Molecular characterization of a pepper C2 domain-containing SRC2 protein implicated in resistance against host and non-host pathogens and abiotic stresses

PmRad23d Interacts With PmSRC2 and PmCAR4 to Mediate the Abscisic Acid-Dependent Drought Response in Prunus mira Koehne

Drought significantly restricts the growth and quality of fruit trees Prunus mira, an ancient wild peach species, exhibits strong drought tolerance; however, the detailed response mechanism remains unknown. The nucleic acid excision repair factor radiation sensitivity 23d (Rad23d) plays a crucial role in plant stress, growth, and development. However, its specific mechanism of action in P. mira is unclear. Here, we report that PmRad23d positively contributes to the abscisic acid (ABA)-dependent drought response in P. mira. Overexpression of PmRad23d enhanced drought tolerance and ABA sensitivity, whereas inhibiting PmRad23d expression reduced the plant's drought tolerance and ABA sensitivity. PmRad23d was found to interact with the C2 domain at the N-terminus of PmSRC2 and PmCAR4, respectively. Together, they regulate the expression of ABA- and drought-related genes, activate ABA signaling, and induce stomatal closure, ultimately enhancing drought resistance in plants. Our findings shed light on the ABA-dependent drought response mechanism of PmRad23d, providing a basis for further exploration of drought tolerance in P. mira. Additionally, this study identifies potential candidate genes for enhancing peach germplasm resources and breeding drought-tolerant cultivars.

Silencing of Putative Plasmodesmata-Associated Genes PDLP and SRC2 Reveals Their Differential Involvement during Plant Infection with Cucumber Mosaic Virus

Plant viruses utilize a subset of host plasmodesmata-associated proteins to establish infection in plants. In the present study, we aimed to understand the role of two plant genes, one encoding a putative plasmodesma located protein (PDLP) and a homolog of soybean gene regulated by cold 2 protein (SRC2) during Cucumber mosaic virus (CMV) infection. Virus-induced gene silencing (VIGS) was used to silence PDLP and SRC2 genes in Nicotiana benthamiana and in two related solanaceous plants, N. tabacum and Capsicum chinense Jacq. (Bhut Jolokia). Up to 50% downregulation in the expression of the PDLP gene using the TRV2-PDLP VIGS construct was observed in N. benthamiana and N. tabacum while, using the same gene construct, 30% downregulation of the target mRNA was observed in C. chinense. Similarly, using the TRV2-SRC2 VIGS construct, a 60% downregulation of the SRC2 mRNA was observed in N. benthamiana, N. tabacum, and a 40% downregulation in C. chinense as confirmed by qRT-PCR analysis. Downregulation of the PDLP gene in N. benthamiana resulted in delayed symptom appearance up to 7-12 days post inoculation with reduced CMV accumulation compared to the control plants expressing TRV2-eGFP. In contrast, SRC2-silenced plants showed enhanced susceptibility to CMV infection compared to the control plants. Our data suggest that the PDLP gene might facilitate infection of CMV, thus being a susceptibility factor, while the SRC2 gene could play a role in resistance to CMV infection in N. benthamiana.

Overexpression of GmSRC2 confers resistance to Phytophthora sojae in soybean

Phytophthora root and stem rot caused by Phytophthora sojae (P. sojae) is one of the most destructive diseases to affect soybean (Glycine max (L.) Merr) production. GmSRC2 that encodes a C2 domain-containing protein can respond to various stresses, however, the molecular mechanism of GmSRC2 in resistance of soybean to P. sojae is yet to be fully elucidated. In this study, GmSRC2 was found to be significantly up-regulated under P. sojae treatment; GmSRC2-overexpression (OE) transgenic lines and GmSRC2-silencing transient plants were generated via Agrobacterium tumefaciens mediated transformation and virus-induced gene silencing (VIGS) system, respectively. Infected leaves and cotyledons of OE-GmSRC2-1 and OE-GmSRC2-2 lines showed significant decreases in the disease symptoms and P. sojae biomass than those of wild type (WT); the activities of superoxide dismutase (SOD) and peroxidase (POD) confirmed the accumulation of reactive oxygen species (ROS) in overexpressed transgenic lines. Whereas, silencing of GmSRC2 severely increased the disease symptoms and the biomass of P. sojae. Further, we confirmed that GmSRC2 interacted with the effector PsAvh23 of P. sojae, and the C2 domain was crucial for the interaction. Overexpression of GmSRC2 upregulated the ADA2/GCN5 module upon P. sojae. The aforementioned results demonstrated that GmSRC2 played vital roles in regulating soybean resistance to oomycetes.

