Molecular characterization of pepper germin-like protein as the novel PR-16 family of pathogenesis-related proteins isolated during the resistance response to viral and bacterial infection

Genomic Exploration: Unraveling the Intricacies of Indica Rice Oryza sativa L. Germin-Like Protein Gene 12-3 (OsGLP12-3) Promoter via Cloning, Sequencing, and In Silico Analysis

Germin and Germin-like proteins (GLPs) are a class of plant proteins that are part of the Cupins superfamily, found in several plant organs including roots, seeds, leaves, and nectar glands. They play a crucial role in plant defense against pathogens and environmental stresses. Herein, this study focused on the promoter analysis of OsGLP12-3 in rice cultivar Swat-1 to elucidate its regulation and functions. The region (1863bp) of the OsGLP12-3 promoter from Swat-1 genomic DNA was amplified, purified, quantified, and cloned using Topo cloning technology, followed by sequencing. Further in silico comparative analysis was conducted between the OsGLP12-3 promoters from Nipponbare and Swat-1 using the Plant CARE database, identifying 24 cis-acting regulatory elements with diverse functions. These elements exhibited distinct distribution patterns in the 2 rice varieties. The OsGLP12-3 promoter revealed an abundance of regulatory elements associated with biotic and abiotic stress responses. Computational tools were employed to analyze the regulatory features of this region. In silico expression analysis of OsGLP12-3, considering various developmental stages, stress conditions, hormones, and expression timing, was performed using the TENOR tool. Pairwise alignment indicated 86% sequence similarity between Nipponbare and Swat-1. Phylogenetic analysis was conducted to explore the evolutionary relationship between the OsGLP12-3 and other plant GLPs. Additionally, 2 unique regulatory elements were modeled and docked, GARE and MBS to understand their hydrogen bonding interactions in gene regulation. The study highlights the importance of OsGLP12-3 in plant defense against biotic and abiotic stresses, supported by its expression patterns in response to various stressors and the presence of specific regulatory elements within its promoter region.

Defense signaling pathways in resistance to plant viruses: Crosstalk and finger pointing

Resistance to infection by plant viruses involves proteins encoded by plant resistance (R) genes, viz., nucleotide-binding leucine-rich repeats (NLRs), immune receptors. These sensor NLRs are activated either directly or indirectly by viral protein effectors, in effector-triggered immunity, leading to induction of defense signaling pathways, resulting in the synthesis of numerous downstream plant effector molecules that inhibit different stages of the infection cycle, as well as the induction of cell death responses mediated by helper NLRs. Early events in this process involve recognition of the activation of the R gene response by various chaperones and the transport of these complexes to the sites of subsequent events. These events include activation of several kinase cascade pathways, and the syntheses of two master transcriptional regulators, EDS1 and NPR1, as well as the phytohormones salicylic acid, jasmonic acid, and ethylene. The phytohormones, which transit from a primed, resting states to active states, regulate the remainder of the defense signaling pathways, both directly and by crosstalk with each other. This regulation results in the turnover of various suppressors of downstream events and the synthesis of various transcription factors that cooperate and/or compete to induce or suppress transcription of either other regulatory proteins, or plant effector molecules. This network of interactions results in the production of defense effectors acting alone or together with cell death in the infected region, with or without the further activation of non-specific, long-distance resistance. Here, we review the current state of knowledge regarding these processes and the components of the local responses, their interactions, regulation, and crosstalk.

Identification of genes governing resistance to PCN (Globodera rostochiensis) through transcriptome analysis in Solanum tuberosum

Potato cyst nematodes (PCNs) are major pests worldwide that affect potato production. The molecular changes happening in the roots upon PCN infection are still unknown. Identification of transcripts and genes governing PCN resistance will help in the development of resistant varieties. Hence, differential gene expression of compatible (Kufri Jyoti) and incompatible (JEX/A-267) potato genotypes was studied before (0 DAI) and after (10 DAI) inoculation of Globodera rostochiensis J2s through RNA sequencing (RNA-Seq). Total sequencing reads generated ranged between 33 and 37 million per sample, with a read mapping of 48-84% to the potato reference genome. In the infected roots of the resistant genotype JEX/A-267, 516 genes were downregulated, and 566 were upregulated. In comparison, in the susceptible genotype Kufri Jyoti, 316 and 554 genes were downregulated and upregulated, respectively. Genes encoding cell wall proteins, zinc finger protein, WRKY transcription factors, MYB transcription factors, disease resistance proteins, and pathogenesis-related proteins were found to be majorly involved in the incompatible reaction after PCN infection in the resistant genotype, JEX/A-267. Furthermore, RNA-Seq results were validated through quantitative real-time PCR (qRT-PCR), and it was observed that ATP, FLAVO, CYTO, and GP genes were upregulated at 5 DAI, which was subsequently downregulated at 10 DAI. The genes encoding ATP, FLAVO, LBR, and GP were present in > 1.5 fold before infection in JEX-A/267 and upregulated 7.9- to 27.6-fold after 5 DAI; subsequently, most of these genes were downregulated to 0.9- to 2.8-fold, except LBR, which was again upregulated to 44.4-fold at 10 DAI.

