and the UPR-dependent splicing of the bZIP60 intron from the mRNA of the 35S::bZIP60-intron:GFP reporter were both significantly induced in the pdi9 mutants, indicating a derepression and hyperactivation of UPR. The inductions of both reporters were substantially attenuated in the ire1a-ire1b mutant. We propose a model in which PDI9 modulates the UPR through two competing activities: secretory protein folding and via interaction with IRE1 to maintain proteostasis in plants.

Integrated Transcriptome and Proteome Analysis Reveals the Regulatory Mechanism of Root Growth by Protein Disulfide Isomerase in Arabidopsis

Protein disulfide isomerase (PDI, EC 5.3.4.1) is a thiol-disulfide oxidoreductase that plays a crucial role in catalyzing the oxidation and rearrangement of disulfides in substrate proteins. In plants, PDI is primarily involved in regulating seed germination and development, facilitating the oxidative folding of storage proteins in the endosperm, and also contributing to the formation of pollen. However, the role of PDI in root growth has not been previously studied. This research investigated the impact of PDI gene deficiency in plants by using 16F16 [2-(2-Chloroacetyl)-2,3,4,9-tetrahydro-1-methyl-1H-pyrido[3,4-b]indole-1-carboxylic acid methyl ester], a small-molecule inhibitor of PDI, to remove functional redundancy. The results showed that the growth of Arabidopsis roots was significantly inhibited when treated with 16F16. To further investigate the effects of 16F16 treatment, we conducted expression profiling of treated roots using RNA sequencing and a Tandem Mass Tag (TMT)-based quantitative proteomics approach at both the transcriptomic and proteomic levels. Our analysis revealed 994 differentially expressed genes (DEGs) at the transcript level, which were predominantly enriched in pathways associated with "phenylpropane biosynthesis", "plant hormone signal transduction", "plant-pathogen interaction" and "starch and sucrose metabolism" pathways. Additionally, we identified 120 differentially expressed proteins (DEPs) at the protein level. These proteins were mainly enriched in pathways such as "phenylpropanoid biosynthesis", "photosynthesis", "biosynthesis of various plant secondary metabolites", and "biosynthesis of secondary metabolites" pathways. The comprehensive transcriptome and proteome analyses revealed a regulatory network for root shortening in Arabidopsis seedlings under 16F16 treatment, mainly involving phenylpropane biosynthesis and plant hormone signal transduction pathways. This study enhances our understanding of the significant role of PDIs in Arabidopsis root growth and provides insights into the regulatory mechanisms of root shortening following 16F16 treatment.

Genome-wide analysis and expression divergence of protein disulfide isomerase (PDI) gene family members in chickpea (Cicer arietinum) under salt stress

Chickpea (Cicer arietinum ) is a grain crop that is an important source of protein, vitamins, carbohydrates and minerals. It is highly sensitive to salt stress, and salt damage to cellular homeostasis and protein folding affects production. Plants have several mechanisms to prevent cellular damages under abiotic stresses, such as proteins in the endoplasmic reticulum (protein isulfide somerases (PDIs) and PDI-like proteins), which help prevent the build-up of mis-folded proteins that are damaged under abiotic stresses. In this study, we completed initial comprehensive genome-wide analysis of the chickpea PDI gene family. We found eight PDI genes are distributed on six out of eight chromosomes. Two pairs of paralogous genes were found to have segmental duplications. The phylogenetic analysis showed that the PDI s have a high degree of homology in C. arietinum, Cicer reticulatum, Lens culinaris, Phaseolus acutifolius, Pisum sativum and Oryza sativa . The gene structure analysis displayed that CaPDI1-CaPDI8 have 9-12 exons except for CaPDI5 , which has 25 exons. Subcellular localisation indicated accumulation of CaPDIs in endoplasmic reticulum. Protein-conserved motifs and domain analysis demonstrated that thioredoxin domains of PDI family is present in all CaPDIs. CaPDI proteins have strong protein-protein interaction. In silico expression analysis showed that four out of eight PDI genes (CPDI2, CaPDI6, CaPDI7 and CaPDI8 ) were expressed under salt stress. Of these, expression of CaPDI2 and CaPDI8 was the highest. This work indicated that PDI genes are involved in salt stress tolerance in chickpea and the CaPDIs may be further studied for their role of inducing salt tolerance.

Protein Disulfide Isomerase FgEps1 Is a Secreted Virulence Factor in Fusarium graminearum

Protein disulfide isomerase (PDI) is a member of the thioredoxin (Trx) superfamily with important functions in cellular stability, ion uptake, and cellular differentiation. While PDI has been extensively studied in humans and animals, its role in fungi remains relatively unknown. In this study, the biological functions of FgEps1, a disulfide bond isomerase in the fungal pathogen Fusarium graminearum, were investigated. It was found that FgEps1 mutation affected nutritional growth, asexual and sexual reproduction, and stress tolerance. Additionally, its deletion resulted in reduced pathogenicity and impaired DON toxin biosynthesis. The involvement of FgEps1 in host infection was also confirmed, as its expression was detected during the infection period. Further investigation using a yeast signal peptide secretion system and transient expression in Nicotiana benthamiana showed that FgEps1 suppressed the immune response of plants and promoted infection. These findings suggest that virulence factor FgEps1 plays a crucial role in growth, development, virulence, secondary metabolism, and host infection in F. graminearum.

An IRE1-proteasome system signalling cohort controls cell fate determination in unresolved proteotoxic stress of the plant endoplasmic reticulum

Excessive accumulation of misfolded proteins in the endoplasmic reticulum (ER) causes ER stress, which is an underlying cause of major crop losses and devastating human conditions. ER proteostasis surveillance is mediated by the conserved master regulator of the unfolded protein response (UPR), Inositol Requiring Enzyme 1 (IRE1), which determines cell fate by controlling pro-life and pro-death outcomes through as yet largely unknown mechanisms. Here we report that Arabidopsis IRE1 determines cell fate in ER stress by balancing the ubiquitin-proteasome system (UPS) and UPR through the plant-unique E3 ligase, PHOSPHATASE TYPE 2CA (PP2CA)-INTERACTING RING FINGER PROTEIN 1 (PIR1). Indeed, PIR1 loss leads to suppression of pro-death UPS and the lethal phenotype of an IRE1 loss-of-function mutant in unresolved ER stress in addition to activating pro-survival UPR. Specifically, in ER stress, PIR1 loss stabilizes ABI5, a basic leucine zipper (bZIP) transcription factor, that directly activates expression of the critical UPR regulator gene, bZIP60, triggering transcriptional cascades enhancing pro-survival UPR. Collectively, our results identify new cell fate effectors in plant ER stress by showing that IRE1's coordination of cell death and survival hinges on PIR1, a key pro-death component of the UPS, which controls ABI5, a pro-survival transcriptional activator of bZIP60.

