Genes encoding plant-specific class III peroxidases are responsible for increased cold tolerance of the brassinosteroid-insensitive 1 mutant

RNA-seq-based comparative transcriptome analysis reveals the role of CsPrx73 in waterlogging-triggered adventitious root formation in cucumber

Abiotic stressors like waterlogging are detrimental to cucumber development and growth. However, comprehension of the highly complex molecular mechanism underlying waterlogging can provide an opportunity to enhance cucumber tolerance under waterlogging stress. We examined the hypocotyl and stage-specific transcriptomes of the waterlogging-tolerant YZ026A and the waterlogging-sensitive YZ106A, which had different adventitious rooting ability under waterlogging. YZ026A performed better under waterlogging stress by altering its antioxidative machinery and demonstrated a greater superoxide ion (O 2-) scavenging ability. KEGG pathway enrichment analysis showed that a high number of differentially expressed genes (DEGs) were enriched in phenylpropanoid biosynthesis. By pairwise comparison and weighted gene co-expression network analysis analysis, 2616 DEGs were obtained which were categorized into 11 gene co-expression modules. Amongst the 11 modules, black was identified as the common module and yielded a novel key regulatory gene, CsPrx73. Transgenic cucumber plants overexpressing CsPrx73 enhance adventitious root (AR) formation under waterlogging conditions and increase reactive oxygen species (ROS) scavenging. Silencing of CsPrx73 expression by virus-induced gene silencing adversely affects AR formation under the waterlogging condition. Our results also indicated that CsERF7-3, a waterlogging-responsive ERF transcription factor, can directly bind to the ATCTA-box motif in the CsPrx73 promoter to initiate its expression. Overexpression of CsERF7-3 enhanced CsPrx73 expression and AR formation. On the contrary, CsERF7-3-silenced plants decreased CsPrx73 expression and rooting ability. In conclusion , our study demonstrates a novel CsERF7-3-CsPrx73 module that allows cucumbers to adapt more efficiently to waterlogging stress by promoting AR production and ROS scavenging.

Genome-Wide Investigation of Class III Peroxidase Genes in Brassica napus Reveals Their Responsiveness to Abiotic Stresses

Brassica napus (B. napus) is susceptible to multiple abiotic stresses that can affect plant growth and development, ultimately reducing crop yields. In the past, many genes that provide tolerance to abiotic stresses have been identified and characterized. Peroxidase (POD) proteins, members of the oxidoreductase enzyme family, play a critical role in protecting plants against abiotic stresses. This study demonstrated a comprehensive investigation of the POD gene family in B. napus. As a result, a total of 109 POD genes were identified across the 19 chromosomes and classified into five distinct subgroups. Further, 44 duplicate events were identified; of these, two gene pairs were tandem and 42 were segmental. Synteny analysis revealed that segmental duplication was more prominent than tandem duplication among POD genes. Expression pattern analysis based on the RNA-seq data of B. napus indicated that BnPOD genes were expressed differently in various tissues; most of them were expressed in roots rather than in other tissues. To validate these findings, we performed RT-qPCR analysis on ten genes; these genes showed various expression levels under abiotic stresses. Our findings not only furnish valuable insights into the evolutionary dynamics of the BnPOD gene family but also serve as a foundation for subsequent investigations into the functional roles of POD genes in B. napus.

MdPRX34L, a class III peroxidase gene, activates the immune response in apple to the fungal pathogen Botryosphaeria dothidea

MAIN CONCLUSION

MdPRX34L enhanced resistance to Botryosphaeria dothidea by increasing salicylic acid (SA) and abscisic acid (ABA) content as well as the expression of related defense genes. The class III peroxidase (PRX) multigene family is involved in complex biological processes. However, the molecular mechanism of PRXs in the pathogen defense of plants against Botryosphaeria dothidea (B. dothidea) remains unclear. Here, we cloned the PRX gene MdPRX34L, which was identified as a positive regulator of the defense response to B. dothidea, from the apple cultivar 'Royal Gala.' Overexpression of MdPRX34L in apple calli decreased sensitivity to salicylic acid (SA) and abscisic acid（ABA). Subsequently, overexpression of MdPRX34L in apple calli increased resistance to B. dothidea infection. In addition, SA contents and the expression levels of genes related to SA synthesis and signaling in apple calli overexpressing MdPRX34L were higher than those in the control after inoculation, suggesting that MdPRX34L enhances resistance to B. dothidea via the SA pathway. Interestingly, infections in apple calli by B. dothidea caused an increase in endogenous levels of ABA followed by induction of ABA-related genes expression. These findings suggest a potential mechanism by which MdPRX34L enhances plant-pathogen defense against B. dothidea by regulating the SA and ABA pathways.

Key candidate genes for male sterility in peppers unveiled via transcriptomic and proteomic analyses

This study aimed to enhance the use of male sterility in pepper to select superior hybrid generations. Transcriptomic and proteomic analyses of fertile line 1933A and nucleic male sterility line 1933B of Capsicum annuum L. were performed to identify male sterility-related proteins and genes. The phylogenetic tree, physical and chemical characteristics, gene structure characteristics, collinearity and expression characteristics of candidate genes were analyzed. The study identified 2,357 differentially expressed genes, of which 1,145 and 229 were enriched in the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases, respectively. A total of 7,628 quantifiable proteins were identified and 29 important proteins and genes were identified. It is worth noting that the existence of CaPRX genes has been found in both proteomics and transcriptomics, and 3 CaPRX genes have been identified through association analysis. A total of 66 CaPRX genes have been identified at the genome level, which are divided into 13 subfamilies, all containing typical CaPRX gene conformal domains. It is unevenly distributed across 12 chromosomes (including the virtual chromosome Chr00). Salt stress and co-expression analysis show that male sterility genes are expressed to varying degrees, and multiple transcription factors are co-expressed with CaPRXs, suggesting that they are involved in the induction of pepper salt stress. The study findings provide a theoretical foundation for genetic breeding by identifying genes, metabolic pathways, and molecular mechanisms involved in male sterility in pepper.

MicroRNA397 regulates tolerance to drought and fungal infection by regulating lignin deposition in chickpea root

Plants deposit lignin in the secondary cell wall as a common response to drought and pathogen attacks. Cell wall localised multicopper oxidase family enzymes LACCASES (LACs) catalyse the formation of monolignol radicals and facilitate lignin formation. We show an upregulation of the expression of several LAC genes and a downregulation of microRNA397 (CamiR397) in response to natural drought in chickpea roots. CamiR397 was found to target LAC4 and LAC17L out of twenty annotated LACs in chickpea. CamiR397 and its target genes are expressed in the root. Overexpression of CamiR397 reduced expression of LAC4 and LAC17L and lignin deposition in chickpea root xylem causing reduction in xylem wall thickness. Downregulation of CamiR397 activity by expressing a short tandem target mimic (STTM397) construct increased root lignin deposition in chickpea. CamiR397-overexpressing and STTM397 chickpea lines showed sensitivity and tolerance, respectively, towards natural drought. Infection with a fungal pathogen Macrophomina phaseolina, responsible for dry root rot (DRR) disease in chickpea, induced local lignin deposition and LAC gene expression. CamiR397-overexpressing and STTM397 chickpea lines showed more sensitivity and tolerance, respectively, to DRR. Our results demonstrated the regulatory role of CamiR397 in root lignification during drought and DRR in an agriculturally important crop chickpea.