Identification of novel resources for panicle blast resistance from wild rice accessions and mutants of cv. Nagina 22 by syringe inoculation under field conditions

Panicle blast is the most severe type of rice blast disease. Screening of rice genotypes for panicle blast resistance at the field level requires an efficient and robust method of inoculation. Here, we standardized a method that can be utilized for both small- and large-scale screening and assessment of panicle blast infection and disease reaction. The method involves inoculation of Magnaporthe oryzae spore culture in the neck of the rice panicle using a syringe and covering the inoculation site with wet cotton wrapped with aluminum foil to provide the required humidity for spore germination. The method was standardized using panicle blast-resistant cv. Tetep and susceptible cv. HP2216 inoculated with Mo-ni-025 isolate of M. oryzae. The method was evaluated at phenotypic as well as molecular level by expression analysis of disease responsive pathogenesis-related (PR) genes. We found this method simple, robust, reliable, and highly efficient for screening of large germplasm sets of rice for panicle blast. This was validated by screening the wild rice germplasm for panicle blast response in the field using three M. oryzae strains and subsequently with the most virulent strain in 45 EMS-induced mutants of Nagina 22 shortlisted based on field screening in a blast hotspot region. We identified five novel blast disease-resistant wild rice genotypes and 15 Nagina 22 mutants that can be used in breeding programmes.

Enhanced thermo-tolerance in transgenic potato (Solanum tuberosum L.) overexpressing hydrogen peroxide-producing germin-like protein (GLP)

Germins and germin-like proteins (GLPs) were reported to participate in plant response to biotic and abiotic stresses involving hydrogen peroxide (H₂O₂) production, but their role in mitigating heat stress is poorly understood. Here, we investigated the ability of a Solanum tuberosum L. GLP (StGLP) gene isolated from the yeast cDNA library generated from heat-stressed potato plants and characterized its role in generating innate and/or acquired thermo-tolerance to potato via genetic transformation. The transgenic plants exhibited enhanced tolerance to gradual heat stress (GHS) compared with sudden heat shock (SHS) in terms of maximal cell viability, minimal ion leakage and reduced chlorophyll breakdown. Further, three StGLP transgenic lines (G9, G12 and G15) exhibited enhanced production of H₂O₂, which was either reduced or blocked by inhibitors of H₂O₂ under normal and heat stress conditions. This tolerance was mediated by up-regulation of antioxidant enzymes (catalase, ascorbate peroxidase and glutathione reductase) and other heat stress-responsive genes (StHSP70, StHSP20 and StHSP90) in transgenic potato plants. These results demonstrate that H₂O₂ produced by over-expression of StGLP in transgenic potato plants triggered the reactive oxygen species (ROS) scavenging signaling pathways controlling antioxidant and heat stress-responsive genes in these plants imparting tolerance to heat stress.

Differential regulation of the durum wheat Pathogenesis-related protein (PR1) by Calmodulin TdCaM1.3 protein

In plants, pathogenesis-related 1 protein (PR1) is considered as important defense protein. The production and accumulation of PR proteins in plants are one of the important responses to several biotic and abiotic stresses. In this regard, PR1 gene was isolated from Triticum turgidum ssp durum and was named as TdPR1.2. The amino acid sequence of TdPR1.2 protein showed 100%, 97.13%, and 44.41% with known PR1 proteins isolated from Triticum aestivum TdPR1-18, PRB1.2 of Aegilops tauschii subsp. tauschii and Arabidopsis thaliana respectively. qRT-PCR showed that TdPR1.2 was induced specially in leaves of durum wheat treated with Salicylic acid for 48 h. Besides, bioinformatic analysis showed that the durum wheat TdPR1.2 harbors a calmodulin binding domain located in it's C-terminal part and that this domain is conserved among different PR1 proteins isolated so far. However, no information is available about the regulation of PR genes by calmodulin and Ca²⁺ complex (CaM/Ca²⁺). Here, we showed that TdPR1.2 gene exhibits an antibacterial effect as revealed by the in vitro tests against 8 different bacteria and against the fungi Septoria tritici. In addition, we demonstrate for the first time that PR1 proteins are able to bind to CaM in a Ca²⁺-dependent manner via a GST-Pull down assay. Finally, in presence of Mn²⁺ cations, CaM/Ca²⁺ complex stimulated the antimicrobial effect of TdPR1.2. Such effects were not reported so far, and raise a possible role for CaM/Ca²⁺ complex in the regulation of plant PRs during cellular response to external signals.