Transcriptome Analysis of Sweet Cherry (Prunus avium L.) Cultivar 'Lapins' upon Infection of Pseudomonas syringae pv. syringae

Bacterial canker caused by Pseudomonas syringae pv. syringae (Pss) is responsible for substantial loss to the production of sweet cherry in Chile. To date, the molecular mechanisms of the Pss-sweet cherry interaction and the disease-related genes in the plant are poorly understood. In order to gain insight into these aspects, a transcriptomic analysis of the sweet cherry cultivar 'Lapins' for differentially expressed genes (DEGs) in response to Pss inoculation was conducted. Three Pss strains, A1M3, A1M197, and 11116_b1, were inoculated in young twigs, and RNA was extracted from tissue samples at the inoculation site and distal sections. RNA sequencing and transcriptomic expression analysis revealed that the three strains induced different patterns of responses in local and distal tissues. In the local tissues, A1M3 triggered a much more extensive response than the other two strains, enriching DEGs especially involved in photosynthesis. In the distal tissues, the three strains triggered a comparable extent of responses, among which 11116_b1 induced a group of DEGs involved in defense responses. Furthermore, tissues from various inoculations exhibited an enrichment of DEGs related to carbohydrate metabolism, terpene metabolism, and cell wall biogenesis. This study opened doors to future research on the Pss-sweet cherry interaction, immunity responses, and disease control.

Genome-wide identification and characterization of the C2 domain family in Sorghum bicolor (L.) and expression profiles in response to saline-alkali stress

The C2 domain family proteins in plants has been recently shown to be involved in the response to abiotic stress such as salt and drought stress. However, less information on C2 domain family members has been reported in Sorghum bicolor (L.), which is a tolerant cereal crop. To elaborate the mechanism of C2 domain family members in response to abiotic stress, bioinformatic methods were used to analyze this family. The results indicated that 69 C2 domain genes belonging to 5 different groups were first identified within the sorghum genome, and each group possessed various gene structures and conserved functional domains. Second, those C2 family genes were localized on 10 chromosomes 3 tandem repeat genes and 1 pair of repeat gene fragments were detected. The family members further presented a variety of stress responsive cis-elements. Third, in addition to being the major integral component of the membrane, sorghum C2 domain family proteins mainly played roles in response to abiotic and biotic stress with their organic transport and catalytic activity by specific location in the cell on the basis of gene ontology analysis. C2 family genes were differentially expressed in root, shoot or leaf, and shown different expression profiling after saline-alkali stress, which indicated that C2 family members played an important role in response to saline-alkali stress based on the transcription profiles of RNA-seq data and expression analysis by quantitative real-time polymerase chain reaction. Besides, most C2 family members were mainly located in cytoplasmi and nucleus. Weighted gene co-expression network analysis revealed three modules (turquoise, dark magenta and pink) that were associated with stress resistance, respectively. Therefore, the present research provides comprehensive information for further analysis of the molecular function of C2 domain family genes in sorghum.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-022-01222-3.

A C2-Domain Abscisic Acid-Related Gene, IbCAR1, Positively Enhances Salt Tolerance in Sweet Potato (Ipomoea batatas (L.) Lam.)

Plant C2-domain abscisic acid-related (CAR) protein family plays an important role in plant growth, abiotic stress responses, and defense regulation. In this study, we cloned the IbCAR1 by homologous cloning method from the transcriptomic data of Xuzishu8, which is a sweet potato cultivar with dark-purple flesh. This gene was expressed in all tissues of sweet potato, with the highest expression level in leaf tissue, and it could be induced by NaCl and ABA. Subcellular localization analyses indicated that IbCAR1 was localized in the nucleus and plasma membrane. The PI staining experiment revealed the distinctive root cell membrane integrity of overexpressed transgenic lines upon salt stress. Salt stress significantly increased the contents of proline, ABA, and the activity of superoxide dismutase (SOD), whereas the content of malondialdehyde (MDA) was decreased in overexpressed lines. On the contrary, RNA interference plants showed sensitivity to salt stress. Overexpression of IbCAR1 in sweet potatoes could improve the salt tolerance of plants, while the RNAi of IbCAR1 significantly increased sensitivity to salt stress in sweet potatoes. Meanwhile, the genes involved in ABA biosynthesis, stress response, and reactive oxygen species (ROS)-scavenging system were upregulated in overexpressed lines under salt stress. Taken together, these results demonstrated that IbCAR1 plays a positive role in salt tolerance by relying on the ABA signal transduction pathway, activating the ROS-scavenging system in sweet potatoes.