Specialist root herbivore modulates plant transcriptome and downregulates defensive secondary metabolites in a brassicaceous plant

Plants face attackers aboveground and belowground. Insect root herbivores can lead to severe crop losses, yet the underlying transcriptomic responses have rarely been studied. We studied the dynamics of the transcriptomic response of Brussels sprouts (Brassica oleracea var. gemmifera) primary roots to feeding damage by cabbage root fly larvae (Delia radicum), alone or in combination with aboveground herbivory by cabbage aphids (Brevicoryne brassicae) or diamondback moth caterpillars (Plutella xylostella). This was supplemented with analyses of phytohormones and the main classes of secondary metabolites; aromatic, indole and aliphatic glucosinolates. Root herbivory leads to major transcriptomic rearrangement that is modulated by aboveground feeding caterpillars, but not aphids, through priming soon after root feeding starts. The root herbivore downregulates aliphatic glucosinolates. Knocking out aliphatic glucosinolate biosynthesis with CRISPR-Cas9 results in enhanced performance of the specialist root herbivore, indicating that the herbivore downregulates an effective defence. This study advances our understanding of how plants cope with root herbivory and highlights several novel aspects of insect-plant interactions for future research. Further, our findings may help breeders develop a sustainable solution to a devastating root pest.

Transcriptomic Analysis Reveals the Correlation between End-of-Day Far Red Light and Chilling Stress in Setaria viridis

Low temperature and end-of-day far-red (EOD-FR) light signaling are two key factors limiting plant production and geographical location worldwide. However, the transcriptional dynamics of EOD-FR light conditions during chilling stress remain poorly understood. Here, we performed a comparative RNA-Seq-based approach to identify differentially expressed genes (DEGs) related to EOD-FR and chilling stress in Setaria viridis. A total of 7911, 324, and 13431 DEGs that responded to low temperature, EOD-FR and these two stresses were detected, respectively. Further DEGs analysis revealed that EOD-FR may enhance cold tolerance in plants by regulating the expression of genes related to cold tolerance. The result of weighted gene coexpression network analysis (WGCNA) using 13431 nonredundant DEGs exhibited 15 different gene network modules. Interestingly, a CO-like transcription factor named BBX2 was highly expressed under EOD-FR or chilling conditions. Furthermore, we could detect more expression levels when EOD-FR and chilling stress co-existed. Our dataset provides a valuable resource for the regulatory network involved in EOD-FR signaling and chilling tolerance in C₄ plants.

Deacclimation-Induced Changes of Photosynthetic Efficiency, Brassinosteroid Homeostasis and BRI1 Expression in Winter Oilseed Rape (Brassica napus L.)—Relation to Frost Tolerance

The objective of this study was to answer the question of how the deacclimation process affects frost tolerance, photosynthetic efficiency, brassinosteroid (BR) homeostasis and BRI1 expression of winter oilseed rape. A comparative study was conducted on cultivars with different agronomic and physiological traits. The deacclimation process can occur when there are periods of higher temperatures, particularly in the late autumn or winter. This interrupts the process of the acclimation (hardening) of winter crops to low temperatures, thus reducing their frost tolerance and becoming a serious problem for agriculture. The experimental model included plants that were non-acclimated, cold acclimated (at 4 ∘C) and deacclimated (at 16 ∘C/9 ∘C, one week). We found that deacclimation tolerance (maintaining a high frost tolerance despite warm deacclimating periods) was a cultivar-dependent trait. Some of the cultivars developed a high frost tolerance after cold acclimation and maintained it after deacclimation. However, there were also cultivars that had a high frost tolerance after cold acclimation but lost some of it after deacclimation (the cultivars that were more susceptible to deacclimation). Deacclimation reversed the changes in the photosystem efficiency that had been induced by cold acclimation, and therefore, measuring the different signals associated with photosynthetic efficiency (based on prompt and delayed chlorophyll fluorescence) of plants could be a sensitive tool for monitoring the deacclimation process (and possible changes in frost tolerance) in oilseed rape. Higher levels of BR were characteristic of the better frost-tolerant cultivars in both the cold-acclimated and deacclimated plants. The relative expression of the BRI1 transcript (encoding the BR-receptor protein) was lower after cold acclimation and remained low in the more frost-tolerant cultivars after deacclimation. The role of brassinosteroids in oilseed rape acclimation/deacclimation is briefly discussed.

Class III Peroxidases in Response to Multiple Abiotic Stresses in Arabidopsis thaliana Pyrenean Populations

Class III peroxidases constitute a plant-specific multigene family, where 73 genes have been identified in Arabidopsis thaliana. These genes are members of the reactive oxygen species (ROS) regulatory network in the whole plant, but more importantly, at the root level. In response to abiotic stresses such as cold, heat, and salinity, their expression is significantly modified. To learn more about their transcriptional regulation, an integrative phenotypic, genomic, and transcriptomic study was executed on the roots of A. thaliana Pyrenean populations. Initially, the root phenotyping highlighted 3 Pyrenean populations to be tolerant to cold (Eaux), heat (Herr), and salt (Grip) stresses. Then, the RNA-seq analyses on these three populations, in addition to Col-0, displayed variations in CIII Prxs expression under stressful treatments and between different genotypes. Consequently, several CIII Prxs were particularly upregulated in the tolerant populations, suggesting novel and specific roles of these genes in plant tolerance against abiotic stresses.

Apoplastic class III peroxidases PRX62 and PRX69 promote Arabidopsis root hair growth at low temperature

Root Hairs (RHs) growth is influenced by endogenous and by external environmental signals that coordinately regulate its final cell size. We have recently determined that RH growth was unexpectedly boosted when Arabidopsis thaliana seedlings are cultivated at low temperatures. It was proposed that RH growth plasticity in response to low temperature was linked to a reduced nutrient availability in the media. Here, we explore the molecular basis of this RH growth response by using a Genome Wide Association Study (GWAS) approach using Arabidopsis thaliana natural accessions. We identify the poorly characterized PEROXIDASE 62 (PRX62) and a related protein PRX69 as key proteins under moderate low temperature stress. Strikingly, a cell wall protein extensin (EXT) reporter reveals the effect of peroxidase activity on EXT cell wall association at 10 °C in the RH apical zone. Collectively, our results indicate that PRX62, and to a lesser extent PRX69, are key apoplastic PRXs that modulate ROS-homeostasis and cell wall EXT-insolubilization linked to RH elongation at low temperature.