Capsicum annum Hsp26.5 promotes defense responses against RNA viruses via ATAF2 but is hijacked as a chaperone for tobamovirus movement protein

The expression of Capsicum annuum HEAT SHOCK PROTEIN 26.5 (CaHsp26.5) was triggered by the inoculation of Tobacco mosaic virus pathotype P0 (TMV-P0) but its function in the defense response of plants is unknown. We used gene silencing and overexpression approaches to investigate the effect of CaHsp26.5 expression on different plant RNA viruses. Moreover, we performed protein-protein and protein-RNA interaction assays to study the mechanism of CaHsp26.5 function. CaHsp26.5 binding to a short poly-cytosine motif in the 3'-untranslated region of the genome of some viruses triggers the expression of several defense-related genes such as PATHOGENESIS-RELATED GENE 1 with the help of a transcription factor, NAC DOMAIN-CONTAINING PROTEIN 81 (ATAF2). Thus, an elevated CaHsp26.5 level was accompanied by increased plant resistance against plant viruses such as Cucumber mosaic virus strain Korea. However, the movement proteins of Pepper mild mottle virus pathotype P1,2,3 and TMV-P0 were shown to be able to interact with CaHsp26.5 to maintain the integrity of their proteins. Our work shows CaHsp26.5 as a positive player in the plant defense response against several plant RNA viruses. However, some tobamoviruses can hijack CaHsp26.5's chaperone activity for their own benefit.

Molecular evidence for the involvement of cotton GhGLP2, in enhanced resistance to Verticillium and Fusarium Wilts and oxidative stress

Germin-like proteins (GLPs) are a diverse and ubiquitous family of plant glycoproteins belonging to the cupin super family; they play considerable roles in plant responses against various abiotic and biotic stresses. Here, we provide evidence that GLP2 protein from cotton (Gossypium hirsutum) functions in plant defense responses against Verticillium dahliae, Fusarium oxysporum and oxidative stress. Purified recombinant GhGLP2 exhibits superoxide dismutase (SOD) activity and inhibits spore germination of pathogens. Virus-induced silencing of GhGLP2 in cotton results in increased susceptibility to pathogens, plants exhibited severe wilt on leaves, enhanced vascular browning and suppressed callose deposition. Transgenic Arabidopsis (Arabidopsis thaliana) plants overexpressing GhGLP2 showed significant resistance to V. dahliae and F. oxysporum, with reduced mycelia growth, increased callose deposition and cell wall lignification at infection sites on leaves. The enhanced tolerance of GhGLP2-transgenic Arabidopsis to oxidative stress was investigated by methyl viologen and ammonium persulfate treatments, along with increased H₂O₂ production. Further, the expression of several defense-related genes (PDF1.2, LOX2, and VSP1) or oxidative stress-related genes (RbohD, RbohF) was triggered by GhGLP2. Thus, our results confirmed the involvement of GhGLP2 in plant defense response against Verticillium and Fusarium wilt pathogens and stress conditions.

Functional characterization of the rice root Germin-like protein gene-1 (OsRGLP1) promoter in Nicotiana tabacum

Germin (GER) and germin-like protein (GLP) genes play a very important role against various stresses. Promoter analysis provide significant insight into gene's function and regulation. Presently, upstream region (1228 bp) of the OsRGLP1 gene was functionally characterized via heterologous expression. It was fused with the Glucuronidase (GUS) reporter gene and the expression cassette was used to transform Nicotiana tabacum using Agrobacterium-mediated transformation. Transgenic plants were examined via quantitative real-time PCR (qPCR) to analyze its role in wounding, salinity, drought, abscisic acid (ABA) and circadian rhythm. OsRGLP1 was highly induced by ABA and drought by showing 28- and 25-fold changes in GUS mRNA level respectively as compared to wounding (fourfold change) and salinity (threefold change). However, no activity was observed in circadian rhythm. Histochemically, strong GUS activity was observed in leaf veins, midrib, epidermal hair, stomata guard cells, stem cortex, root hairs, xylem and phloem and at cellular level in cell wall, cytoplasm and its periphery. OsRGLP1 promoter can be used to develop agronomically important transgenic plants in future food program.

Comparative Proteomic Analysis of Wheat Carrying Pm40 Response to Blumeria graminis f. sp. tritici Using Two-Dimensional Electrophoresis

Wheat powdery mildew caused by Blumeria graminis f. sp. tritici (Bgt) is considered a major wheat leaf disease in the main wheat producing regions of the world. Although many resistant wheat cultivars to this disease have been developed, little is known about their resistance mechanisms. Pm40 is a broad, effective resistance gene against powdery mildew in wheat line L699. The aim of this study was to investigate the resistance proteins after Bgt inoculation in wheat lines L699, Neimai836, and Chuannong26. Neimai836 with Pm21 was used as the resistant control, and Chuannong26 without any effective Pm genes was the susceptible control. Proteins were extracted from wheat leaves sampled 2, 4, 8, 12, and 24 h after Bgt inoculation, separated by two-dimensional electrophoresis, and stained with Coomassie brilliant blue G-250. The results showed that different proteins were upregulated and downregulated in three wheat cultivars at different time points. For the wheat cultivar L699, a total of 62 proteins were upregulated and 71 proteins were downregulated after Bgt inoculation. Among these, 46 upregulated proteins were identified by mass spectrometry analysis using the NCBI nr database of Triticum. The identified proteins were predicted to be associated with the defense response, photosynthesis, signal transduction, carbohydrate metabolism, energy pathway, protein turnover, and cell structure functions. It is inferred that the proteins are not only involved in defense response, but also other physiological and cellular processes to confer wheat resistance against Bgt. Therefore, the resistance products potentially mediate the immune response and coordinate other physiological and cellular processes during the resistance response to Bgt. The lipoxygenase, glucan exohydrolase, glucose adenylyltransferasesmall, phosphoribulokinase, and phosphoglucomutase are first reported to be involved in the interactions of wheat-Bgt at early stage. The further study of these proteins will deepen our understanding of their detailed functions and potentially develop more efficient disease control strategies.