Laser capture microdissection-based spatiotemporal transcriptomes uncover regulatory networks during seed abortion in seedless Ponkan (Citrus reticulata)

Seed abortion is an important process in the formation of seedless characteristics in citrus fruits. However, the molecular regulatory mechanism underlying citrus seed abortion is poorly understood. Laser capture microdissection-based RNA-seq combined with Pacbio-seq was used to profile seed development in the Ponkan cultivars 'Huagan No. 4' (seedless Ponkan) (Citrus reticulata) and 'E'gan No. 1' (seeded Ponkan) (C. reticulata) in two types of seed tissue across three developmental stages. Through comparative transcriptome and dynamic phytohormone analyses, plant hormone signal, cell division and nutrient metabolism-related processes were revealed to play critical roles in the seed abortion of 'Huagan No. 4'. Moreover, several genes may play indispensable roles in seed abortion of 'Huagan No. 4', such as CrWRKY74, CrWRKY48 and CrMYB3R4. Overexpression of CrWRKY74 in Arabidopsis resulted in severe seed abortion. By analyzing the downstream regulatory network, we further determined that CrWRKY74 participated in seed abortion regulation by inducing abnormal programmed cell death. Of particular importance is that a preliminary model was proposed to depict the regulatory networks underlying seed abortion in citrus. The results of this study provide novel insights into the molecular mechanism across citrus seed development, and reveal the master role of CrWRKY74 in seed abortion of 'Huagan No. 4'.

Exploring the Potential Role of Ribosomal Proteins to Enhance Potato Resilience in the Face of Changing Climatic Conditions

Potatoes have emerged as a key non-grain crop for food security worldwide. However, the looming threat of climate change poses significant risks to this vital food source, particularly through the projected reduction in crop yields under warmer temperatures. To mitigate potential crises, the development of potato varieties through genome editing holds great promise. In this study, we performed a comprehensive transcriptomic analysis to investigate microtuber development and identified several differentially expressed genes, with a particular focus on ribosomal proteins-RPL11, RPL29, RPL40 and RPL17. Our results reveal, by protein-protein interaction (PPI) network analyses, performed with the highest confidence in the STRING database platform (v11.5), the critical involvement of these ribosomal proteins in microtuber development, and highlighted their interaction with PEBP family members as potential microtuber activators. The elucidation of the molecular biological mechanisms governing ribosomal proteins will help improve the resilience of potato crops in the face of today's changing climatic conditions.

Cadmium treatment induces endoplasmic reticulum stress and unfolded protein response in Arabidopsisthaliana

We report about the response of Arabidopsis thaliana to chronic and temporary Cd²⁺ stress, and the Cd²⁺ induced activation of ER stress and unfolded protein response (UPR). Cd²⁺-induced UPR proceeds mainly through the bZIP60 arm, which in turn activates relevant ER stress marker genes such as BiP3, CNX, PDI5 and ERdj3B in a concentration- (chronic stress) or time- (temporary stress) dependent manner. A more severe Cd-stress triggers programmed cell death (PCD) through the activation of the NAC089 transcription factor. Toxic effects of Cd²⁺ exposure are reduced in the Atbzip28/bzip60 double mutant in terms of primary root length and fresh shoot weight, likely due to reduced UPR and PCD activation. We also hypothesised that the enhanced Cd²⁺ tolerance of the Atbzip28/bzip60 double mutant is due to an increase in brassinosteroids signaling, since the amount of the brassinosteroid insensitive1 receptor (BRI1) protein decreases under Cd²⁺ stress only in Wt plants. These data highlight the complexity of the UPR pathway, since the ER stress response is strictly related to the type of the treatment applied and the multifaceted connections of ER signaling. The reduced sensing of Cd²⁺ stress in plants with UPR defects can be used as a novel strategy for phytoremediation.

QTL Mapping and a Transcriptome Integrative Analysis Uncover the Candidate Genes That Control the Cold Tolerance of Maize Introgression Lines at the Seedling Stage

Chilling injury owing to low temperatures severely affects the growth and development of maize (Zea mays.L) seedlings during the early and late spring seasons. The existing maize germplasm is deficient in the resources required to improve maize's ability to tolerate cold injury. Therefore, it is crucial to introduce and identify excellent gene/QTLs that confer cold tolerance to maize for sustainable crop production. Wild relatives of maize, such as Z. perennis and Tripsacum dactyloides, are strongly tolerant to cold and can be used to improve the cold tolerance of maize. In a previous study, a genetic bridge among maize that utilized Z. perennis and T. dactyloides was created and used to obtain a highly cold-tolerant maize introgression line (MIL)-IB030 by backcross breeding. In this study, two candidate genes that control relative electrical conductivity were located on MIL-IB030 by forward genetics combined with a weighted gene co-expression network analysis. The results of the phenotypic, genotypic, gene expression, and functional verification suggest that two candidate genes positively regulate cold tolerance in MIL-IB030 and could be used to improve the cold tolerance of cultivated maize. This study provides a workable route to introduce and mine excellent genes/QTLs to improve the cold tolerance of maize and also lays a theoretical and practical foundation to improve cultivated maize against low-temperature stress.

Thiol-disulfide oxidoreductase PDI1;1 regulates actin structures in Oryza sativa root cells

The polarized and dynamic actin cytoskeleton is essential for root cell growth. Here, we report the key role of thiol-disulfide oxidoreductase PDI1;1 in actin structures. Microscopic analyses revealed that after Oryza sativa roots were exposed to H₂ O₂ , both actin and PDI1;1 were depolarized and arranged in a meshwork. In H₂ O₂ -exposed cells, actin formed intermolecularly disulfide-bonded high-molecular-weight structures, which were thiol-trapped by PDI1;1. Recombinant PDI1;1 exhibited the ability to recognize actin in an in vitro binding assay. During recovery from H₂ O₂ exposure, the amount of disulfide-bonded high-molecular-weight structures of actin decreased over time, but deficiency of PDI1;1 inhibited the decrease. These results suggest a PDI1;1-dependent pathway that reduces disulfide bonds in high-molecular-weight structures of actin, thus promoting their degradation.

Interference of Arabidopsis N-Acetylglucosamine-1-P Uridylyltransferase Expression Impairs Protein N-Glycosylation and Induces ABA-Mediated Salt Sensitivity During Seed Germination and Early Seedling Development

N-acetylglucosamine (GlcNAc) is the fundamental amino sugar moiety that is essential for protein glycosylation. UDP-GlcNAc, an active form of GlcNAc, is synthesized through the hexosamine biosynthetic pathway (HBP). Arabidopsis N-acetylglucosamine-1-P uridylyltransferases (GlcNAc1pUTs), encoded by GlcNA.UTs, catalyze the last step in the HBP pathway, but their biochemical and molecular functions are less clear. In this study, the GlcNA.UT1 expression was knocked down by the double-stranded RNA interference (dsRNAi) in the glcna.ut2 null mutant background. The RNAi transgenic plants, which are referred to as iU1, displayed the reduced UDP-GlcNAc biosynthesis, altered protein N-glycosylation and induced an unfolded protein response under salt-stressed conditions. Moreover, the iU1 transgenic plants displayed sterility and salt hypersensitivity, including delay of both seed germination and early seedling establishment, which is associated with the induction of ABA biosynthesis and signaling. These salt hypersensitive phenotypes can be rescued by exogenous fluridone, an inhibitor of ABA biosynthesis, and by introducing an ABA-deficient mutant allele nced3 into iU1 transgenic plants. Transcriptomic analyses further supported the upregulated genes that were involved in ABA biosynthesis and signaling networks, and response to salt stress in iU1 plants. Collectively, these data indicated that GlcNAc1pUTs are essential for UDP-GlcNAc biosynthesis, protein N-glycosylation, fertility, and the response of plants to salt stress through ABA signaling pathways during seed germination and early seedling development.