The IbBBX24-IbTOE3-IbPRX17 module enhances abiotic stress tolerance by scavenging reactive oxygen species in sweet potato

Soil salinity and drought limit sweet potato yield. Scavenging of reactive oxygen species (ROS) by peroxidases (PRXs) is essential during plant stress responses, but how PRX expression is regulated under abiotic stress is not well understood. Here, we report that the B-box (BBX) family transcription factor IbBBX24 activates the expression of the class III peroxidase gene IbPRX17 by binding to its promoter. Overexpression of IbBBX24 and IbPRX17 significantly improved the tolerance of sweet potato to salt and drought stresses, whereas reducing IbBBX24 expression increased their susceptibility. Under abiotic stress, IbBBX24- and IbPRX17-overexpression lines showed higher peroxidase activity and lower H₂ O₂ accumulation compared with the wild-type. RNA sequencing analysis revealed that IbBBX24 modulates the expression of genes encoding ROS scavenging enzymes, including PRXs. Moreover, interaction between IbBBX24 and the APETALA2 (AP2) protein IbTOE3 enhances the ability of IbBBX24 to activate IbPRX17 transcription. Overexpression of IbTOE3 improved the tolerance of tobacco plants to salt and drought stresses by scavenging ROS. Together, our findings elucidate the mechanism underlying the IbBBX24-IbTOE3-IbPRX17 module in response to abiotic stress in sweet potato and identify candidate genes for developing elite crop varieties with enhanced abiotic stress tolerance.

Genome-wide characterization and functional analysis of class III peroxidase gene family in soybean reveal regulatory roles of GsPOD40 in drought tolerance

Class III peroxidases (PODs) are plant-specific glycoproteins, that play essential roles in various plant physiological processes and defence responses. To date, scarce information is available about the POD gene family in soybean. Hence, the present study is the first comprehensive report about the genome-wide characterization of GmPOD gene family in soybean (Glycine max L.). Here, we identified a total of 124 GmPOD genes in soybean, that are unevenly distributed across the genome. Phylogenetic analysis classified them into six distinct sub-groups (A-F), with one soybean specific subgroup. Exon-intron and motif analysis suggested the existence of structural and functional diversity among the sub-groups. Duplication analysis identified 58 paralogous gene pairs; segmental duplication and positive/Darwinian selection were observed as the major factors involved in the evolution of GmPODs. Furthermore, RNA-seq analysis revealed that 23 out of a total 124 GmPODs showed differential expression between drought-tolerant and drought-sensitive genotypes under stress conditions; however, two of them (GmPOD40 and GmPOD42) revealed the maximum deregulation in all contrasting genotypes. Overexpression (OE) lines of GsPOD40 showed considerably higher drought tolerance compared to wild type (WT) plants under stress treatment. Moreover, the OE lines showed enhanced photosynthesis and enzymatic antioxidant activities under drought stress, resulting in alleviation of ROS induced oxidative damage. Hence, the GsPOD40 enhanced drought tolerance in soybean by regulating the key physiological and biochemical pathways involved in the defence response. Lastly, the results of our study will greatly assist in further functional characterization of GsPODs in plant growth and stress tolerance in soybean.

Evaluation of high salinity tolerance in Pongamia pinnata (L.) Pierre by a systematic analysis of hormone-metabolic network

Salinity stress results in significant losses in plant productivity and loss of cultivable lands. Although Pongamia pinnata is reported to be a salt-tolerant semiarid biofuel tree, the adaptive mechanisms to saline environments are elusive. Despite a reduction in carbon exchange rate (CER), the unchanged relative water content provides no visible salinity induced symptoms in leaves of hydroponic cultivated Pongamia seedlings for 8 days. Our Na⁺ -specific fluorescence results demonstrated that there was an effective apoplastic sodium sequestration in the roots. Salinity stress significantly increased zeatin (~5.5-fold), and jasmonic acid (~3.8-fold) levels in leaves while zeatin (~2.5-fold) content increased in leaves as well as in roots of salt-treated plants. Metabolite analysis suggested that osmolytes such as myo-inositol and mannitol were enhanced by ~12-fold in leaves and roots of salt-treated plants. Additionally, leaves of Pongamia showed a significant enhancement in carbohydrate content, while fatty acids were accumulated in roots under salt stress condition. At the molecular level, salt stress enhanced the expression of genes related to transporters, including the Salt Overly Sensitive 2 gene (SOS2), SOS3, vacuolar-cation/proton exchanger, and vacuolar-proton/ATPase exclusively in leaves, whereas the Sodium Proton Exchanger1 (NHX1), Cation Calcium Exchanger (CCX), and Cyclic Nucleotide Gated Channel 5 (CNGC5) were up-regulated in roots. Antioxidant gene expression analysis clearly demonstrated that peroxidase levels were significantly enhanced by ~10-fold in leaves, while Catalase and Fe-superoxide Dismutase (Fe-SOD) genes were increased in roots under salt stress. The correlation interaction studies between phytohormones and metabolites revealed new insights into the molecular and metabolic adaptations that confer salinity tolerance to Pongamia.

Evolutionary Implications of a Peroxidase with High Affinity for Cinnamyl Alcohols from Physcomitrium patens, a Non-Vascular Plant

Physcomitrium (Physcomitrella) patens is a bryophyte highly tolerant to different stresses, allowing survival when water supply is a limiting factor. This moss lacks a true vascular system, but it has evolved a primitive water-conducting system that contains lignin-like polyphenols. By means of a three-step protocol, including ammonium sulfate precipitation, adsorption chromatography on phenyl Sepharose and cationic exchange chromatography on SP Sepharose, we were able to purify and further characterize a novel class III peroxidase, PpaPrx19, upregulated upon salt and H₂O₂ treatments. This peroxidase, of a strongly basic nature, shows surprising homology to angiosperm peroxidases related to lignification, despite the lack of true lignins in P. patens cell walls. Moreover, PpaPrx19 shows catalytic and kinetic properties typical of angiosperm peroxidases involved in oxidation of monolignols, being able to efficiently use hydroxycinnamyl alcohols as substrates. Our results pinpoint the presence in P. patens of peroxidases that fulfill the requirements to be involved in the last step of lignin biosynthesis, predating the appearance of true lignin.

Genome-wide expression and network analyses of mutants in key brassinosteroid signaling genes

BACKGROUND

Brassinosteroid (BR) signaling regulates plant growth and development in concert with other signaling pathways. Although many genes have been identified that play a role in BR signaling, the biological and functional consequences of disrupting those key BR genes still require detailed investigation.

RESULTS

Here we performed phenotypic and transcriptomic comparisons of A. thaliana lines carrying a loss-of-function mutation in BRI1 gene, bri1-5, that exhibits a dwarf phenotype and its three activation-tag suppressor lines that were able to partially revert the bri1-5 mutant phenotype to a WS2 phenotype, namely bri1-5/bri1-1D, bri1-5/brs1-1D, and bri1-5/bak1-1D. From the three investigated bri1-5 suppressors, bri1-5/bak1-1D was the most effective suppressor at the transcriptional level. All three bri1-5 suppressors showed altered expression of the genes in the abscisic acid (ABA signaling) pathway, indicating that ABA likely contributes to the partial recovery of the wild-type phenotype in these bri1-5 suppressors. Network analysis revealed crosstalk between BR and other phytohormone signaling pathways, suggesting that interference with one hormone signaling pathway affects other hormone signaling pathways. In addition, differential expression analysis suggested the existence of a strong negative feedback from BR signaling on BR biosynthesis and also predicted that BRS1, rather than being directly involved in signaling, might be responsible for providing an optimal environment for the interaction between BRI1 and its ligand.

CONCLUSIONS

Our study provides insights into the molecular mechanisms and functions of key brassinosteroid (BR) signaling genes, especially BRS1.