Effect of Smut Infection on the Photosynthetic Physiological Characteristics and Related Defense Enzymes of Sugarcane

Pathogen infection seriously affects plant development and crop productivity, sometimes causing total crop failure. In this study, artificial stab inoculation was used to inoculate sugarcane smut. The changes in leaf gas exchange, chlorophyll fluorescence variables, and related defense enzyme activities were measured in sugarcane cultivar ROC22 after pathogen infection. The results showed that the net photosynthetic rate (Pn), stomatal conductance (gs), and transpiration rate (Tr) downregulated in the first three days after smut infection and upregulated on the fourth day; intercellular CO₂ concentration (Ci) increased in the first three days of smut infection and reduced on the fourth day. The chlorophyll fluorescence parameters, i.e., Fo, Fm, Fv/Fm, Fs, and Fv′/Fm′ decreased at the initial stage of pathogen infection but increased rapidly up to 3 days after smut infection. It can be seen that sugarcane seedlings showed a positive response to pathogen infection. The correlation coefficient relationship between Pn, gs, and Tr reached above 0.800, showing a significant correlation; Ci was positively correlated with Fv′/Fm′ and ΦPSII, reaching above 0.800 and showing a significant correlation; Fo positively correlated with Fv/Fm, Fs, and ETR; Fv /Fm was positively correlated with Fv′/Fm′; Fs significantly correlated with Fv′/Fm′; and Fv′/Fm′ positively correlated with ΦPSII. After inoculation with smut, the related defense enzymes, i.e., POD, SOD, PPO, and PAL, were increased and upregulated; photosynthetic parameters can be associated with an increase in enzymatic activities. The results of this study will help to further study of the response mechanism to smut in the sugarcane growing period and provide a theoretical reference for sugarcane resistance to smut breeding.

Large-Scale Integrative Analysis of Soybean Transcriptome Using an Unsupervised Autoencoder Model

Plant tissues are distinguished by their gene expression patterns, which can help identify tissue-specific highly expressed genes and their differential functional modules. For this purpose, large-scale soybean transcriptome samples were collected and processed starting from raw sequencing reads in a uniform analysis pipeline. To address the gene expression heterogeneity in different tissues, we utilized an adversarial deconfounding autoencoder (AD-AE) model to map gene expressions into a latent space and adapted a standard unsupervised autoencoder (AE) model to help effectively extract meaningful biological signals from the noisy data. As a result, four groups of 1,743, 914, 2,107, and 1,451 genes were found highly expressed specifically in leaf, root, seed and nodule tissues, respectively. To obtain key transcription factors (TFs), hub genes and their functional modules in each tissue, we constructed tissue-specific gene regulatory networks (GRNs), and differential correlation networks by using corrected and compressed gene expression data. We validated our results from the literature and gene enrichment analysis, which confirmed many identified tissue-specific genes. Our study represents the largest gene expression analysis in soybean tissues to date. It provides valuable targets for tissue-specific research and helps uncover broader biological patterns. Code is publicly available with open source at https://github.com/LingtaoSu/SoyMeta.

A Novel Glycerol Kinase Gene OsNHO1 Regulates Resistance to Bacterial Blight and Blast Diseases in Rice

Glycerol-induced resistance to various pathogens has been reported in different plants. Glycerol kinase (GK), a vital rate-limiting enzyme that catalyzes glycerol conversion to glycerol-3-phosphate (G3P), participates in responses to both abiotic and biotic stresses. However, its physiological importance in rice defenses against pathogens remains unclear. In this research, quantification analysis revealed that GK levels were significantly induced in rice leaves infected by Xanthomonas oryzae pv. oryzae (Xoo) strain PXO99. A typical GK-encoding gene OsNHO1 was cloned in rice. The transcriptional levels of OsNHO1 were significantly induced by salicylic acid, jasmonic acid, and Xoo-PXO99. Ectopic expression of OsNHO1 partially rescued the resistance to P. s. pv. phaseolicola in the Arabidopsis nho1 mutant. In the overexpressing transgenic rice lines (OsNHO1-OE), the content of GK and the transcriptional level of OsNHO1 were increased and the resistance to bacterial blight and blast was improved, while reduced OsNHO1 expression impaired the resistance in OsNHO1-RNAi lines. The wax contents and expression of the wax synthesis regulatory genes were significantly increased in the overexpression lines but decreased in the OsNHO1-RNAi lines. We then confirmed the interaction partner of OsNHO1 using yeast two-hybrid and bimolecular fluorescence complementation assays. The transcription of the interaction partner-encoding genes OsSRC2 and OsPRs in OsNHO1-RNAi lines was downregulated but upregulated in OsNHO1-OE lines. Thus, we concluded that OsNHO1 provided disease resistance by affecting the wax content and modulating the transcription levels of PR genes.