The Use of Fluorescent Protein Fusions to Monitor the Unfolded Protein Response and Protein Foldase-Substrate Interactions in Plant Protoplasts

Endoplasmic reticulum (ER) stress and the resulting unfolded protein response (UPR) are critical stress response pathways in eukaryotes. To study these types of interactions in plants, a wide range of methods have been used, including generation of transgenic plants, subcellular immunolocalization of protein foldases, and co-immunoprecipitation (co-IP) assays. Although these more time-consuming methods have been successfully implemented, there is a need for a versatile and rapid in vivo system to investigate ER stress and UPR. Here, we describe a transient expression system that uses plant protoplasts to define in vivo subcellular localizations and protein-protein interactions of protein foldases and their substrates fused to fluorescent protein reporters. This accurate and robust assay utilizes a variety of analyses, such as subcellular localization, FLIM-FRET, co-IP, mutagenesis, and RT-PCR in the genetically amenable Arabidopsis model system. We demonstrate the methodology by using the representative protein foldase, protein disulfide isomerase-9 (PDI9), as well as subcellular markers, secretory proteins, and dithiothreitol (DTT)-mediated induction of the UPR as monitored by RT-PCR. Together, these methods yield reliable high output results for investigating subcellular localization and protein-protein interactions in plants to decipher the UPR pathways.

Expression Characterization of AtPDI11 and Functional Analysis of AtPDI11 D Domain in Oxidative Protein Folding

The formation and isomerization of disulfide bonds mediated by protein disulfide isomerase (PDI) in the endoplasmic reticulum (ER) is of fundamental importance in eukaryotes. Canonical PDI structure comprises four domains with the order of a-b-b′-a′. In Arabidopsis thaliana, the PDI-S subgroup contains only one member, AtPDI11, with an a-a′-D organization, which has no orthologs in mammals or yeast. However, the expression pattern of AtPDI11 and the functioning mechanism of AtPDI11 D domain are currently unclear. In this work, we found that PDI-S is evolutionarily conserved between land plants and algal organisms. AtPDI11 is expressed in various tissues and its induction by ER stress is disrupted in bzip28/60 and ire1a/b mutants that are null mutants of key components in the unfolded protein response (UPR) signal transduction pathway, suggesting that the induction of AtPDI11 by ER stress is mediated by the UPR signaling pathway. Furthermore, enzymatic activity assays and genetic evidence showed that the D domain is crucially important for the activities of AtPDI11. Overall, this work will help to further understand the working mechanism of AtPDI11 in catalyzing disulfide formation in plants.

Proteome Changes in Stem Tissues of Sunflower Lines Inoculated with Culture Filtrate of Sclerotinia sclerotiorum

BACKGROUND

Sclerotinia sclerotiorum (Lib.) de Bary cause a deleterious disease on sunflower plants. Oxalic acid is the main pathogenicity factor of S. sclerotiorum. Two dimensional gel electrophoresis and mass spectrometry have been used in several studies to investigate molecular changes that occur in the plants in response to S. sclerotiorum infection. Comparing responses of resistant and susceptible lines upon pathogen infection provided novel information regarding defense mechanisms against this necrotrophic pathogen.

OBJECTIVES

The present study reports proteome changes of partially resistant and susceptible sunflower lines under pathogen's culture filtrate treatment, resulting in the characterization of up- and down- regulated proteins.

MATERIAL AND METHODS

Sunflower partially resistant and susceptible lines with two true leaves were exposed to fungus culture filtrate. The stems of treated and untreated plants were sampled at 24, 48 and 72 hours after treatment for two-dimensional electrophoresis. Twenty spots showed more than 1.5-fold change in abundance were subjected to MALDI/TOF-TOF MS for further analysis.

RESULTS

The identified proteins were categorized into several classes including carbohydrate and energy metabolism (25%), cellular metabolic process (15%), stress response (15%), plant cell wall biogenesis (10%), photosynthesis (10%), protein metabolism (10%), unknown function (10%) and redox homeostasis (5%).

CONCLUSIONS

Our proteomic investigation demonstrates an increase in the expression of proteins only in partially resistant line, such as proteins involved in carbohydrate metabolism and plant defense responses (malate dehydrogenase and peroxidase), metabolic process (adenosine kinase), regulating cell redox homeostasis (disulfide isomerase) and lignin biosynthetic process (laccase). Moreover, the expression of pyrroline-5-carboxylate reductase, involved in proline biosynthesis, was significantly changed in both sunflower lines in response to pathogen culture filtrate. Proteins which were only up-regulated in the partially resistant lines might have a significant role in mediating the defense against Sclerotinia and could be considered for enhancing resistance against this devastating pathogen.

Biochemical aspects of seeds from Cannabis sativa L. plants grown in a mountain environment

Cannabis sativa L. (hemp) is a versatile plant which can adapt to various environmental conditions. Hempseeds provide high quality lipids, mainly represented by polyunsaturated acids, and highly digestible proteins rich of essential aminoacids. Hempseed composition can vary according to plant genotype, but other factors such as agronomic and climatic conditions can affect the presence of nutraceutic compounds. In this research, seeds from two cultivars of C. sativa (Futura 75 and Finola) grown in a mountain environment of the Italian Alps were analyzed. The main purpose of this study was to investigate changes in the protein profile of seeds obtained from such environments, using two methods (sequential and total proteins) for protein extraction and two analytical approaches SDS-PAGE and 2D-gel electrophoresis, followed by protein identification by mass spectrometry. The fatty acids profile and carotenoids content were also analysed. Mountain environments mainly affected fatty acid and protein profiles of Finola seeds. These changes were not predictable by the sole comparison of certified seeds from Futura 75 and Finola cultivars. The fatty acid profile confirmed a high PUFA content in both cultivars from mountain area, while protein analysis revealed a decrease in the protein content of Finola seeds from the experimental fields.

The Arabidopsis Protein Disulfide Isomerase Subfamily M Isoform, PDI9, Localizes to the Endoplasmic Reticulum and Influences Pollen Viability and Proper Formation of the Pollen Exine During Heat Stress

Plants adapt to heat via thermotolerance pathways in which the activation of protein folding chaperones is essential. In eukaryotes, protein disulfide isomerases (PDIs) facilitate the folding of nascent and misfolded proteins in the secretory pathway by catalyzing the formation and isomerization of disulfide bonds and serving as molecular chaperones. In Arabidopsis, several members of the PDI family are upregulated in response to chemical inducers of the unfolded protein response (UPR), including both members of the non-classical PDI-M subfamily, PDI9 and PDI10. Unlike classical PDIs, which have two catalytic thioredoxin (TRX) domains separated by two non-catalytic TRX-fold domains, PDI-M isoforms are orthologs of mammalian P5/PDIA6 and possess two tandem catalytic domains. Here, PDI9 accumulation was found to be upregulated in pollen in response to heat stress. Histochemical staining of plants harboring the PDI9 and PDI10 promoters fused to the gusA gene indicated they were actively expressed in the anthers of flowers, specifically in the pollen and tapetum. Immunoelectron microscopy revealed that PDI9 localized to the endoplasmic reticulum in root and pollen cells. transfer DNA (T-DNA) insertional mutations in the PDI9 gene disrupted pollen viability and development in plants exposed to heat stress. In particular, the pollen grains of pdi9 mutants exhibited disruptions in the reticulated pattern of the exine and an increased adhesion of pollen grains. Pollen in the pdi10 single mutant did not display similar heat-associated defects, but pdi9 pdi10 double mutants (DMs) completely lost exine reticulation. Interestingly, overexpression of PDI9 partially led to heat-associated defects in the exine. We conclude that PDI9 plays an important role in pollen thermotolerance and exine biogenesis. Its role fits the mechanistic theory of proteostasis in which an ideal balance of PDI isoforms is required in the endoplasmic reticulum (ER) for normal exine formation in plants subjected to heat stress.