Brassinosteroids application induces phosphatidic acid production and modify antioxidant enzymes activity in tobacco in calcium-dependent manner

Brassinosteroids (BRs) are steroid hormones regulating various aspects of plant metabolism, including growth, development and stress responses. However, little is known about the mechanism of their impact on antioxidant systems and phospholipid turnover. Using tobacco plants overexpressing H+/Ca2+vacuolar Arabidopsis antiporter CAX1, we showed the role of Ca2+ ion balance in the reactive oxygen species production and rapid phosphatidic acid accumulation induced by exogenous BR. Combination of our experimental results with public transcriptomic and proteomic data revealed a particular role of Ca2+-dependent phospholipid metabolizing enzymes in BR signaling. Here we provide novel insights into the role of calcium balance and lipid-derived second messengers in plant responses to exogenous BRs and propose a complex model integrating BR-mediated metabolic changes with phospholipid turnover.

Natural population re-sequencing detects the genetic basis of local adaptation to low temperature in a woody plant

Total of 14 SNPs associated with overwintering-related traits and 75 selective regions were detected. Important candidate genes were identified and a possible network of cold-stress responses in woody plants was proposed. Local adaptation to low temperature is essential for woody plants to against changeable climate and safely survive the winter. To uncover the specific molecular mechanism of low temperature adaptation in woody plants, we sequenced 134 core individuals selected from 494 paper mulberry (Broussonetia papyrifera), which naturally distributed in different climate zones and latitudes. The population structure analysis, PCA analysis and neighbor-joining tree analysis indicated that the individuals were classified into three clusters, which showed forceful geographic distribution patterns because of the adaptation to local climate. Using two overwintering phenotypic data collected at high latitudes of 40°N and one bioclimatic variable, genome-phenotype and genome-environment associations, and genome-wide scans were performed. We detected 75 selective regions which possibly undergone temperature selection and identified 14 trait-associated SNPs that corresponded to 16 candidate genes (including LRR-RLK, PP2A, BCS1, etc.). Meanwhile, low temperature adaptation was also supported by other three trait-associated SNPs which exhibiting significant differences in overwintering traits between alleles within three geographic groups. To sum up, a possible network of cold signal perception and responses in woody plants were proposed, including important genes that have been confirmed in previous studies while others could be key potential candidates of woody plants. Overall, our results highlighted the specific and complex molecular mechanism of low temperature adaptation and overwintering of woody plants.

Class III peroxidase: an indispensable enzyme for biotic/abiotic stress tolerance and a potent candidate for crop improvement

Class III peroxidases are secretory enzymes which belong to a ubiquitous multigene family in higher plants and have been identified to play role in a broad range of physiological and developmental processes. Potentially, it is involved in generation and detoxification of hydrogen peroxide (H₂O₂), and their subcellular localization reflects through three different cycles, namely peroxidative cycle, oxidative and hydroxylic cycles to maintain the ROS level inside the cell. Being an antioxidant, class III peroxidases are an important initial defence adapted by plants to cope with biotic and abiotic stresses. Both these stresses have become a major concern in the field of agriculture due to their devastating effect on plant growth and development. Despite numerous studies on plant defence against both the stresses, only a handful role of class III peroxidases have been uncovered by its functional characterization. This review will cover our current understanding on class III peroxidases and the signalling involved in their regulation under both types of stresses. The review will give a view of class III peroxidases and highlights their indispensable role under stress conditions. Its future application will be discussed to showcase their importance in crop improvement by genetic manipulation and by transcriptome analysis.

Integrated Analysis of the Transcriptome and Metabolome of Cecropia obtusifolia: A Plant with High Chlorogenic Acid Content Traditionally Used to Treat Diabetes Mellitus

This investigation cultured Cecropia obtusifolia cells in suspension to evaluate the effect of nitrate deficiency on the growth and production of chlorogenic acid (CGA), a secondary metabolite with hypoglycemic and hypolipidemic activity that acts directly on type 2 diabetes mellitus. Using cell cultures in suspension, a kinetics time course was established with six time points and four total nitrate concentrations. The metabolites of interest were quantified by high-performance liquid chromatography (HPLC), and the metabolome was analyzed using directed and nondirected approaches. Finally, using RNA-seq methodology, the first transcript collection for C. obtusifolia was generated. HPLC analysis detected CGA at all sampling points, while metabolomic analysis confirmed the identity of CGA and of precursors involved in its biosynthesis. Transcriptome analysis identified differentially expressed genes and enzymes involved in the biosynthetic pathway of CGA. C. obtusifolia probably expresses a key enzyme with bifunctional activity, the hydroxycinnamoyl-CoA quinate hydroxycinnamoyl transferase and hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase (HQT/HCT), which recognizes shikimic acid or quinic acid as a substrate and incorporates either into one of the two routes responsible for CGA biosynthesis.

Molecular basis for neofunctionalization of duplicated E3 ubiquitin ligases underlying adaptation to drought tolerance in Arabidopsis thaliana

Multigene families in plants expanded from ancestral genes via gene duplication mechanisms constitute a significant fraction of the coding genome. Although most duplicated genes are lost over time, many are retained in the genome. Clusters of tandemly arrayed genes are commonly found in the plant genome where they can promote expansion of gene families. In the present study, promoter fusion to the GUS reporter gene was used to examine the promoter architecture of duplicated E3 ligase genes that are part of group C in the Arabidopsis thaliana ATL family. Acquisition of gene expression by AtATL78, possibly generated from defective AtATL81 expression, is described. AtATL78 expression was purportedly enhanced by insertion of a TATA box within the core promoter region after a short tandem duplication that occurred during evolution of Brassicaceae lineages. This gene is associated with an adaptation to drought tolerance of A. thaliana. These findings also suggest duplicated genes could serve as a reservoir of tacit genetic information, and expression of these duplicated genes is activated upon acquisition of core promoter sequences. Remarkably, drought transcriptome profiling in response to rehydration suggests that ATL78-dependent gene expression predominantly affects genes with root-specific activities.

Genome-wide identification of the class III POD gene family and their expression profiling in grapevine (Vitis vinifera L)

BACKGROUND

The class III peroxidases (PODs) are involved in a broad range of physiological activities, such as the formation of lignin, cell wall components, defense against pathogenicity or herbivore, and abiotic stress tolerance. The POD family members have been well-studied and characterized by bioinformatics analysis in several plant species, but no previous genome-wide analysis has been carried out of this gene family in grapevine to date.

RESULTS

We comprehensively identified 47 PODs in the grapevine genome and are further classified into 7 subgroups based on their phylogenetic analysis. Results of motif composition and gene structure organization analysis revealed that PODs in the same subgroup shared similar conjunction while the protein sequences were highly conserved. Intriguingly, the integrated analysis of chromosomal mapping and gene collinearity analysis proposed that both dispersed and tandem duplication events contributed to the expansion of PODs in grapevine. Also, the gene duplication analysis suggested that most of the genes (20) were dispersed followed by (15) tandem, (9) segmental or whole-genome duplication, and (3) proximal, respectively. The evolutionary analysis of PODs, such as Ka/Ks ratio of the 15 duplicated gene pairs were less than 1.00, indicated that most of the gene pairs exhibiting purifying selection and 7 pairs underwent positive selection with value greater than 1.00. The Gene Ontology Enrichment (GO), Kyoto Encyclopedia of Genes Genomics (KEGG) analysis, and cis-elements prediction also revealed the positive functions of PODs in plant growth and developmental activities, and response to stress stimuli. Further, based on the publically available RNA-sequence data, the expression patterns of PODs in tissue-specific response during several developmental stages revealed diverged expression patterns. Subsequently, 30 genes were selected for RT-PCR validation in response to (NaCl, drought, and ABA), which showed their critical role in grapevine.