Use of a Network-Based Method to Identify Latent Genes Associated with Hearing Loss in Children

Hearing loss is a total or partial inability to hear. Approximately 5% of people worldwide experience this condition. Hearing capacity is closely related to language, social, and basic emotional development; hearing loss is particularly serious in children. The pathogenesis of childhood hearing loss remains poorly understood. Here, we sought to identify new genes potentially associated with two types of hearing loss in children: congenital deafness and otitis media. We used a network-based method incorporating a random walk with restart algorithm, as well as a protein-protein interaction framework, to identify genes potentially associated with either pathogenesis. A following screening procedure was performed and 18 and 87 genes were identified, which potentially involved in the development of congenital deafness or otitis media, respectively. These findings provide novel biomarkers for clinical screening of childhood deafness; they contribute to a genetic understanding of the pathogenetic mechanisms involved.

OsC2DP, a Novel C2 Domain-Containing Protein Is Required for Salt Tolerance in Rice

Salt stress is one of the major factors limiting crop production globally, including rice (Oryza sativa). Although a number of genes involved in salt tolerance have been functionally identified, the mechanism underlying salt tolerance in rice is still poorly understood. Here, we reported a novel C2 domain-containing protein, OsC2DP required for salt tolerance in rice. OsC2DP was predominately expressed in the roots and its expression was repressed by salt stress. Transient expression of OsC2DP in rice protoplast cells showed that it was localized in the cytosol. Immunostaining further showed that OsC2DP was able to translocate from the cytosol to plasma membrane under salt conditions. Knockout of OsC2DP did not affect Na+ concentration in the roots, but increased shoot Na+ concentration, resulting in a significant sensitivity of rice to salt stress. Furthermore, the quantitative Real-time PCR and transcriptomic analysis showed that the expression level of some genes related to salt tolerance were indirectly regulated by OsC2DP, especially OsSOS1 and OsNHX4. These results indicate that OsC2DP has an important role in salt tolerance and these findings provide new insights into the regulation of OsC2DP gene for rice breeding with high salt tolerance.

C2 domain plays critical roles in localization of novel C2 domain-containing protein OsC2DP

OsC2DP is a cytosolic protein containing a C2 domain recently identified in rice, which is translocated to the plasma membrane in response to salt stress. Here, we further investigated the subcellular localization of OsC2DP by truncation analysis. In consistent with OsC2DP, OsC2DP^1-165 containing C2 domain at the N-terminus was localized to the cytosol. In contrast to OsC2DP^1-165, OsC2DP^166-290 lack of C2 domain at the C-terminus was localized to the cytosol and nucleus, which was similar to the GFP control. Under salt conditions, subcellular localization of both OsC2DP^1-165 and OsC2DP^166-290 was not altered and failed to migrate to plasma membrane. These results indicated that the subcellular localization was determined by C2 domain of OsC2DP under normal conditions and that both N- and C-terminus of OsC2DP are essential for its cytosol-plasma membrane translocation in response to salt stress.

The P1 gene of Cauliflower mosaic virus is responsible for breaking resistance in Arabidopsis thaliana ecotype Enkheim (En-2)

Arabidopsis thaliana ecotype En-2 is resistant to several strains of Cauliflower mosaic virus (CaMV), including strain W260, but is susceptible to strain NY8153. Resistance in En-2 is conditioned by a single, semi-dominant gene called CAR1. We constructed several recombinant infectious clones between W260 and NY8153 and evaluated their capability to infect En-2. This analysis showed that the capacity of NY8153 to break resistance in En-2 was conditioned by mutations within the CaMV gene 1, a gene that encodes a protein dedicated to cell-to-cell movement (P1), and conversely, that P1 of W260 is responsible for eliciting the plant defense response. A previous study had shown that P6 of W260 was responsible for overcoming resistance in Arabidopsis ecotype Tsu-0 and that P6 of CaMV strain CM1841 was responsible for triggering resistance. The present study now shows that a second gene of CaMV is targeted by Arabidopsis for plant immunity.

Regulation of Long Noncoding RNAs Responsive to Phytoplasma Infection in Paulownia tomentosa

Paulownia witches' broom caused by phytoplasma infection affects the production of Paulownia trees worldwide. Emerging evidence showed that long noncoding RNAs (lncRNA) play a protagonist role in regulating the expression of genes in plants. So far, the identification of lncRNAs has been limited to a few model plant species, and their roles in mediating responses to Paulownia tomentosa that free of phytoplasma infection are yet to be characterized. Here, whole-genome identification of lncRNAs, based on strand-specific RNA sequencing, from four Paulownia tomentosa samples, was performed and identified 3689 lncRNAs. These lncRNAs showed low conservation among plant species and some of them were miRNA precursors. Further analysis revealed that the 112 identified lncRNAs were related to phytoplasma infection. We predicted the target genes of these phytoplasma-responsive lncRNAs, and our analysis showed that 51 of the predicted target genes were alternatively spliced. Moreover, we found the expression of the lncRNAs plays vital roles in regulating the genes involved in the reactive oxygen species induced hypersensitive response and effector-triggered immunity in phytoplasma-infected Paulownia. This study indicated that diverse sets of lncRNAs were responsive to Paulownia witches' broom, and the results will provide a starting point to understand the functions and regulatory mechanisms of Paulownia lncRNAs in the future.