Catalytic and Structural Characterization of a Browning-Related Protein in Oriental Sweet Melon (Cucumis Melo var. Makuwa Makino)

Polyphenol oxidase (PPO) in plants plays an important role in browning reactions and may affect the quality of sweet melon products. In this study, a browning-related protein (BRP) with PPO activity was partially purified from oriental sweet melon (Cucumis melo var. makuwa Makino) by salt precipitation and column chromatography. The BRP possessed a high degree of identity with several chitinase proteins, particularly defense-related proteins, by MS identification. Pyrogallol was determined as the most appropriate substrate for BRP (K_m = 0.04278 M). BRP exhibited extreme resistance under alkaline and high temperature conditions when pyrogallol was used as substrate. Polyacrylamide gel electrophoresis (PAGE) analysis indicated that BRP was a homo-dimer of two subunits and had a molecular weight of 37 kDa. Structural analysis indicated that the α-helix was the dominant conformation of BRP. The active site of the protein might be buried deeply in the protein, and BRP might be monodispersed in an aqueous system.

New reference genome sequences of hot pepper reveal the massive evolution of plant disease-resistance genes by retroduplication

BACKGROUND

Transposable elements are major evolutionary forces which can cause new genome structure and species diversification. The role of transposable elements in the expansion of nucleotide-binding and leucine-rich-repeat proteins (NLRs), the major disease-resistance gene families, has been unexplored in plants.

RESULTS

We report two high-quality de novo genomes (Capsicum baccatum and C. chinense) and an improved reference genome (C. annuum) for peppers. Dynamic genome rearrangements involving translocations among chromosomes 3, 5, and 9 were detected in comparison between C. baccatum and the two other peppers. The amplification of athila LTR-retrotransposons, members of the gypsy superfamily, led to genome expansion in C. baccatum. In-depth genome-wide comparison of genes and repeats unveiled that the copy numbers of NLRs were greatly increased by LTR-retrotransposon-mediated retroduplication. Moreover, retroduplicated NLRs are abundant across the angiosperms and, in most cases, are lineage-specific.

CONCLUSIONS

Our study reveals that retroduplication has played key roles for the massive emergence of NLR genes including functional disease-resistance genes in pepper plants.

Transcriptome Analysis of Capsicum Chlorosis Virus-Induced Hypersensitive Resistance Response in Bell Capsicum

BACKGROUND

Capsicum chlorosis virus (CaCV) is an emerging pathogen of capsicum, tomato and peanut crops in Australia and South-East Asia. Commercial capsicum cultivars with CaCV resistance are not yet available, but CaCV resistance identified in Capsicum chinense is being introgressed into commercial Bell capsicum. However, our knowledge of the molecular mechanisms leading to the resistance response to CaCV infection is limited. Therefore, transcriptome and expression profiling data provide an important resource to better understand CaCV resistance mechanisms.

METHODOLOGY/PRINCIPAL FINDINGS

We assembled capsicum transcriptomes and analysed gene expression using Illumina HiSeq platform combined with a tag-based digital gene expression system. Total RNA extracted from CaCV/mock inoculated CaCV resistant (R) and susceptible (S) capsicum at the time point when R line showed a strong hypersensitive response to CaCV infection was used in transcriptome assembly. Gene expression profiles of R and S capsicum in CaCV- and buffer-inoculated conditions were compared. None of the genes were differentially expressed (DE) between R and S cultivars when mock-inoculated, while 2484 genes were DE when inoculated with CaCV. Functional classification revealed that the most highly up-regulated DE genes in R capsicum included pathogenesis-related genes, cell death-associated genes, genes associated with hormone-mediated signalling pathways and genes encoding enzymes involved in synthesis of defense-related secondary metabolites. We selected 15 genes to confirm DE expression levels by real-time quantitative PCR.

CONCLUSION/SIGNIFICANCE

DE transcript profiling data provided comprehensive gene expression information to gain an understanding of the underlying CaCV resistance mechanisms. Further, we identified candidate CaCV resistance genes in the CaCV-resistant C. annuum x C. chinense breeding line. This knowledge will be useful in future for fine mapping of the CaCV resistance locus and potential genetic engineering of resistance into CaCV-susceptible crops.