CONCLUSIONS

In conclusion, we predict that these results will lead to novel insights regarding genetic improvement of grapevine.

The ethylene responsive factor CdERF1 from bermudagrass (Cynodon dactylon) positively regulates cold tolerance

Cold stress is one of the major environmental factors that limit growth and utilization of bermudagrass [Cynodon dactylon (L.) Pers], a prominent warm-season turfgrass. However, the molecular mechanism of cold response in bermudagrass remains largely unknown. In this study, we characterized a cold-responsive ERF (ethylene responsive factor) transcription factor, CdERF1, from bermudagrass. CdERF1 expression was induced by cold, drought and salinity stresses. The CdERF1 protein was nucleus-localized and encompassed transcriptional activation activity. Transgenic Arabidopsis plants overexpressing CdERF1 showed enhanced cold tolerance, whereas CdERF1-underexpressing bermudagrass plants via virus induced gene silencing (VIGS) method exhibited reduced cold resistance compared with control, respectively. Under cold stress, electrolyte leakage (EL), malondialdehyde (MDA), H₂O₂ and O₂^- contents were reduced, while the activities of SOD and POD were elevated in transgenic Arabidopsis. By contrast, these above physiological indicators in CdERF1-underexpressing bermudagrass exhibited the opposite trend. To further explore the possible molecular mechanism of bermudagrass cold stress response, the RNA-Seq analyses were performed. The result indicated that overexpression of CdERF1 activated a subset of stress-related genes in transgenic Arabidopsis, such as CBF2, pEARLI1 (lipid transfer protein), PER71 (peroxidase) and LTP (lipid transfer protein). Interestingly, under-expression of CdERF1 suppressed the transcription of many genes in CdERF1-underexpressing bermudagrass, also including pEARLI1 (lipid transfer protein) and PER70 (peroxidase). All these results revealed that CdERF1 positively regulates plant cold response probably by activating stress-related genes, PODs, CBF2 and LTPs. This study also suggests that CdERF1 may be an ideal candidate in the effort to improve cold tolerance of bermudagrass in the further molecular breeding.

The TIR-NB-LRR pair DSC1 and WRKY19 contributes to basal immunity of Arabidopsis to the root-knot nematode Meloidogyne incognita

BACKGROUND

Root-knot nematodes transform vascular host cells into permanent feeding structures to withdraw nutrients from the host plant. Ecotypes of Arabidopsis thaliana can display large quantitative variation in susceptibility to the root-knot nematode Meloidogyne incognita, which is thought to be independent of dominant major resistance genes. However, in an earlier genome-wide association study of the interaction between Arabidopsis and M. incognita we identified a quantitative trait locus harboring homologs of dominant resistance genes but with minor effect on susceptibility to the M. incognita population tested.

RESULTS

Here, we report on the characterization of two of these genes encoding the TIR-NB-LRR immune receptor DSC1 (DOMINANT SUPPRESSOR OF Camta 3 NUMBER 1) and the TIR-NB-LRR-WRKY-MAPx protein WRKY19 in nematode-infected Arabidopsis roots. Nematode infection studies and whole transcriptome analyses using the Arabidopsis mutants showed that DSC1 and WRKY19 co-regulate susceptibility of Arabidopsis to M. incognita.

CONCLUSION

Given the head-to-head orientation of DSC1 and WRKY19 in the Arabidopsis genome our data suggests that both genes may function as a TIR-NB-LRR immune receptor pair. Unlike other TIR-NB-LRR pairs involved in dominant disease resistance in plants, DSC1 and WRKY19 most likely regulate basal levels of immunity to root-knot nematodes.

Phytohormones enabled endophytic Penicillium funiculosum LHL06 protects Glycine max L. from synergistic toxicity of heavy metals by hormonal and stress-responsive proteins modulation

This study investigates the stress-mitigating effects of endophytic Penicillium funiculosum LHL06 on soybean roots via modulation of physio-biochemical, molecular, and proteomic responses to combined heavy metal (Ni, Cu, Pb, Cr, and Al) toxicity. Preliminary screening revealed that LHL06 can tolerate and remediate combined heavy metal contamination in its media and upregulate gibberellins (GA1, GA3, GA4, GA7 and GA9) and indole-3-acetic acid (IAA) production. Inoculation of LHL06 resulted in marked reduction of metals uptake in roots and shoots by downregulating heavy metal ATPase genes (GmHMA13, GmHMA14, GmHMA19) and GmMATE1 compared to non-inoculated plants; in turn, this decreased abscisic acid and jasmonic acid levels. Moreover, triggering of free amino acid metabolism in LHL06-inoculated roots significantly upregulated expression of stress-related proteins (glutathione S-transferase L3, isoflavone reductase-like, chalcone isomerase A, NAD(P)H dehydrogenase (quinone), FQR1-like 1 isoform X2, and Peroxidase 3) to combat metals toxicity. Compared to non-inoculated-plants, LHL06-inoculated-plants exhibited higher antioxidant activity and transcript accumulation of glutathione S-transferase (GmGST8 and GmGST3), G6PDH, and GmSOD1[Cu-Zn], which decreased metal-induced reactive oxygen species. Therefore, LHL06-inoculation remediate combined metal contamination in soil, activate signaling network of stress-responsive hormones and antioxidant systems for promoting growth and tolerance, and reduce metal-accumulation, thereby making plants safer for consumption.

Genome-wide and evolutionary analysis of the class III peroxidase gene family in wheat and Aegilops tauschii reveals that some members are involved in stress responses

Background

The class III peroxidase (PRX) gene family is a plant-specific member of the PRX superfamily that is closely related to various physiological processes, such as cell wall loosening, lignification, and abiotic and biotic stress responses. However, its classification, evolutionary history and gene expression patterns are unclear in wheat and Aegilops tauschii.

Results

Here, we identified 374, 159 and 169 PRXs in Triticum aestivum, Triticum urartu and Ae. tauschii, respectively. Together with PRXs detected from eight other plants, they were classified into 18 subfamilies. Among subfamilies V to XVIII, a conserved exon-intron structure within the “001” exon phases was detected in the PRX domain. Based on the analysis, we proposed a phylogenetic model to infer the evolutionary history of the exon-intron structures of PRX subfamilies. A comparative genomics analysis showed that subfamily VII could be the ancient subfamily that originated from green algae (Chlamydomonas reinhardtii). Further integrated analysis of chromosome locations and collinearity events of PRX genes suggested that both whole genome duplication (WGD) and tandem duplication (TD) events contributed to the expansion of T. aestivum PRXs (TaePRXs) during wheat evolution. To validate functions of these genes in the regulation of various physiological processes, the expression patterns of PRXs in different tissues and under various stresses were studied using public microarray datasets. The results suggested that there were distinct expression patterns among different tissues and PRXs could be involved in biotic and abiotic responses in wheat. qRT-PCR was performed on samples exposed to drought, phytohormone treatments and Fusarium graminearum infection to validate the microarray predictions. The predicted subcellular localizations of some TaePRXs were consistent with the confocal microscopy results. We predicted that some TaePRXs had hormone-responsive cis-elements in their promoter regions and validated these predicted cis-acting elements by sequencing promoters.