The Tomato Hybrid Proline-rich Protein regulates the abscission zone competence to respond to ethylene signals

The Tomato Hybrid Proline-rich Protein (THyPRP) gene was specifically expressed in the tomato (Solanum lycopersicum) flower abscission zone (FAZ), and its stable antisense silencing under the control of an abscission zone (AZ)-specific promoter, Tomato Abscission Polygalacturonase4, significantly inhibited tomato pedicel abscission following flower removal. For understanding the THyPRP role in regulating pedicel abscission, a transcriptomic analysis of the FAZ of THyPRP-silenced plants was performed, using a newly developed AZ-specific tomato microarray chip. Decreased expression of THyPRP in the silenced plants was already observed before abscission induction, resulting in FAZ-specific altered gene expression of transcription factors, epigenetic modifiers, post-translational regulators, and transporters. Our data demonstrate that the effect of THyPRP silencing on pedicel abscission was not mediated by its effect on auxin balance, but by decreased ethylene biosynthesis and response. Additionally, THyPRP silencing revealed new players, which were demonstrated for the first time to be involved in regulating pedicel abscission processes. These include: gibberellin perception, Ca²⁺-Calmodulin signaling, Serpins and Small Ubiquitin-related Modifier proteins involved in post-translational modifications, Synthaxin and SNARE-like proteins, which participate in exocytosis, a process necessary for cell separation. These changes, occurring in the silenced plants early after flower removal, inhibited and/or delayed the acquisition of the competence of the FAZ cells to respond to ethylene signaling. Our results suggest that THyPRP acts as a master regulator of flower abscission in tomato, predominantly by playing a role in the regulation of the FAZ cell competence to respond to ethylene signals.

An Apple Protein Kinase MdSnRK1.1 Interacts with MdCAIP1 to Regulate ABA Sensitivity

ABA is a crucial phytohormone for development and stress responses in plants. Snf1-related protein kinase 1.1 (SnRK1.1) is involved in the ABA response. However, the molecular mechanism underlying the SnRK1.1 response to ABA is largely unknown. Here, it was found that overexpression of the apple MdSnRK1.1 gene enhanced ABA sensitivity in both transgenic apple calli and Arabidopsis seedlings. Subsequently, a yeast two-hybrid screen demonstrated that MdCAIP1 (C2-domain ABA Insensitive Protein1) interacted with MdSnRK1.1. Their interaction was further confirmed by pull-down and co-immunoprecipitation assays. Expression of the MdCAIP1 gene was positively induced by ABA. Its overexpression enhanced ABA sensitivity in transgenic apple calli. Furthermore, it was found that MdSnRK1.1 phosphorylated the MdCAIP1 protein in vivo and promoted its degradation in vitro and in vivo. As a result, MdSnRK1.1 inhibited MdCAIP1-mediated ABA sensitivity, and MdCAIP1 partially reduced MdSnRK1.1-mediated ABA sensitivity. Our findings indicate that MdSnRK1.1 plays an important role in the ABA response, partially by controlling the stability of the MdCAIP1 protein.

Viral protein suppresses oxidative burst and salicylic acid-dependent autophagy and facilitates bacterial growth on virus-infected plants

Virus interactions with plant silencing and innate immunity pathways can potentially alter the susceptibility of virus-infected plants to secondary infections with nonviral pathogens. We found that Arabidopsis plants infected with Cauliflower mosaic virus (CaMV) or transgenic for CaMV silencing suppressor P6 exhibit increased susceptibility to Pseudomonas syringae pv. tomato (Pst) and allow robust growth of the Pst mutant hrcC-, which cannot deploy effectors to suppress innate immunity. The impaired antibacterial defense correlated with the suppressed oxidative burst, reduced accumulation of the defense hormone salicylic acid (SA) and diminished SA-dependent autophagy. The viral protein domain required for suppression of these plant defense responses is dispensable for silencing suppression but essential for binding and activation of the plant target-of-rapamycin (TOR) kinase which, in its active state, blocks cellular autophagy and promotes CaMV translation. Our findings imply that CaMV P6 is a versatile viral effector suppressing both silencing and innate immunity. P6-mediated suppression of oxidative burst and SA-dependent autophagy may predispose CaMV-infected plants to bacterial infection.