Genome-Wide Identification and Expression Profiling of the PDI Gene Family Reveals Their Probable Involvement in Abiotic Stress Tolerance in Tomato (Solanum Lycopersicum L.)

Protein disulfide isomerases (PDI) and PDI-like proteins catalyze the formation and isomerization of protein disulfide bonds in the endoplasmic reticulum and prevent the buildup of misfolded proteins under abiotic stress conditions. In the present study, we conducted the first comprehensive genome-wide exploration of the PDI gene family in tomato (Solanum lycopersicum L.). We identified 19 tomato PDI genes that were unevenly distributed on 8 of the 12 tomato chromosomes, with segmental duplications detected for 3 paralogous gene pairs. Expression profiling of the PDI genes revealed that most of them were differentially expressed across different organs and developmental stages of the fruit. Furthermore, most of the PDI genes were highly induced by heat, salt, and abscisic acid (ABA) treatments, while relatively few of the genes were induced by cold and nutrient and water deficit (NWD) stresses. The predominant expression of SlPDI1-1, SlPDI1-3, SlPDI1-4, SlPDI2-1, SlPDI4-1, and SlPDI5-1 in response to abiotic stress and ABA treatment suggested they play regulatory roles in abiotic stress tolerance in tomato in an ABA-dependent manner. Our results provide new insight into the structure and function of PDI genes and will be helpful for the selection of candidate genes involved in fruit development and abiotic stress tolerance in tomato.

Identification of tannic cell walls at the outer surface of the endosperm upon Arabidopsis seed coat rupture

The seed coat is specialized dead tissue protecting the plant embryo from mechanical and oxidative damage. Tannins, a type of flavonoids, are antioxidants known to accumulate in the Arabidopsis seed coat and transparent testa mutant seeds, deficient in flavonoid synthesis, exhibit low viability. However, their precise contribution to seed coat architecture and biophysics remains evasive. A seed coat cuticle, covering the endosperm outer surface and arising from the seed coat inner integument 1 cell layer was, intriguingly, previously shown to be more permeable in transparent testa mutants deficient not in cuticular component synthesis, but rather in flavonoid synthesis. Investigating the role of flavonoids in cuticle permeability led us to identify periclinal inner integument 1 tannic cell walls being attached, together with the cuticle, to the endosperm surface upon seed coat rupture. Hence, inner integument 1 tannic cell walls and the cuticle form two fused layers present at the surface of the exposed endosperm upon seed coat rupture, regulating its permeability. Their potential physiological role during seed germination is discussed.

The root-knot nematode effector MiPDI1 targets a stress-associated protein (SAP) to establish disease in Solanaceae and Arabidopsis

Large amounts of effectors are secreted by the oesophageal glands of plant-parasitic nematodes, but their molecular mode of action remains largely unknown. We characterized a Meloidogyne incognita protein disulphide isomerase (PDI)-like effector protein (MiPDI1) that facilitates nematode parasitism. In situ hybridization showed that MiPDI1 was expressed specifically in the subventral glands of M. incognita. It was significantly upregulated during parasitic stages. Immunolocalization demonstrated MiPDI1 secretion in planta during nematode migration and within the feeding cells. Host-induced silencing of the MiPDI1 gene affected the ability of the nematode to infect the host, whereas MiPDI1 expression in Arabidopsis increased susceptibility to M. incognita, providing evidence for a key role of MiPDI1 in M. incognita parasitism. Yeast two-hybrid, bimolecular fluorescence complementation and coimmunoprecipitation assays showed that MiPDI1 interacted with a tomato stress-associated protein (SlSAP12) orthologous to the redox-regulated AtSAP12, which plays an important role in plant responses to abiotic and biotic stresses. SAP12 silencing or knocking out in Nicotiana benthamiana and Arabidopsis increased susceptibility to M. incognita. Our results suggest that MiPDI1 acts as a pathogenicity factor promoting disease by fine-tuning SAP-mediated responses at the interface of redox signalling, defence and stress acclimation in Solanaceae and Arabidopsis.

Differential proteomic analysis of soybean anthers by iTRAQ under high-temperature stress

High-temperature has severe impacts on the functionality and development of soybean male reproductive organs. However, the molecular mechanism of thermo-tolerance in soybean remains unclear. In this study, a differential proteomic analysis was conducted between the anthers of heat-tolerant (JD21) and heat-sensitive (HD14) cultivars using an iTRAQ based approach. In total, 371, 479, and 417 differentially abundant proteins were identified between HD14 anthers treated with high-temperature stress vs HD14 anthers in the natural field conditions, JD21 anthers treated with high-temperature stress vs JD21 anthers in the natural field conditions, and HD14 vs JD21 anthers treated with high-temperature stress, respectively. The differentially abundant proteins associated with thermo-tolerance were predominantly involved in carbohydrate and energy metabolism, protein synthesis and degradation, nitrogen assimilation, and ROS detoxification. Sixteen common differentially abundant proteins were involved in known protein-protein interaction networks in three comparisons associated with heat, which may strongly influence anther growth and development. The qRT-PCR analysis validated the reliability of the iTRAQ results. In conclusion, the heat-tolerant cultivar performed better under stress than heat-sensitive cultivar through modulation of HSP family proteins, pectinesterase, profilin, S-adenosylmethionine synthase, peroxidase, GST, peptidylprolyl isomerase, and disulfide-isomerase. The results provide novel insight into the mechanism of high-temperature stress response of soybean. SIGNIFICANCE: In recent years, with the high temperature (HT) stress brought by climate change frequently occurs at anthesis and negatively affects soybean productivity. The molecular mechanism underlying the response of soybean anthers to HT is a relatively complex process and thus difficult to elucidate; however, it is possible to identify differentially expressed genes or proteins between heat-sensitive and heat-tolerant cultivars under HT stress. The potential candidate genes or proteins may then be utilized in elucidating the molecular mechanism underlying the response of soybean to HT stress, as well as provide genetic resource for the improvement of heat-tolerant characteristics in soybean. In present study, quantitative and qualitative proteomic changes occurring in anthers were compared between the heat-tolerant (JD21) and heat-sensitive (HD14) cultivars under HT stress using iTRAQ-based proteomics strategy. Our results provide new insight into translational alterations in HT-resistant and HT-sensitive soybean cultivars under HT stress, which helps to address the underlying molecular mechanism of soybean in response to HT stress.