Conclusion

In this study, identification, classification, evolution, and expression patterns of PRXs in wheat and relative plants were performed. Our results will provide information for further studies on the evolution and molecular mechanisms of wheat PRXs.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-6006-5) contains supplementary material, which is available to authorized users.

Detection of First Marker Trait Associations for Resistance Against Sclerotinia sclerotiorum in Brassica juncea-Erucastrum cardaminoides Introgression Lines

A set of 96 Brassica juncea-Erucastrum cardaminoides introgression lines (ILs) were developed with genomic regions associated with Sclerotinia stem rot (Sclerotinia sclerotiorum) resistance from a wild Brassicaceous species E. cardaminoides. ILs were assessed for their resistance responses to stem inoculation with S. sclerotiorum, over three crop seasons (season I, 2011/2012; II, 2014/2015; III, 2016-2017). Initially, ILs were genotyped with transferable SSR markers and subsequently through genotyping by sequencing. SSR based association mapping identified six marker loci associated to resistance in both A and B genomes. Subsequent genome-wide association analysis (GWAS) of 84 ILs recognized a large number of SNPs associated to resistance, in chromosomes A03, A06, and B03. Chromosomes A03 and A06 harbored the maximum number of resistance related SNPs. Annotation of linked genomic regions highlighted an array of resistance mechanisms in terms of signal transduction pathways, hypersensitive responses and production of anti-fungal proteins and metabolites. Of major importance was the clustering of SNPs, encoding multiple resistance genes on small regions spanning approximately 885 kb region on chromosome A03 and 74 kb on B03. Five SNPs on chromosome A03 (6,390,210-381) were associated with LRR-RLK (receptor like kinases) genes that encode LRR-protein kinase family proteins. Genetic factors associated with pathogen-associated molecular patterns (PAMPs) and effector-triggered immunity (ETI) were predicted on chromosome A03, exhibiting 11 SNPs (6,274,763-994). These belonged to three R-Genes encoding TIR-NBS-LRR proteins. Marker trait associations (MTAs) identified will facilitate marker assisted introgression of these critical resistances, into new cultivars of B. juncea initially and, subsequently, into other crop Brassica species.

ERF109 of trifoliate orange (Poncirus trifoliata (L.) Raf.) contributes to cold tolerance by directly regulating expression of Prx1 involved in antioxidative process

Ethylene-responsive factors (ERFs) have been revealed to play essential roles in a variety of physiological and biological processes in higher plants. However, functions and regulatory pathways of most ERFs in cold stress remain largely unclear. Here, we identified PtrERF109 of trifoliate orange (Poncirus trifoliata (L.) Raf.) and deciphered its role in cold tolerance. PtrERF109 was drastically up-regulated by cold, ethylene and dehydration, but repressed by salt. PtrERF109 was localized in the nucleus and displayed transcriptional activity, and the C terminus is required for the activation. Overexpression of PtrERF109 conferred enhanced cold tolerance in transgenic tobacco and lemon plants, whereas VIGS (virus-induced gene silencing)-mediated suppression of PtrERF109 in trifoliate orange led to increased cold susceptibility. PtrERF109 overexpression caused extensive transcriptional reprogramming of several suites of stress-responsive genes. Prx1 encoding class III peroxidase (POD) was one of the antioxidant genes exhibiting the greatest induction. PtrERF109 was shown to directly bind to the promoter of PtrPrx1 (trifoliate orange Prx1 homologue) and positively activated its expression. In addition, the PtrERF109-overexpressing plants exhibited significantly higher POD activity and accumulated dramatically less H₂ O₂ and were more tolerant to oxidative stress, whereas the VIGS plants exhibited opposite trends, in comparison with wild type. Taken together, these results indicate that PtrERF109 as a positive regulator contributes to imparting cold tolerance by, at least partly, directly regulating the POD-encoding gene to maintain a robust antioxidant capacity for effectively scavenging the reactive oxygen species. Our findings gain insight into better understanding of transcriptional regulation of antioxidant genes in response to cold stress.

Plant Cell Wall Proteomics: A Focus on Monocot Species, Brachypodium distachyon, Saccharum spp. and Oryza sativa

Plant cell walls mostly comprise polysaccharides and proteins. The composition of monocots' primary cell walls differs from that of dicots walls with respect to the type of hemicelluloses, the reduction of pectin abundance and the presence of aromatic molecules. Cell wall proteins (CWPs) differ among plant species, and their distribution within functional classes varies according to cell types, organs, developmental stages and/or environmental conditions. In this review, we go deeper into the findings of cell wall proteomics in monocot species and make a comparative analysis of the CWPs identified, considering their predicted functions, the organs analyzed, the plant developmental stage and their possible use as targets for biofuel production. Arabidopsis thaliana CWPs were considered as a reference to allow comparisons among different monocots, i.e., Brachypodium distachyon, Saccharum spp. and Oryza sativa. Altogether, 1159 CWPs have been acknowledged, and specificities and similarities are discussed. In particular, a search for A. thaliana homologs of CWPs identified so far in monocots allows the definition of monocot CWPs characteristics. Finally, the analysis of monocot CWPs appears to be a powerful tool for identifying candidate proteins of interest for tailoring cell walls to increase biomass yield of transformation for second-generation biofuels production.

Brassinosteroid signaling in plant development and adaptation to stress

Brassinosteroids (BRs) are steroid hormones that are essential for plant growth and development. These hormones control the division, elongation and differentiation of various cell types throughout the entire plant life cycle. Our current understanding of the BR signaling pathway has mostly been obtained from studies using Arabidopsis thaliana as a model. In this context, the membrane steroid receptor BRI1 (BRASSINOSTEROID INSENSITIVE 1) binds directly to the BR ligand, triggering a signal cascade in the cytoplasm that leads to the transcription of BR-responsive genes that drive cellular growth. However, recent studies of the primary root have revealed distinct BR signaling pathways in different cell types and have highlighted cell-specific roles for BR signaling in controlling adaptation to stress. In this Review, we summarize our current knowledge of the spatiotemporal control of BR action in plant growth and development, focusing on BR functions in primary root development and growth, in stem cell self-renewal and death, and in plant adaption to environmental stress.

Summary: This Review summarizes current knowledge of the spatiotemporal control of brassinosteroid function in plants, focusing on primary root development and growth, stem cell self-renewal and death, and adaptation to environmental stress.