SRC2-1 is required in PcINF1-induced pepper immunity by acting as an interacting partner of PcINF1

Elicitins are elicitors that can trigger hypersensitive cell death in most Nicotiana spp., but their underlying molecular mechanism is not well understood. The gene Phytophthora capsici INF1 (PcINF1) coding for an elicitin from P. capsici was characterized in this study. Transient overexpression of PcINF1 triggered cell death in pepper (Capsicum annuum L.) and was accompanied by upregulation of the hypersensitive response marker, Hypersensitive Induced Reaction gene 1 (HIR1), and the pathogenesis-related genes SAR82, DEF1, BPR1, and PO2. A putative PcINF1-interacting protein, SRC2-1, was isolated from a pepper cDNA library by yeast two-hybrid screening and was observed to target the plasma membrane. The interaction between PcINF1 and SRC2-1 was confirmed by bimolecular fluorescence complementation and co-immunoprecipitation. Simultaneous transient overexpression of SRC2-1 and PcINF1 in pepper plants triggered intensive cell death, whereas silencing of SRC2-1 by virus-induced gene silencing blocked the cell death induction of PcINF1 and increased the susceptibility of pepper plants to P. capsici infection. Additionally, membrane targeting of the PcINF1-SRC2-1 complex was required for cell death induction. The C2 domain of SRC2-1 was crucial for SRC2-1 plasma membrane targeting and the PcINF1-SRC2-1 interaction. These results suggest that SRC2-1 interacts with PcINF1 and is required in PcINF1-induced pepper immunity.

Comprehensive insights on how 2,4-dichlorophenoxyacetic acid retards senescence in post-harvest citrus fruits using transcriptomic and proteomic approaches

Auxin-like 2,4-dichlorophenoxyacetic acid (2,4-D), a high-efficiency anti-stalling agent for the post-harvest fresh fruit industry, has had its use restricted due to environmental concerns. However, no other substitutes for 2,4-D are available to the post-harvest industry. Insights into the molecular mechanism underlying the effects of 2,4-D on fruit quality preservation will provide a theoretical basis for exploring new safe and effective anti-stalling agents. This study comprehensively analysed changes in the peel of Olinda Valencia orange [Citrus sinensis (L.) Osbeck] induced by 500 ppm 2,4-D using 'omic'-driven approaches. Transcriptional profiling revealed that transcriptional factor (mainly AP2/ERF, WRKY, and NAC family members), transport, and hormone metabolism genes were over-represented and up-regulated within 24h post-treatment (HPT). Stress defence genes were up-regulated, while cell wall metabolism genes were down-regulated after 48 HPT. However, secondary metabolism genes, especially phenylpropanoid and lignin biosynthesis-related genes, were over-represented at all the time points. Comparative proteomic analysis indicated that the expression of proteins implicated in stress responses (25%), hormone metabolism, and signal transduction (12%) significantly accumulated at the post-transcriptional level. Hormone levels detected by high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) showed that abscisic acid, salicylic acid, and 2,4-D significantly increased, while ethylene production (detected by gas chromatography) decreased after 2,4-D treatment. In addition, lignin and water content in the fruit peel also increased and the epicuticle wax ultrastructure was modified. In conclusion, 2,4-D retarded fruit senescence by altering the levels of many endogenous hormones and by improving stress defence capabilities by up-regulating defence-related genes and proteins.

Differentially delayed root proteome responses to salt stress in sugar cane varieties

Soil salinity is a limiting factor to sugar cane crop development, although in general plants present variable mechanisms of tolerance to salinity stress. The molecular basis underlying these mechanisms can be inferred by using proteomic analysis. Thus, the objective of this work was to identify differentially expressed proteins in sugar cane plants submitted to salinity stress. For that, a greenhouse experiment was established with four sugar cane varieties and two salt conditions, 0 mM (control) and 200 mM NaCl. Physiological and proteomics analyses were performed after 2 and 72 h of stress induction by salt. Distinct physiological responses to salinity stress were observed in the varieties and linked to tolerance mechanisms. In proteomic analysis, the roots soluble protein fraction was extracted, quantified, and analyzed through bidimensional electrophoresis. Gel images analyses were done computationally, where in each contrast only one variable was considered (salinity condition or variety). Differential spots were excised, digested by trypsin, and identified via mass spectrometry. The tolerant variety RB867515 showed the highest accumulation of proteins involved in growth, development, carbohydrate and energy metabolism, reactive oxygen species metabolization, protein protection, and membrane stabilization after 2 h of stress. On the other hand, the presence of these proteins in the sensitive variety was verified only in stress treatment after 72 h. These data indicate that these stress responses pathways play a role in the tolerance to salinity in sugar cane, and their effectiveness for phenotypical tolerance depends on early stress detection and activation of the coding genes expression.