A novel soybean protein disulphide isomerase family protein possesses dithiol oxidation activity: identification and characterization of GmPDIL6

Secretory and membrane proteins synthesized in the endoplasmic reticulum (ER) are folded with intramolecular disulphide bonds, viz. oxidative folding, catalysed by the protein disulphide isomerase (PDI) family proteins. Here, we identified a novel soybean PDI family protein, GmPDIL6. GmPDIL6 has a single thioredoxin-domain with a putative N-terminal signal peptide and an active centre (CKHC). Recombinant GmPDIL6 forms various oligomers binding iron. Oligomers with or without iron binding and monomers exhibited a dithiol oxidase activity level comparable to those of other soybean PDI family proteins. However, they displayed no disulphide reductase and extremely low oxidative refolding activity. Interestingly, GmPDIL6 was mainly expressed in the cotyledon during synthesis of seed storage proteins and GmPDIL6 mRNA was up-regulated under ER stress. GmPDIL6 may play a role in the formation of disulphide bonds in nascent proteins for oxidative folding in the ER.

Programmed cell death (PCD) control in plants: New insights from the Arabidopsis thaliana deathosome

Programmed cell death (PCD) is a genetically controlled process that leads to cell suicide in both eukaryotic and prokaryotic organisms. In plants PCD occurs during development, defence response and when exposed to adverse conditions. PCD acts controlling the number of cells by eliminating damaged, old, or unnecessary cells to maintain cellular homeostasis. Unlike in animals, the knowledge about PCD in plants is limited. The molecular network that controls plant PCD is poorly understood. Here we present a review of the current mechanisms involved with the genetic control of PCD in plants. We also present an updated version of the AtLSD1 deathosome, which was previously proposed as a network controlling HR-mediated cell death in Arabidopsis thaliana. Finally, we discuss the unclear points and open questions related to the AtLSD1 deathosome.

A Poplar Rust Effector Protein Associates with Protein Disulfide Isomerase and Enhances Plant Susceptibility

Melampsora larici-populina (Mlp), the causal agent of Populus leaf rust, secretes an array of effectors into the host through the haustorium to gain nutrients and suppress immunity. The precise mechanisms by which these effectors promote virulence remain unclear. To address this question, we developed a transgenic Arabidopsis line expressing a candidate effector, Mlp124357. Constitutive expression of the effector increased plant susceptibility to pathogens. A GxxxG motif present in Mlp124357 is required for its subcellular localization at the vacuolar membrane of the plant cell, as replacement of the glycine residues with alanines led to the delocalization of Mlp124357 to the nucleus and cytoplasm. We used immunoprecipitation and mass spectrometry (MS) to identify Mlp124357 interaction partners. Only one of the putative interaction partners knock-out line caused delocalization of the effector, indicating that Arabidopsis protein disulfide isomerase-11 (AtPDI-11) is required for the effector localization. This interaction was further confirmed by a complementation test, a yeast-two hybrid assay and a molecular modeling experiment. Moreover, localization results and infection assays suggest that AtPDI-11 act as a helper for Mlp124357. In summary, our findings established that one of Mlp effectors resides at the vacuole surface and modulates plant susceptibility.

A novel plant protein-disulfide isomerase participates in resistance response against the TYLCV in tomato

Overexpression or silencing of the SlPDI could increase plants resistance or sensitivity to TYLCV through enhancing or reducing the plant's antioxidant capacity. Tomato yellow leaf curl virus (TYLCV), a plant virus that could infect a variety of crops, is particularly destructive to tomato growth. Protein disulfide isomerase (PDI) is a member of the thioredoxin (Trx) superfamily, is capable of catalyzing the formation and heterogeneity of protein disulfide bonds and inhibiting the aggregation of misfolded proteins. Studies have shown that PDI plays important roles in plant response to abiotic stress, there is no research report on the function of PDI in response to biotic stress, especially TYLCV infection. Here, we identified a tomato PDI gene, SlPDI, was involved in regulating tomato plants resistance to TYLCV. Subcellular localization results showed that SlPDI was located at the endoplasmic reticulum (ER), and its location remained unchanged after infection with TYLCV virus. Overexpression or silencing of SlPDI could increase plants resistance or sensitivity to TYLCV. Transgenic plants that overexpressing SlPDI exhibit enhanced antioxidant activity evidenced by lower hydrogen peroxide (H₂O₂) level and higher activity of superoxide dismutase (SOD) and peroxidase (POD) in comparison with WT plants, after infected by TYLCV. Moreover, the SlPDI-silencing plants showed opposite results. The promoter analyzes result showed that SlPDI was involved in response to salicylic acid (SA), and our experimental results also showed that the expression level of SlPDI was induced by SA. Taken together, our results indicated that SlPDI could regulate plant resistance to TYLCV through enhancing the protein folding function of ER and promoting the synthesis and conformation of antioxidant-related proteins.

A TMT-Based Quantitative Proteome Analysis to Elucidate the TSWV Induced Signaling Cascade in Susceptible and Resistant Cultivars of Solanum lycopersicum

Tomato spotted wilt virus (TSWV), transmitted by small insects known as thrips, is one of the major threats to tomato productivity across the globe. In addition to tomato, this virus infects more than 1000 other plants belonging to 85 families and is a cause of serious concern. Very little, however, is known about the molecular mechanism of TSWV induced signaling in plants. Here, we used a tandem mass tags (TMT)-based quantitative proteome approach to investigate the protein profiles of tomato leaves of two cultivars (cv 2621 and 2689; susceptible and resistant to TSWV infection, respectively) following TSWV inoculation. This approach resulted in the identification of 5112 proteins of which 1022 showed significant changes in response to TSWV. While the proteome of resistant cultivar majorly remains unaltered, the proteome of susceptible cultivar showed distinct differences following TSWV inoculation. TSWV modulated proteins in tomato included those with functions previously implicated in plant defense including secondary metabolism, reactive oxygen species (ROS) detoxification, mitogen-activated protein (MAP) kinase signaling, calcium signaling and jasmonate biosynthesis, among others. Taken together, results reported here provide new insights into the TSWV induced signaling in tomato leaves and may be useful in the future to manage this deadly disease of plants.

Comparative acetylomic analysis reveals differentially acetylated proteins regulating anther and pollen development in kenaf cytoplasmic male sterility line

Cytoplasmic male sterility (CMS) is widely used in plant breeding and represents a perfect model to understand cyto-nuclear interactions and pollen development research. Lysine acetylation in proteins is a dynamic and reversible posttranslational modification (PTM) that plays an important roles in diverse cell processes and signaling. However, studies addressing acetylation PTM regarding to anther and pollen development in CMS background are largely lacking. To reveal the possible mechanism of kenaf (Hibiscus cannabinus L.) CMS and pollen development, we performed a label-free-based comparative acetylome analysis in kenaf anther of a CMS line and wild-type (Wt). Using whole transcriptome unigenes of kenaf as the reference genome, we identified a total of 1204 Kac (lysin acetylation) sites on 1110 peptides corresponding to 672 unique proteins. Futher analysis showed 56 out of 672 proteins were differentially acetylated between CMS and Wt line, with 13 and 43 of those characterized up- and downregulated, respectively. Thirty-eight and 82 proteins were detected distinctively acetylated in CMS and Wt lines, respectively. And evaluation of the acetylomic and proteomic results indicated that the most significantly acetylated proteins were not associated with abundant changes at the protein level. Bioinformatics analysis demonstrated that many of these proteins were involved in various biological processes which may play key roles in pollen development, inculding tricarboxylic acid (TCA) cycle and energy metabolism, protein folding, protein metabolism, cell signaling, gene expression regulation. Taken together, our results provide insight into the CMS molecular mechanism and pollen development in kenaf from a protein acetylation perspective.