Oryza sativa class III peroxidase (OsPRX38) overexpression in Arabidopsis thaliana reduces arsenic accumulation due to apoplastic lignification

ClassIII peroxidases are multigene family of plant-specific peroxidase enzyme. They are involved in various physiological and developmental processes like auxin catabolism, cell metabolism, various biotic, abiotic stresses and cell elongation. In the present study, we identified a class III peroxidase (OsPRX38) from rice which is upregulated several folds in both arsenate (AsV) and arsenite (AsIII) stresses. The overexpression of OsPRX38 in Arabidopsis thaliana significantly enhances Arsenic (As) tolerance by increasing SOD, PRX GST activity and exhibited low H₂O_2, electrolyte leakage and malondialdehyde content. OsPRX38 overexpression also affect the plant growth by increasing total biomass and seeds production in transgenics than WT under As stress condition. Confocal microscopy revealed that the OsPRX38-YFP fusion protein was localized to the apoplast of the onion epidermal cells. In addition, lignification was positively correlated with an increase in cell-wall-associated peroxidase activities in transgenic plants. This study indicates the role of OsPRX38 in lignin biosynthesis, where lignin act as an apoplastic barrier for As entry in root cells leading to reduction of As accumulation in transgenic. Overall the study suggests that overexpression of OsPRX38 in Arabidopsis thaliana activates the signaling network of different antioxidant systems under As stress condition, enhancing the plant tolerance by reducing As accumulation due to high lignification.

Arabidopsis thaliana responds to colonisation of Piriformospora indica by secretion of symbiosis-specific proteins

Plants interact with a wide variety of fungi in a mutualistic, parasitic or neutral way. The associations formed depend on the exchange of nutrients and signalling molecules between the partners. This includes a diverse set of protein classes involved in defence, nutrient uptake or establishing a symbiotic relationship. Here, we have analysed the secretomes of the mutualistic, root-endophytic fungus Piriformospora indica and Arabidopsis thaliana when cultivated alone or in a co-culture. More than one hundred proteins were identified as differentially secreted, including proteins associated with growth, development, abiotic and biotic stress response and mucilage. While some of the proteins have been associated before to be involved in plant-microbial interaction, other proteins are newly described in this context. One plant protein found in the co-culture is PLAT1 (Polycystin, Lipoxygenase, Alpha-toxin and Triacylglycerol lipase). PLAT1 has not been associated with plant-fungal-interaction and is known to play a role in abiotic stress responses. In colonised roots PLAT1 shows an altered gene expression in a stage specific manner and plat1 knock-out plants are colonised stronger. It co-localises with Brassicaceae-specific endoplasmic reticulum bodies (ER-bodies) which are involved in the formation of the defence compound scopolin. We observed degraded ER-bodies in infected Arabidopsis roots and a change in the scopolin level in response to the presence of the fungus.

An atypical R2R3 MYB transcription factor increases cold hardiness by CBF-dependent and CBF-independent pathways in apple

Apple (Malus × domestica) trees are vulnerable to freezing temperatures. However, there has been only limited success in developing cold-hardy cultivars. This lack of progress is due at least partly to lack of understanding of the molecular mechanisms of freezing tolerance in apple. In this study, we evaluated the potential roles for two R2R3 MYB transcription factors (TFs), MYB88 and the paralogous FLP (MYB124), in cold stress in apple and Arabidopsis. We found that MYB88 and MYB124 positively regulate freezing tolerance and cold-responsive gene expression in both apple and Arabidopsis. Chromatin-Immunoprecipitation-qPCR and electrophoretic mobility shift assays showed that MdMYB88/MdMYB124 act as direct regulators of the COLD SHOCK DOMAIN PROTEIN 3 (MdCSP3) and CIRCADIAN CLOCK ASSOCIATED 1 (MdCCA1) genes. Dual luciferase reporter assay indicated that MdCCA1 but not MdCSP3 activated the expression of MdCBF3 under cold stress. Moreover, MdMYB88 and MdMYB124 promoted anthocyanin accumulation and H₂ O₂ detoxification in response to cold. Taken together, our results suggest that MdMYB88 and MdMYB124 positively regulate cold hardiness and cold-responsive gene expression under cold stress by C-REPEAT BINDING FACTOR (CBF)-dependent and CBF-independent pathways.

Functional Characterization of the Steroid Reductase Genes GmDET2a and GmDET2b form Glycine max

Brassinosteroids are important phytohormones for plant growth and development. In soybean (Glycine max), BR receptors have been identified, but the genes encoding BR biosynthesis-related enzymes remain poorly understood. Here, we found that the soybean genome encodes eight steroid reductases (GmDET2a to GmDET2h). Phylogenetic analysis grouped 105 steroid reductases from moss, fern and higher plants into five subgroups and indicated that the steroid reductase family has experienced purifying selection. GmDET2a and GmDET2b, homologs of the Arabidopsis thaliana steroid 5 α -reductase AtDET2, are proteins of 263 amino acids. Ectopic expression of GmDET2a and GmDET2b rescued the defects of the Atdet2-1 mutant in both darkness and light. Compared to the mutant, the hypocotyl length and plant height of the transgenic lines GmDET2a and GmDET2b increased significantly, in both darkness and light, and the transcript levels of the BR biosynthesis-related genes CPD, DWF4, BR6ox-1 and BR6ox-2 were downregulated in GmDET2aOX-23 and GmDET2bOX-16 lines compared to that in Atdet2-1. Quantitative real-time PCR revealed that GmDET2a and GmDET2b are ubiquitously expressed in all tested soybean organs, including roots, leaves and hypocotyls. Moreover, epibrassinosteroid negatively regulated GmDET2a and GmDET2b expression. Sulfate deficiency downregulated GmDET2a in leaves and GmDET2b in leaves and roots; by contrast, phosphate deficiency upregulated GmDET2b in roots and leaves. Taken together, our results revealed that GmDET2a and GmDET2b function as steroid reductases.

Selective responses of class III plant peroxidase isoforms to environmentally relevant UV-B doses

Efficient hydrogen peroxide detoxification is an essential aspect of plant defence against a large variety of stressors. Among others, class III peroxidase (POD, EC 1.11.1.7) enzymes provide this function. Previous studies have shown that PODs are present in several isoforms and have in general low substrate specificities. The aim of our work was to study how various assays based on using various substrates reflect differences in peroxidase activities of tobacco leaves due to either developmental or environmental factors. The former factor was studied comparing fully developed leaves of the 3rd and 5th nodes; and the latter was achieved using plants acclimated to low doses of supplementary UV-B (280-315 nm) in growth chambers. To investigate the above, POD activities were measured using three different, commonly used chromophore substrates: ABTS (2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid)), guaiacol (2-methoxyphenol), OPD (o-phenylenediamine) and a fourth substrate, the secondary metabolite quercetin. All substrates registered a UV-B induced increase in leaf peroxidases as compared to untreated controls, although to different extents. However, age-related differences between upper and lower leaves were only detectable when either ABTS or quercetin were used as substrates. Additionally, native PAGE separation of POD isoforms followed by visualisation using one of the substrates showed that leaf acclimation to supplementary UV-B is realized via a selective activation of POD isoforms.

Bound by Fate: The Role of Reactive Oxygen Species in Receptor-Like Kinase Signaling

In plants, receptor-like kinases (RLKs) and extracellular reactive oxygen species (ROS) contribute to the communication between the environment and the interior of the cell. Apoplastic ROS production is a frequent result of RLK signaling in a multitude of cellular processes; thus, by their nature, these two signaling components are inherently linked. However, it is as yet unclear how ROS signaling downstream of receptor activation is executed. In this review, we provide a broad view of the intricate connections between RLKs and ROS signaling and describe the regulatory events that control and coordinate extracellular ROS production. We propose that concurrent initiation of ROS-dependent and -independent signaling linked to RLKs might be a critical element in establishing cellular responses. Furthermore, we discuss the possible ROS sensing mechanisms in the context of the biochemical environment in the apoplast. We suggest that RLK-dependent modulation of apoplastic and intracellular conditions facilitates ROS perception and signaling. Based on data from plant and animal models, we argue that specific RLKs could be components of the ROS sensing machinery or ROS sensors. The importance of the crosstalk between RLK and ROS signaling is discussed in the context of stomatal immunity. Finally, we highlight challenges in the understanding of these signaling processes and provide perspectives for future research.