Laser Microdissection of Grapevine Leaves Reveals Site-Specific Regulation of Transcriptional Response to Plasmopara viticola

Grapevine is one of the most important fruit crops in the world, and it is highly susceptible to downy mildew caused by the biotrophic oomycete Plasmopara viticola. Gene expression profiling has been used extensively to investigate the regulation processes of grapevine-P. viticola interaction, but all studies to date have involved the use of whole leaves. However, only a small fraction of host cells is in contact with the pathogen, so highly localized transcriptional changes of infected cells may be masked by the large portion of non-infected cells when analyzing the whole leaf. In order to understand the transcriptional regulation of the plant reaction at the sites of pathogen infection, we optimized a laser microdissection protocol and analyzed the transcriptional changes in stomata cells and surrounding areas of grapevine leaves at early stages of P. viticola infection. The results indicate that the expression levels of seven P. viticola-responsive genes were greater in microdissected cells than in whole leaves, highlighting the site-specific transcriptional regulation of the host response. The gene modulation was restricted to the stomata cells and to the surrounding areas of infected tissues, indicating that the host response is mainly located at the infection sites and that short-distance signals are implicated. In addition, due to the high sensitivity of the laser microdissection technique, significant modulations of three genes that were completely masked in the whole tissue analysis were detected. The protocol validated in this study could greatly increase the sensitivity of further transcriptomic studies of the grapevine-P. viticola interaction.

Silencing of a Germin-Like Protein Gene (CchGLP) in Geminivirus-Resistant Pepper (Capsicum chinense Jacq.) BG-3821 Increases Susceptibility to Single and Mixed Infections by Geminiviruses PHYVV and PepGMV

Germin-like proteins (GLPs) are encoded by a family of genes found in all plants, and in terms of function, the GLPs are implicated in the response of plants to biotic and abiotic stresses. CchGLP is a gene encoding a GLP identified in a geminivirus-resistant Capsicum chinense Jacq accession named BG-3821, and it is important in geminivirus resistance when transferred to susceptible tobacco in transgenic experiments. To characterize the role of this GLP in geminivirus resistance in the original accession from which this gene was identified, this work aimed at demonstrating the possible role of CchGLP in resistance to geminiviruses in Capsicum chinense Jacq. BG-3821. Virus-induced gene silencing studies using a geminiviral vector based in PHYVV component A, displaying that silencing of CchGLP in accession BG-3821, increased susceptibility to geminivirus single and mixed infections. These results suggested that CchGLP is an important factor for geminivirus resistance in C. chinense BG-3821 accession.

Isolation and Characterization of a Novel Pathogenesis-Related Protein Gene (GmPRP) with Induced Expression in Soybean (Glycine max) during Infection with Phytophthora sojae

Pathogenesis-related proteins (PR proteins) play crucial roles in the plant defense system. A novel PRP gene was isolated from highly resistant soybean infected with Phytophthora sojae (P. sojae) and was named GmPRP (GenBank accession number: KM506762). The amino acid sequences of GmPRP showed identities of 74%, 73%, 72% and 69% with PRP proteins from Vitis vinifera, Populus trichocarpa, Citrus sinensis and Theobroma cacao, respectively. Quantitative real-time reverse transcription PCR (qRT-PCR) data showed that the expression of GmPRP was highest in roots, followed by the stems and leaves. GmPRP expression was upregulated in soybean leaves infected with P. sojae. Similarly, GmPRP expression also responded to defense/stress signaling molecules, including salicylic acid (SA), ethylene (ET), abscisic acid (ABA) and jasmonic acid (JA). GmPRP was localized in the cell plasma membrane and cytoplasm. Recombinant GmPRP protein exhibited ribonuclease activity and significant inhibition of hyphal growth of P. sojae 1 in vitro. Overexpression of the GmPRP gene in T2 transgenic tobacco and T2 soybean plants resulted in enhanced resistance to Phytophthora nicotianae (P. nicotianae) and P. sojae race 1, respectively. These results indicated that the GmPRP protein played an important role in the defense of soybean against P. sojae infection.

Developmental stimuli and stress factors affect expression of ClGLP1, an emerging allergen-related gene in Citrus limon

Germins and germin-like proteins (GLPs) constitute an ubiquitous family of plant proteins that seem to be involved in many developmental and stress related processes. A novel GLP cDNA was isolated from Citrus limon and structural features and genomic organization were investigated by in silico and Southern blots analysis. In lemon, the ClGLP1 encodes a 24.38 kDa which possesses a conserved motif of plant GLPs proteins. A phylogetic analysis mapped ClGLP1 as belonging to the GER3 subfamily into the GLP1 group of large GLP family. ClGLP1 was differentially expressed in the various organs and was highest in mature fruit. Moreover, expression in the fruit was tissue- and stage-related as well as dependent on agricultural practice (organic vs conventional). ClGLP1 transcripts increased during the transition from the green (180 days after blooming) to the yellow (240 days after blooming) mature fruit and were strongly enhanced in yellow mature fruit from organic compared with conventional culture. A sudden and systemic increase in ClGLP1 expression level was observed in leaves injured by wounding, together with an increase of endogenous H2O2 amount. Notably, an enhancement of H202 was observed in fruit peel during transition from green to yellow fruit stage. All together our data showed that ClGLP1 expression can be modulated in relation to both developmental stimuli and culture practices; evidence is also provided that through an oxidase activity this gene could play a role in fruit maturation as well as in stress responses.