A DIGE-based quantitative proteomic analysis of grape berry flesh development and ripening reveals key events in sugar and organic acid metabolism

Grapevine (Vitis vinifera L.) is an economically important fruit crop. Quality-determining grape components, such as sugars, acids, flavours, anthocyanins, tannins, etc., are accumulated during the different grape berry development stages. Thus, correlating the proteomic profiles with the biochemical and physiological changes occurring in grape is of paramount importance to advance the understanding of the berry development and ripening processes. Here, the developmental analysis of V. vinifera cv. Muscat Hamburg berries is reported at protein level, from fruit set to full ripening. A top-down proteomic approach based on differential in-gel electrophoresis (DIGE) followed by tandem mass spectrometry led to identification and quantification of 156 and 61 differentially expressed proteins in green and ripening phases, respectively. Two key points in development, with respect to changes in protein level, were detected: end of green development and beginning of ripening. The profiles of carbohydrate metabolism enzymes were consistent with a net conversion of sucrose to malate during green development. Pyrophosphate-dependent phosphofructokinase is likely to play a key role to allow an unrestricted carbon flow. The well-known change of imported sucrose fate at the beginning of ripening from accumulation of organic acid (malate) to hexoses (glucose and fructose) was well correlated with a switch in abundance between sucrose synthase and soluble acid invertase. The role of the identified proteins is discussed in relation to their biological function, grape berry development, and to quality traits. Another DIGE experiment comparing fully ripe berries from two vintages showed very few spots changing, thus indicating that protein changes detected throughout development are specific.

Response of living tissues of Pinus sylvestris to the saprotrophic biocontrol fungus Phlebiopsis gigantea

The saprotrophic fungus Phlebiopsis gigantea has been used for several years as a biocontrol agent against the conifer pathogen Heterobasidion annosum. Although the effectiveness of P. gigantea in biocontrol has been shown empirically, the long-term effect on living conifer trees as well as the mechanism underlying its antagonistic activity is still unknown. An additional concern is the potential of P. gigantea to acquire a necrotrophic habit through adaptation to living wood tissues. By using a combination of histochemical, molecular and transcript profiling (454 sequencing), we investigated under in vitro conditions the necrotrophic capability of P. gigantea and induced localized resistance as a mechanism for its biocontrol action. Pinus sylvestris seedlings (10 years old) were challenged on the xylem surface with P. gigantea or H. annosum. Both fungi provoked strong necrotic lesions, but after prolonged incubation, P. gigantea lesions shrank and ceased to expand further. Tree seedlings pre-treated with P. gigantea further restricted H. annosum-induced necrosis and had more lignified cells. The 454 sequencing revealed elevated transcript levels of genes important for lignification, cell death regulation and jasmonic acid signalling. The results suggest that induced localized resistance is a contributory factor for the biocontrol efficacy of P. gigantea, and it has a limited necrotrophic capability compared with H. annosum.

Overexpression of a rice gene encoding a small C2 domain protein OsSMCP1 increases tolerance to abiotic and biotic stresses in transgenic Arabidopsis

Plant growth and crop production are limited by environmental stress. We used a large population of transgenic Arabidopsis expressing rice full-length cDNAs to isolate the rice genes that improve the tolerance of plants to environmental stress. By sowing T2 seeds of the transgenic lines under conditions of salinity stress, the salt-tolerant line R07047 was isolated. It expressed a rice gene, OsSMCP1, which encodes a small protein with a single C2 domain, a Ca(2+)-dependent membrane-targeting domain. Retransformation of wild-type Arabidopsis revealed that OsSMCP1 is responsible for conferring the salt tolerance. It is particularly interesting that R07047 and newly constructed OsSMCP1-overexpressing Arabidopsis showed enhanced tolerance not only to high salinity but also to osmotic, dehydrative, and oxidative stresses. Furthermore, R07047 showed improved resistance to Pseudomonas syringae. The OsSMCP1 expression in rice is constitutive. Particle-bombardment-mediated transient expression analysis revealed that OsSMCP1 is targeted to plastids in rice epidermal cells. It induced overexpression of several nuclear encoded genes, including the stress-associated genes, in transgenic Arabidopsis. No marked morphological change or growth retardation was observed in R07047 or retransformants. For molecular breeding to improve the tolerance of crops against environmental stress, OsSMCP1 is a promising candidate.