Overexpression of BAK1 causes salicylic acid accumulation and deregulation of cell death control genes

Since the BRI1-Associated Receptor Kinase 1 (BAK1) was firstly identified as a co-receptor of BRI1 that mediates brassinosteroids (BR) signaling, the functional roles of BAK1, as a versatile co-receptor for various ligand-binding leucine-rich repeat (LRR)-containing receptor-like kinase (RLKs), are being extended to involvement with plant immunity, cell death, stomatal development and ABA signaling in plants. During more than a decade of research on the BAK1, it has been known that transgenic Arabidopsis plants overexpressing BAK1 tagged with various reporters do not fully represent its natural functions. Therefore, in this study, we characterized the transgenic plants in which native BAK1 is overexpressed driven by its own promoter. We found that those transgenic plants were more sensitive to BR signaling but showed reduced growth patterns accompanied with spontaneous cell death features that are different from those seen in BR-related mutants. We demonstrated that more salicylic acid (SA) and hydrogen peroxide were accumulated and that expressions of the genes that are known to regulate cell death, such as BONs, BIRs, and SOBIR, were increased in the BAK1-overexpressing transgenic plants. These results suggest that pleiotropic phenotypic alterations shown in the BAK1- overexpressing transgenic plants result from the constitutive activation of SA-mediated defense responses.

Proteome quantification of cotton xylem sap suggests the mechanisms of potassium-deficiency-induced changes in plant resistance to environmental stresses

Proteomics was employed to investigate the molecular mechanisms of apoplastic response to potassium(K)-deficiency in cotton. Low K (LK) treatment significantly decreased the K and protein contents of xylem sap. Totally, 258 peptides were qualitatively identified in the xylem sap of cotton seedlings, of which, 90.31% were secreted proteins. Compared to the normal K (NK), LK significantly decreased the expression of most environmental-stress-related proteins and resulted in a lack of protein isoforms in the characterized proteins. For example, the contents of 21 Class Ш peroxidase isoforms under the LK were 6 to 44% of those under the NK and 11 its isoforms were lacking under the LK treatment; the contents of 3 chitinase isoforms under LK were 11–27% of those under the NK and 2 its isoforms were absent under LK. In addition, stress signaling and recognizing proteins were significantly down-regulated or disappeared under the LK. In contrast, the LK resulted in at least 2-fold increases of only one peroxidase, one protease inhibitor, one non-specific lipid-transfer protein and histone H₄ and in the appearance of H₂A. Therefore, K deficiency decreased plant tolerance to environmental stresses, probably due to the significant and pronounced decrease or disappearance of a myriad of stress-related proteins.

Reverse function of ROS-induced CBL10 during salt and drought stress responses

Cellular levels of Ca(2+) and reactive oxygen species (ROS) are maintained at low levels in the cytosol but fluctuate greatly when acting as second messengers to decode environmental and developmental signals. Phytohormones are primary signals leading to various changes in ROS or Ca(2+) signaling during synergistic and antagonistic cross-talk. In this study, we found that brassinosteroids (BRs), hormones involved in diverse plant developmental processes, promote ROS production. To identify downstream signaling components of ROS during BR-mediated plant development, we searched for genes whose expression remained unchanged by ROS only in BR- signaling mutants and found calcineurin B-like (CBL) 10, which encodes a CBL should be changed to CBL10. protein that senses calcium. ROS-induced CBL10 expression was nullified and endogenous CBL10 expression in the shoot was low in the BR-signaling mutant. Using a cbl10 mutant and a transgenic plant overexpressing CBL10, we showed that BR sensitivity during hypocotyl growth decreased in the cbl10 mutant under salt stress, providing an additional mechanism for positive regulation of salt stress by CBL10. We also demonstrated that CBL10 negatively affects tolerance to drought and is not mediated by abscisic acid-induced signaling. Our results suggest that Ca(2+) signaling through CBL10 differently affects the response to abiotic stresses, partly by regulating BR sensitivity of plant tissues.

BRI1-EMS-suppressor 1 gain-of-function mutant shows higher susceptibility to necrotrophic fungal infection

Brassinosteroids (BRs) are plant-specific steroids that are involved in plant growth and defense responses. However, the exact roles of BR in plant defense are unclear. We used the bes1-D gain-of-function mutant to define the underlying relationship between plant growth and defense through BR signaling and innate immunity. In bes1-D, further downstream component BES1 transcription factor is stabilized, leading to the activation of BR signaling. Previous reports on BES1 target genes showed that approximately 10% are related to biotic stress responses. Therefore, the bes1-D PTI responses were examined. The bes1-D mutant was specifically susceptible to Alternaria brassicicola, a necrotrophic fungus, which successfully produced spore, resulting in considerable cell death. However, it was not affected by a biotrophic pathogen, Pseudomonas syringae pv. tomato (Pst) DC3000. Instead of a ROS burst, a representative initial PTI responses, higher ROS accumulation was sustained in bes1-D than in the wild type plant. PDF1.2 expression was not induced in response to fungal pathogen infection in bes1-D. These results suggest that BES1 is also involved in JA-related defense responses, especially in response to necrotrophic pathogens.

Freezing tolerance of sea urchin embryonic cells: Differentiation commitment and cytoskeletal disturbances in culture

This study focuses on the freezing tolerance of sea urchin embryonic cells. To significantly reduce the loss of physiological activity of these cells that occurs after cryopreservation and to study the effects of ultra-low temperatures on sea urchin embryonic cells, we tested the ability of the cells to differentiate into spiculogenic or pigment directions in culture, including an evaluation of the expression of some genes involved in pigment differentiation. A morphological analysis of cytoskeletal disturbances after freezing in a combination of penetrating (dimethyl sulfoxide and ethylene glycol) and non-penetrating (trehalose and polyvinylpyrrolidone) cryoprotectants revealed that the distribution pattern of filamentous actin and tubulin was similar to that in the control cultures. In contrast, very rare spreading cells and a small number of cells with filamentous actin and tubulin were detected after freezing in the presence of only non-penetrating cryoprotectants. The largest number of pigment cells was found in cultures frozen with trehalose or trehalose and dimethyl sulfoxide. The ability to induce the spicule formation was lost in the cells frozen only with non-penetrating cryoprotectants, while it was maximal in cultures frozen in a cryoprotective mixture containing both non-penetrating and penetrating cryoprotectants (particularly, when ethylene glycol was present). Using different markers for cell state assessment, an effective cryopreservation protocol for sea urchin cells was developed: three-step freezing with a low cooling rate (1-2°C/min) and a combination of non-penetrating and penetrating cryoprotectants made it possible to obtain a high level of cell viability (up to 65-80%).