Characterization of peanut germin-like proteins, AhGLPs in plant development and defense

Background

Germin-like superfamily members are ubiquitously expressed in various plant species and play important roles in plant development and defense. Although several GLPs have been identified in peanut (Arachis hypogaea L.), their roles in development and defense remain unknown. In this research, we study the spatiotemporal expression of AhGLPs in peanut and their functions in plant defense.

Results

We have identified three new AhGLP members (AhGLP3b, AhGLP5b and AhGLP7b) that have distinct but very closely related DNA sequences. The spatial and temporal expression profiles revealed that each peanut GLP gene has its distinct expression pattern in various tissues and developmental stages. This suggests that these genes all have their distinct roles in peanut development. Subcellular location analysis demonstrated that AhGLP2 and 5 undergo a protein transport process after synthesis. The expression of all AhGLPs increased in responding to Aspergillus flavus infection, suggesting AhGLPs' ubiquitous roles in defense to A. flavus. Each AhGLP gene had its unique response to various abiotic stresses (including salt, H₂O₂ stress and wound), biotic stresses (including leaf spot, mosaic and rust) and plant hormone stimulations (including SA and ABA treatments). These results indicate that AhGLPs have their distinct roles in plant defense. Moreover, in vivo study of AhGLP transgenic Arabidopsis showed that both AhGLP2 and 3 had salt tolerance, which made transgenic Arabidopsis grow well under 100 mM NaCl stress.

Conclusions

For the first time, our study analyzes the AhGLP gene expression profiles in peanut and reveals their roles under various stresses. These results provide an insight into the developmental and defensive roles of GLP gene family in peanut.

Comparisons of protein profiles of beech bark disease resistant and susceptible American beech (Fagus grandifolia)

BACKGROUND

Beech bark disease is an insect-fungus complex that damages and often kills American beech trees and has major ecological and economic impacts on forests of the northeastern United States and southeastern Canadian forests. The disease begins when exotic beech scale insects feed on the bark of trees, and is followed by infection of damaged bark tissues by one of the Neonectria species of fungi. Proteomic analysis was conducted of beech bark proteins from diseased trees and healthy trees in areas heavily infested with beech bark disease. All of the diseased trees had signs of Neonectria infection such as cankers or fruiting bodies. In previous tests reported elsewhere, all of the diseased trees were demonstrated to be susceptible to the scale insect and all of the healthy trees were demonstrated to be resistant to the scale insect. Sixteen trees were sampled from eight geographically isolated stands, the sample consisting of 10 healthy (scale-resistant) and 6 diseased/infested (scale-susceptible) trees.

RESULTS

Proteins were extracted from each tree and analysed in triplicate by isoelectric focusing followed by denaturing gel electrophoresis. Gels were stained and protein spots identified and intensity quantified, then a statistical model was fit to identify significant differences between trees. A subset of BBD differential proteins were analysed by mass spectrometry and matched to known protein sequences for identification. Identified proteins had homology to stress, insect, and pathogen related proteins in other plant systems. Protein spots significantly different in diseased and healthy trees having no stand or disease-by-stand interaction effects were identified.

CONCLUSIONS

Further study of these proteins should help to understand processes critical to resistance to beech bark disease and to develop biomarkers for use in tree breeding programs and for the selection of resistant trees prior to or in early stages of BBD development in stands. Early identification of resistant trees (prior to the full disease development in an area) will allow forest management through the removal of susceptible trees and their root-sprouts prior to the onset of disease, allowing management and mitigation of costs, economic impact, and impacts on ecological systems and services.

Members of the germin-like protein family in Brassica napus are candidates for the initiation of an oxidative burst that impedes pathogenesis of Sclerotinia sclerotiorum