Flower bud proteome reveals modulation of sex-biased proteins potentially associated with sex expression and modification in dioecious Coccinia grandis

BACKGROUND

Dioecy is an important sexual system wherein, male and female flowers are borne on separate unisexual plants. Knowledge of sex-related differences can enhance our understanding in molecular and developmental processes leading to unisexual flower development. Coccinia grandis is a dioecious species belonging to Cucurbitaceae, a family well-known for diverse sexual forms. Male and female plants have 22A + XY and 22A + XX chromosomes, respectively. Previously, we have reported a gynomonoecious form (22A + XX) of C. grandis bearing morphologically hermaphrodite flowers (GyM-H) and female flowers (GyM-F). Also, we have showed that foliar spray of AgNO₃ on female plant induces morphologically hermaphrodite bud development (Ag-H) despite the absence of Y-chromosome.

RESULTS

To identify sex-related differences, total proteomes from male, female, GyM-H and Ag-H flower buds at early and middle stages of development were analysed by label-free proteomics. Protein search against the cucumber protein sequences (Phytozome) as well as in silico translated C. grandis flower bud transcriptome database, resulted in the identification of 2426 and 3385 proteins (FDR ≤ 1%), respectively. The latter database was chosen for further analysis as it led to the detection of higher number of proteins. Identified proteins were annotated using BLAST2GO pipeline. SWATH-MS-based comparative abundance analysis between Female_Early_vs_Male_Early, Ag_Early_vs_Female_Early, GyM-H_Middle_vs_Male_Middle and Ag_Middle_vs_ Male_Middle led to the identification of 650, 1108, 905 and 805 differentially expressed proteins, respectively, at fold change ≥1.5 and P ≤ 0.05. Ethylene biosynthesis-related candidates as highlighted in protein interaction network were upregulated in female buds compared to male buds. AgNO₃ treatment on female plant induced proteins related to pollen development in Ag-H buds. Additionally, a few proteins governing pollen germination and tube growth were highly enriched in male buds compared to Ag-H and GyM-H buds.

CONCLUSION

Overall, current proteomic analysis provides insights in the identification of key proteins governing dioecy and unisexual flower development in cucurbitaceae, the second largest horticultural family in terms of economic importance. Also, our results suggest that the ethylene-mediated stamen inhibition might be conserved in dioecious C. grandis similar to its monoecious cucurbit relatives. Further, male-biased proteins associated with pollen germination and tube growth identified here can help in understanding pollen fertility.

Oxidative protein folding in the plant endoplasmic reticulum

For most of the proteins synthesized in the endoplasmic reticulum (ER), disulfide bond formation accompanies protein folding in a process called oxidative folding. Oxidative folding is catalyzed by a number of enzymes, including the family of protein disulfide isomerases (PDIs), as well as other proteins that supply oxidizing equivalents to PDI family proteins, like ER oxidoreductin 1 (Ero1). Oxidative protein folding in the ER is a basic vital function, and understanding its molecular mechanism is critical for the application of plants as protein production tools. Here, I review the recent research and progress related to the enzymes involved in oxidative folding in the plant ER. Firstly, nine groups of plant PDI family proteins are introduced. Next, the enzymatic properties of plant Ero1 are described. Finally, the cooperative folding by multiple PDI family proteins and Ero1 is described.

Proteolysis and nitrogen: emerging insights

Nitrogen (N) is a core component of fertilizers used in modern agriculture to increase yields and thus to help feed a growing global population. However, this comes at a cost to the environment, through run-off of excess N as a result of poor N-use efficiency (NUE) by crops. An obvious remedy to this problem would therefore be the improvement of NUE, which requires advancing our understanding on N homeostasis, sensing, and uptake. Proteolytic pathways are linked to N homeostasis as they recycle proteins that contain N and carbon; however, emerging data suggest that their functions extend beyond this simple recycling. Here, we highlight roles of proteolytic pathways in non-symbiotic and symbiotic N uptake and in systemic N sensing. We also offer a novel view in which we suggest that proteolytic pathways have roles in N homeostasis that differ from their accepted function in recycling.

Plant proteases during developmental programmed cell death

Proteases are among the key regulators of most forms of programmed cell death (PCD) in animals. Many PCD processes have also been associated with protease expression or activation in plants, However, functional evidence for the roles and actual modes of action of plant proteases in PCD remains surprisingly limited. In this review, we provide an update on protease involvement in the context of developmentally regulated plant PCD. To illustrate the diversity of protease functions, we focus on several prominent developmental PCD processes, including xylem and tapetum maturation, suspensor elimination, endosperm degradation, and seed coat formation, as well as plant senescence processes. Despite the substantial advances in the field, protease functions are often only correlatively linked to developmental PCD, and the specific molecular roles of proteases in many developmental PCD processes remain to be elucidated.

Protein Disulfide Isomerase (PDI1-1) differential expression and modification in Mexican malting barley cultivars

Barley malting quality depends on seed characteristics achieved during grain development and germination. One important parameter is protein accumulation in the mature seed, which may vary between cultivars. Here we conducted a protein pattern analysis in the range of pI 4–7 of mature grains from five Mexican barley cultivars, commonly used for malt and beer production. Reproducibly distinct protein spots, separated by 2D SDS PAGE, were identified by mass spectrometry and considered as potential markers for cultivars with distinct seed protein accumulation. The expression patterns of glutamate decarboxylase (GAD) and protein disulfide isomerase (PDI1-1) were followed at transcript level during grain development for three independent growth cycles to establish whether differences between cultivars were reproducible. Quantitative determination of PDI1-1 protein levels by ELISA confirmed a reproducibly, distinctive accumulation and post-translational modifications between cultivars, which were independent of plant growth regimes. According to its impact on differential storage protein accumulation, we propose the PDI1-1 protein as potential biomarker for Mexican malting barley cultivars.