Patterns of defence gene expression in the tomato–Verticilliuminteraction

In a tomato plant infected by Verticillium dahliae , race 1, compatibility or incompatibility appears to be determined in the stem, but little is known about the genes that either regulate or effect critical cellular events. In the present study, microarray and RT-PCR analyses were used to assess changes in tomato mRNA populations during both interactions. Initially, a commercially available DNA chip was used to screen gene expression at a single critical time point after inoculation of resistant and susceptible plants. From the results, the most-affected genes were selected to develop a tomato Verticillium response (TVR) DNA chip for detailed analyses of gene expression for 15 d after inoculation. Taken together, over half of the genes on the TVR array exhibited one of three distinct patterns of change, one reflecting a resistant phenotype and two being consistent with a susceptible phenotype. Of particular interest was a cluster of strongly expressed genes belonging to groups 2 and 3 that appeared to be co-ordinately down regulated in infected resistant plants relative to susceptible. Many of these genes encode pathogenesis related (PR) proteins. The data demonstrate that even though complex, the biological system can be standardized sufficiently to allow the reproducible analysis of gene expression in a whole plant system and provide patterns of transcriptional variation that can be used to assess the significance of specific genes in pathogenesis and resistance.

A protein containing an XYPPX repeat and a C2 domain is associated with virally induced hypersensitive cell death in plants

In this study, we characterized a Capsicum hypersensitive response (HR)-associated gene, SS52, which encodes a protein that contains an N-terminal C2 domain and a C-terminal XYPPX repeat. Expression analyses revealed that SS52 and its homologue in Arabidopsis were induced by infection with incompatible viruses, indicating the conserved function of this gene. SS52 was not induced by treatment with defense-related hormones, but was induced by abiotic stresses, including wounding. Overexpression of SS52 in tobacco plants suppressed the spread of HR cell death and restricted the spread of an incompatible virus from local lesions. Collectively, the results suggest that SS52 negatively regulates plant HR cell death.

Comparison of the transcriptomes of American chestnut (Castanea dentata) and Chinese chestnut (Castanea mollissima) in response to the chestnut blight infection

BACKGROUND1471-2229-9-51: American chestnut (Castanea dentata) was devastated by an exotic pathogen in the beginning of the twentieth century. This chestnut blight is caused by Cryphonectria parasitica, a fungus that infects stem tissues and kills the trees by girdling them. Because of the great economic and ecological value of this species, significant efforts have been made over the century to combat this disease, but it wasn't until recently that a focused genomics approach was initiated. Prior to the Genomic Tool Development for the Fagaceae project, genomic resources available in public databases for this species were limited to a few hundred ESTs. To identify genes involved in resistance to C. parasitica, we have sequenced the transcriptome from fungal infected and healthy stem tissues collected from blight-sensitive American chestnut and blight-resistant Chinese chestnut (Castanea mollissima) trees using ultra high throughput pyrosequencing.

RESULTS

We produced over a million 454 reads, totaling over 250 million bp, from which we generated 40,039 and 28,890 unigenes in total from C. mollissima and C. dentata respectively. The functions of the unigenes, from GO annotation, cover a diverse set of molecular functions and biological processes, among which we identified a large number of genes associated with resistance to stresses and response to biotic stimuli. In silico expression analyses showed that many of the stress response unigenes were expressed more in canker tissues versus healthy stem tissues in both American and Chinese chestnut. Comparative analysis also identified genes belonging to different pathways of plant defense against biotic stresses that are differentially expressed in either American or Chinese chestnut canker tissues.

CONCLUSION

Our study resulted in the identification of a large set of cDNA unigenes from American chestnut and Chinese chestnut. The ESTs and unigenes from this study constitute an important resource to the scientific community interested in the discovery of genes involved in various biological processes in Chestnut and other species. The identification of many defense-related genes differentially expressed in canker vs. healthy stem in chestnuts provides many new candidate genes for developing resistance to the chestnut blight and for studying pathways involved in responses of trees to necrotrophic pathogens. We also identified several candidate genes that may underline the difference in resistance to Cryphonectria parasitica between American chestnut and Chinese chestnut.

Heme-independent soluble and membrane-associated peroxidase activity of a Zea mays annexin preparation

Annexins are cytosolic proteins capable of reversible, Ca(2+)-dependent membrane binding or insertion. Animal annexins form and regulate Ca(2+)-permeable ion channels and may therefore participate in signaling. Zea mays (maize) annexins (ZmANN33 and ZmANN35) have recently been shown to form a Ca(2+)-permeable conductance in planar lipid bilayers and also exhibit in vitro peroxidase activity. Peroxidases form a superfamily of intra- or extracellular heme-containing enzymes that use H(2)O(2) as the electron acceptor in a number of oxidative reactions. Maize annexin peroxidase activity appears independent of heme and persists after membrane association, the latter suggesting a role in reactive oxygen species signaling.