Germin-like proteins (GLPs) are defined by their sequence homology to germins from barley and are present ubiquitously in plants. Analyses of corresponding genes have revealed diverse functions of GLPs in plant development and biotic and abiotic stresses. This study describes the identification of a family of 14 germin-like genes from Brassica napus (BnGLP) designated BnGLP1-BnGLP14 and investigated potential functions of BnGLPs in plant defense against the necrotrophic fungus Sclerotinia sclerotiorum. Sequence alignment and phylogenetic analyses classify the 14 BnGLPs into four groups, which were clearly distinguished from known germin oxalic acid oxidases. Transcriptional responses of the BnGLP genes to S. sclerotiorum infection was determined by comparing cultivars of susceptible B. napus 'Falcon' and partially resistant B. napus 'Zhongshuang 9'. Of the 14 BnGLP genes tested, BnGLP3 was transcriptionally upregulated in both B. napus cultivars at 6h after S. sclerotiorum infection, while upregulation of BnGLP12 was restricted to resistant B. napus 'Zhongshuang 9'. Biochemical analysis of five representative BnGLP members identified a H(2)O(2)-generating superoxide dismutase activity only for higher molecular weight complexes of BnGLP3 and BnGLP12. By analogy, H(2)O(2) formation at infected leaf sites increased after 6h, with even higher H(2)O(2) production in B. napus 'Zhongshuang 9' compared with B. napus 'Falcon'. Conversely, exogenous application of H(2)O(2) significantly reduced the susceptibility of B. napus 'Falcon'. These data suggest that early induction of BnGLP3 and BnGLP12 participates in an oxidative burst that may play a pivotal role in defence of B. napus against S. sclerotiorum.

Dissecting Phaseolus vulgaris innate immune system against Colletotrichum lindemuthianum infection

Background

The genus Colletotrichum is one of the most economically important plant pathogens, causing anthracnose on a wide range of crops including common beans (Phaseolus vulgaris L.). Crop yield can be dramatically decreased depending on the plant cultivar used and the environmental conditions. This study aimed to identify potential genetic components of the bean immune system to provide environmentally friendly control measures against this fungus.

Methodology and Principal Findings

As the common bean is not amenable to reverse genetics to explore functionality and its genome is not fully curated, we used putative Arabidopsis orthologs of bean expressed sequence tag (EST) to perform bioinformatic analysis and experimental validation of gene expression to identify common bean genes regulated during the incompatible interaction with C. lindemuthianum. Similar to model pathosystems, Gene Ontology (GO) analysis indicated that hormone biosynthesis and signaling in common beans seem to be modulated by fungus infection. For instance, cytokinin and ethylene responses were up-regulated and jasmonic acid, gibberellin, and abscisic acid responses were down-regulated, indicating that these hormones may play a central role in this pathosystem. Importantly, we have identified putative bean gene orthologs of Arabidopsis genes involved in the plant immune system. Based on experimental validation of gene expression, we propose that hypersensitive reaction as part of effector-triggered immunity may operate, at least in part, by down-regulating genes, such as FLS2-like and MKK5-like, putative orthologs of the Arabidopsis genes involved in pathogen perception and downstream signaling.

Conclusions/Significance

We have identified specific bean genes and uncovered metabolic processes and pathways that may be involved in the immune response against pathogens. Our transcriptome database is a rich resource for mining novel defense-related genes, which enabled us to develop a model of the molecular components of the bean innate immune system regulated upon pathogen attack.

Nitrogen under- and over-supply induces distinct protein responses in maize xylem sap

Xylem sap primarily transports water and mineral nutrients such as nitrogen (N) from roots to shoots in vascular plants. However, it remains largely unknown how nitrogenous compounds, especially proteins in xylem sap, respond to N under- or over-supply. We found that reducing N supply increased amino-N percentage of total N in maize (Zea mays L.) xylem sap. Proteomic analysis showed that 23 proteins in the xylem sap of maize plants, including 12 newly identified ones, differentially accumulated in response to various N supplies. Fifteen of these 23 proteins were primarily involved in general abiotic or biotic stress responses, whereas the other five proteins appeared to respond largely to N under- or over-supply, suggesting distinct protein responses in maize xylem upon N under- and over-supply. Furthermore, one putative xylanase inhibitor and two putative O-glycosyl hydrolases had preferential gene expression in shoots.

A germin-like protein gene (CchGLP) of Capsicum chinense Jacq. is induced during incompatible interactions and displays Mn-superoxide dismutase activity

A germin-like gene (CchGLP) cloned from geminivirus-resistant pepper (Capsicum chinense Jacq. Line BG-3821) was characterized and the enzymatic activity of the expressed protein analyzed. The predicted protein consists of 203 amino acids, similar to other germin-like proteins. A highly conserved cupin domain and typical germin boxes, one of them containing three histidines and one glutamate, are also present in CchGLP. A signal peptide was predicted in the first 18 N-terminal amino acids, as well as one putative N-glycosylation site from residues 44-47. CchGLP was expressed in E. coli and the recombinant protein displayed manganese superoxide dismutase (Mn-SOD) activity. Molecular analysis showed that CchGLP is present in one copy in the C. chinense Jacq. genome and was induced in plants by ethylene (Et) and salicylic acid (SA) but not jasmonic acid (JA) applications in the absence of pathogens. Meanwhile, incompatible interactions with either Pepper golden mosaic virus (PepGMV) or Pepper huasteco yellow vein virus (PHYVV) caused local and systemic CchGLP induction in these geminivirus-resistant plants, but not in a susceptible accession. Compatible interactions with PHYVV, PepGMV and oomycete Phytophthora capsici did not induce CchGLP expression. Thus, these results indicate that CchGLP encodes a Mn-SOD, which is induced in the C. chinense geminivirus-resistant line BG-3821, likely using SA and Et signaling pathways during incompatible interactions with geminiviruses PepGMV and PHYVV.