Identification and Functional Analysis of a Protein Disulfide Isomerase (AtPDI1) in Arabidopsis thaliana

Protein disulfide isomerase (PDI) catalyzes the conversion of thiol-disulfide and plays an important role in various physiological events in animals. A PDI (OaPDI) from a tropical plant was detailed studied and it was found to be involved in response of biotic stress (Gruber et al., 2007). However, the activities of PDI related to physiological functions in plants are poorly understood. In the present study, a homolog of human PDI in Arabidopsis (AtPDI1), encoded by the gene (At3g54960), was characterized. The recombinant AtPDI1 protein had disulfide isomerase activity in vitro and two pairs of conservative cysteines in catalytic domains play a crucial role in the PDI activities. Expression of AtPDI1 in Escherichia coli significantly enhanced stress tolerance of cells and the mutations of critical cysteines almost lose this function. In plants, AtPDI1 was strongly induced by abiotic stresses and exogenous abscisic acid. An ArabidopsisAtPDI1 knockdown mutant (pdi1) and overexpression lines of transgenic plants obtained by this investigation were used to further examine the function of AtPDI1. The mutant line was more sensitive to stresses than the wild-type, while overexpressing AtPDI1 increased tolerance of seedlings to abiotic stresses, with a higher germination ratio and longer length of roots than the wild-type. Our results suggested AtPDI1 played roles in anti-stresses in Arabidopsis, which relate to the activities of PDI.

A Maternally Deposited Endosperm Cuticle Contributes to the Physiological Defects of transparent testa Seeds

Mature dry seeds are highly resilient plant structures where the encapsulated embryo is kept protected and dormant to facilitate its ultimate dispersion. Seed viability is heavily dependent on the seed coat's capacity to shield living tissues from mechanical and oxidative stress. In Arabidopsis (Arabidopsis thaliana), the seed coat, also called the testa, arises after the differentiation of maternal ovular integuments during seed development. We recently described a thick cuticle tightly embedded in the mature seed's endosperm cell wall. We show here that it is produced by the maternal inner integument 1 layer and, remarkably, transferred to the developing endosperm. Arabidopsis transparent testa (tt) mutations cause maternally derived seed coat pigmentation defects. TT gene products encode proteins involved in flavonoid metabolism and regulators of seed coat development. tt mutants have abnormally high seed coat permeability, resulting in lower seed viability and dormancy. However, the biochemical basis of this high permeability is not fully understood. We show that the cuticles of developing tt mutant integuments have profound structural defects, which are associated with enhanced cuticle permeability. Genetic analysis indicates that a functional proanthocyanidin synthesis pathway is required to limit cuticle permeability, and our results suggest that proanthocyanidins could be intrinsic components of the cuticle. Together, these results show that the formation of a maternal cuticle is an intrinsic part of the normal integumental differentiation program leading to testa formation and is essential for the seed's physiological properties.

Vacuolar processing enzyme 4 contributes to maternal control of grain size in barley by executing programmed cell death in the pericarp

The angiosperm embryo and endosperm are limited in space because they grow inside maternal seed tissues. The elimination of cell layers of the maternal seed coat by programmed cell death (PCD) could provide space and nutrition to the filial organs. Using the barley (Hordeum vulgare L.) seed as a model, we elucidated the role of vacuolar processing enzyme 4 (VPE4) in cereals by using an RNAi approach and targeting the enzymatic properties of the recombinant protein. A comparative characterization of transgenic versus wild-type plants included transcriptional and metabolic profiling, flow cytometry, histology and nuclear magnetic imaging of grains. The recombinant VPE4 protein exhibited legumain and caspase-1 properties in vitro. Pericarp disintegration was delayed in the transgenic grains. Although the VPE4 gene and enzymatic activity was decreased in the early developing pericarp, storage capacity and the size of the endosperm and embryo were reduced in the mature VPE4-repressed grains. The persistence of the pericarp in the VPE4-affected grains constrains endosperm and embryo growth and leads to transcriptional reprogramming, perturbations in signalling and adjustments in metabolism. We conclude that VPE4 expression executes PCD in the pericarp, which is required for later endosperm filling, and argue for a role of PCD in maternal control of seed size in cereals.

Protein Quality Control in the Endoplasmic Reticulum of Plants

The endoplasmic reticulum (ER) is the site of maturation for roughly one-third of all cellular proteins. ER-resident molecular chaperones and folding catalysts promote folding and assembly in a diverse set of newly synthesized proteins. Because these processes are error-prone, all eukaryotic cells have a quality-control system in place that constantly monitors the proteins and decides their fate. Proteins with potentially harmful nonnative conformations are subjected to assisted folding or degraded. Persistent folding-defective proteins are distinguished from folding intermediates and targeted for degradation by a specific process involving clearance from the ER. Although the basic principles of these processes appear conserved from yeast to animals and plants, there are distinct differences in the ER-associated degradation of misfolded glycoproteins. The general importance of ER quality-control events is underscored by their involvement in the biogenesis of diverse cell surface receptors and their crucial maintenance of protein homeostasis under diverse stress conditions.

Protein Quality Control in the Endoplasmic Reticulum of Plants

The endoplasmic reticulum (ER) is the site of maturation for roughly one-third of all cellular proteins. ER-resident molecular chaperones and folding catalysts promote folding and assembly in a diverse set of newly synthesized proteins. Because these processes are error-prone, all eukaryotic cells have a quality-control system in place that constantly monitors the proteins and decides their fate. Proteins with potentially harmful nonnative conformations are subjected to assisted folding or degraded. Persistent folding-defective proteins are distinguished from folding intermediates and targeted for degradation by a specific process involving clearance from the ER. Although the basic principles of these processes appear conserved from yeast to animals and plants, there are distinct differences in the ER-associated degradation of misfolded glycoproteins. The general importance of ER quality-control events is underscored by their involvement in the biogenesis of diverse cell surface receptors and their crucial maintenance of protein homeostasis under diverse stress conditions.

Transcriptional Roadmap to Seasonal Variation in Wood Formation of Norway Spruce

Seasonal cues influence several aspects of the secondary growth of tree stems, including cambial activity, wood chemistry, and transition to latewood formation. We investigated seasonal changes in cambial activity, secondary cell wall formation, and tracheid cell death in woody tissues of Norway spruce (Picea abies) throughout one seasonal cycle. RNA sequencing was performed simultaneously in both the xylem and cambium/phloem tissues of the stem. Principal component analysis revealed gradual shifts in the transcriptomes that followed a chronological order throughout the season. A notable remodeling of the transcriptome was observed in the winter, with many genes having maximal expression during the coldest months of the year. A highly coexpressed set of monolignol biosynthesis genes showed high expression during the period of secondary cell wall formation as well as a second peak in midwinter. This midwinter peak in expression did not trigger lignin deposition, as determined by pyrolysis-gas chromatography/mass spectrometry. Coexpression consensus network analyses suggested the involvement of transcription factors belonging to the ASYMMETRIC LEAVES2/LATERAL ORGAN BOUNDARIES and MYELOBLASTOSIS-HOMEOBOX families in the seasonal control of secondary cell wall formation of tracheids. Interestingly, the lifetime of the latewood tracheids stretched beyond the winter dormancy period, correlating with a lack of cell death-related gene expression. Our transcriptomic analyses combined with phylogenetic and microscopic analyses also identified the cellulose and lignin biosynthetic genes and putative regulators for latewood formation and tracheid cell death in Norway spruce, providing a toolbox for further physiological and functional assays of these important phase transitions.

Ten Prominent Host Proteases in Plant-Pathogen Interactions

Proteases are enzymes integral to the plant immune system. Multiple aspects of defence are regulated by proteases, including the hypersensitive response, pathogen recognition, priming and peptide hormone release. These processes are regulated by unrelated proteases residing at different subcellular locations. In this review, we discuss 10 prominent plant proteases contributing to the plant immune system, highlighting the diversity of roles they perform in plant defence.

A guideline for leaf senescence analyses: from quantification to physiological and molecular investigations

Leaf senescence is not a chaotic breakdown but a dynamic process following a precise timetable. It enables plants to economize with their resources and control their own viability and integrity. The onset as well as the progression of leaf senescence are co-ordinated by a complex genetic network that continuously integrates developmental and environmental signals such as biotic and abiotic stresses. Therefore, studying senescence requires an integrative and multi-scale analysis of the dynamic changes occurring in plant physiology and metabolism. In addition to providing an automated and standardized method to quantify leaf senescence at the macroscopic scale, we also propose an analytic framework to investigate senescence at physiological, biochemical, and molecular levels throughout the plant life cycle. We have developed protocols and suggested methods for studying different key processes involved in senescence, including photosynthetic capacities, membrane degradation, redox status, and genetic regulation. All methods presented in this review were conducted on Arabidopsis thaliana Columbia-0 and results are compared with senescence-related mutants. This guideline includes experimental design, protocols, recommendations, and the automated tools for leaf senescence analyses that could also be applied to other species.

Retarded germination of Nicotiana tabacum seeds following insertion of exogenous DNA mimics the seed persistent behavior

Tobacco seeds show a coat-imposed dormancy in which the seed envelope tissues (testa and endosperm) impose a physical constraint on the radicle protrusion. The germination-limiting process is represented by the endosperm rupture which is induced by cell-wall weakening. Transgenic tobacco seeds, obtained by insertion of exogenous genes codifying for seed-based oral vaccines (F18 and VT2eB), showed retarded germination with respect to the wild type and modified the expression of endogenous proteins. Morphological and proteomic analyses of wild type and transgenic seeds revealed new insights into factors influencing seed germination. Our data showed that the interference of exogenous DNA influences the germination rather than the dormancy release, by modifying the maturation process. Dry seeds of F18 and VT2eB transgenic lines accumulated a higher amount of reserve and stress-related proteins with respect to the wild type. Moreover, the storage proteins accumulated in tobacco F18 and VT2eB dry seeds have structural properties that do not enable the early limited proteolysis observed in the wild type. Morphological observations by electron and light microscopy revealed a retarded mobilization of the storage material from protein and lipid bodies in transgenic seeds, thus impairing water imbibition and embryo elongation. In addition, both F18 and VT2eB dry seeds are more rounded than the wild type. Both the morphological and biochemical characteristics of transgenic seeds mimic the seed persistent profile, in which their roundness enables them to be buried in the soil, while the higher content of storage material enables the hypocotyl to elongate more and the cotyledons to emerge.

RiceAntherNet: a gene co-expression network for identifying anther and pollen development genes

In plants, normal anther and pollen development involves many important biological events and complex molecular regulatory coordination. Understanding gene regulatory relationships during male reproductive development is essential for fundamental biology and crop breeding. In this work, we developed a rice gene co-expression network for anther development (RiceAntherNet) that allows prediction of gene regulatory relationships during pollen development. RiceAntherNet was generated from 57 rice anther tissue microarrays across all developmental stages. The microarray datasets from nine rice male sterile mutants, including msp1-4, ostdl1a, gamyb-2, tip2, udt1-1, tdr, eat1-1, ptc1 and mads3-4, were used to explore and test the network. Among the changed genes, three clades showing differential expression patterns were constructed to identify genes associated with pollen formation. Many of these have known roles in pollen development, for example, seven genes in Clade 1 (OsABCG15, OsLAP5, OsLAP6, DPW, CYP703A3, OsNP1 and OsCP1) are involved in rice pollen wall formation. Furthermore, Clade 1 contained 12 genes whose predicted orthologs in Arabidopsis have been reported as key during pollen development and may play similar roles in rice. Genes in Clade 2 are expressed earlier than Clade 1 (anther stages 2-9), while genes in Clade 3 are expressed later (stages 10-12). RiceAntherNet serves as a valuable tool for identifying novel genes during plant anther and pollen development. A website is provided (https://www.cpib.ac.uk/anther/riceindex.html) to present the expression profiles for gene characterization. This will assist in determining the key relationships between genes, thus enabling characterization of critical genes associated with anther and pollen regulatory networks.

A Non-Classical Member of the Protein Disulfide Isomerase Family, PDI7 of Arabidopsis thaliana, Localizes to the cis-Golgi and Endoplasmic Reticulum Membranes

Members of the protein disulfide isomerase (PDI)-C subfamily are chimeric proteins containing the thioredoxin (Trx) domain of PDIs, and the conserved N- and C-terminal Pfam domains of Erv41p/Erv46p-type cargo receptors. They are unique to plants and chromalveolates. The Arabidopsis genome encodes three PDI-C isoforms: PDI7, PDI12 and PDI13. Here we demonstrate that PDI7 is a 65 kDa integral membrane glycoprotein expressed throughout many Arabidopsis tissues. Using a PDI7-specific antibody, we show through immunoelectron microscopy that PDI7 localizes to the endoplasmic reticulum (ER) and Golgi membranes in wild-type root tip cells, and was also detected in vesicles. Tomographic modeling of the Golgi revealed that PDI7 was confined to the cis-Golgi, and accumulated primarily at the cis-most cisterna. Shoot apical meristem cells from transgenic plants overexpressing PDI7 exhibited a dramatic increase in anti-PDI7 labeling at the cis-Golgi. When N- or C-terminal fusions between PDI7 and the green fluorescent protein variant, GFP(S65T), were expressed in mesophyll protoplasts, the fusions co-localized with the ER marker, ER-mCherry. However, when GFP(S65T) was positioned internally within PDI7 (PDI7-GFPint), the fusion strongly co-localized with the cis-Golgi marker, mCherry-SYP31, and faintly labeled the ER. In contrast to the Golgi-resident fusion protein (Man49-mCherry), PDI7-GFPint did not redistribute to the ER after brefeldin A treatment. Protease protection experiments indicated that the Trx domain of PDI7 is located within the ER/Golgi lumen. We propose a model where PDI-C isoforms function as cargo receptors for proteins containing exposed cysteine residues, cycling them from the Golgi back to the ER.

Nitrogen remobilization during leaf senescence: lessons from Arabidopsis to crops

As a result of climate changes, land use and agriculture have to adapt to new demands. Agriculture is responsible for a large part of the greenhouse gas (GHG) emissions that have to be urgently reduced in order to protect the environment. At the same time, agriculture has to cope with the challenges of sustainably feeding a growing world population. Reducing the use of the ammonia-nitrate fertilizers that are responsible for a large part of the GHGs released and that have a negative impact on carbon balance is one of the objectives of precision agriculture. One way to reduce N fertilizers without dramatically affecting grain yields is to improve the nitrogen recycling and remobilization performances of plants. Mechanisms involved in nitrogen recycling, such as autophagy, are essential for nutrient remobilization at the whole-plant level and for seed quality. Studies on leaf senescence and nutrient recycling provide new perspectives for improvement. The aim of this review is to give an overview of the mechanisms involved in nitrogen recycling and remobilization during leaf senescence and to present the different approaches undertaken to improve nitrogen remobilization efficiency using both model plants and crop species.