Use of a secretion trap screen in pepper following Phytophthora capsici infection reveals novel functions of secreted plant proteins in modulating cell death

In plants, the primary defense against pathogens is mostly inducible and associated with cell wall modification and defense-related gene expression, including many secreted proteins. To study the role of secreted proteins, a yeast-based signal-sequence trap screening was conducted with the RNA from Phytophthora capsici-inoculated root of Capsicum annuum 'Criollo de Morelos 334' (CM334). In total, 101 Capsicum annuum secretome (CaS) clones were isolated and identified, of which 92 were predicted to have a secretory signal sequence at their N-terminus. To identify differences in expressed CaS genes between resistant and susceptible cultivars of pepper, reverse Northern blots and real-time reverse-transcription polymerase chain reaction were performed with RNA samples isolated at different time points following P. capsici inoculation. In an attempt to assign biological functions to CaS genes, we performed in planta knock-down assays using the Tobacco rattle virus-based gene-silencing method. Silencing of eight CaS genes in pepper resulted in suppression of the cell death induced by the non-host bacterial pathogen (Pseudomonas syringae pv. tomato T1). Three CaS genes induced phenotypic abnormalities in silenced plants and one, CaS259 (PR4-l), caused both cell death suppression and perturbed phenotypes. These results provide evidence that the CaS genes may play important roles in pathogen defense as well as developmental processes.

Regulation of two germin-like protein genes during plum fruit development

Germin-like proteins (GLPs) have several proposed roles in plant development and defence. Two novel genes (Ps-GLP1 and 2) encoding germin-like protein were isolated from plum (Prunus salicina). Their regulation was studied throughout fruit development and during ripening of early and late cultivars. These two genes exhibited similar expression patterns throughout the various stages of fruit development excluding two important stages, pit hardening (S2) and fruit ripening (S4). During fruit development until the ripening phase, the accumulation of both Ps-GLPs is related to the evolution of auxin. However, during the S2 stage only Ps-GLP1 is induced and this could putatively be in a H(2)O(2)-dependent manner. On the other hand, the diversity in the Ps-GLPs accumulation profile during the ripening process seems to be putatively due to the variability of endogenous auxin levels among the two plum cultivars, which consequently change the levels of autocatalytic ethylene available for the fruit to co-ordinate ripening. The effect of auxin on stimulating ethylene production and in regulating Ps-GLPs transcripts was also investigated. These data, supported by their localization in the extracellular matrix, suggest that auxin is somehow involved in the regulation of both transcripts throughout fruit development and ripening.

Molecular cloning of a PR-5 like protein gene from cherry tomato and analysis of the response of this gene to abiotic stresses

LePR-5, a putative PR5 like protein gene was amplified from a cherry tomato (Lycopersicon esculentum), which encodes a precursor protein of 250 amino acid residues, and shares high degrees of homology with a number of other PR5 genes. Expression of LePR-5 in different tomato organs was analyzed with Semi-quantitative RT-PCR, showing that LePR-5 expressed at different levels in leaves, stems, roots, flowers and fruits. In addition, expression of LePR-5 under different abiotic stresses was carried out at different time points. Three of the four tested abiotic stimuli, ethophen, salicylic acid and methyl jasmonate, triggered a significant induction of LePR-5 after treatment. However, LePR-5 was weaker induced by abscisic acid than by others. The positive responses of LePR-5 to the three abiotic stimuli suggested that LePR-5 may play an important role in response to abiotic stresses, and it may also be involved in plant defense system against pathogens. In addition, different expression patterns between tomato fruit and seedling suggested that LePR-5 may play a distinctive role in the defensive system protecting tomato fruit and seedling.

Molecular characterization of a novel soybean gene encoding a neutral PR-5 protein induced by high-salt stress

In this study, we characterized a novel soybean gene encoding a neutral PR-5 protein and compared it to two acidic isoforms of soybean PR-5 protein. This gene, designated as Glycine max osmotin-like protein, b isoform (GmOLPb, accession no. AB370233), encoded a putative protein having the greatest similarity to chickpea PR-5b (89% identity). Unlike the two acidic PR-5, GmOLPa and P21, the protein had a C-terminal elongation responsible for possible vacuolar targeting and after maturation showed a calculated molecular mass of 21.9kDa with pI 6.0. The 3D models, predicted by the homology modeling, contained four alpha-helixes and 16 beta-strands and formed three characteristic domains. The two acidic PR-5 proteins also showed a 3D structure very similar to GmOLPb, although the electrostatic potential on molecular surface of each PR-5 was significantly different. In the study of the gene expression under conditions of high-salt stress, GmOLPb was highly induced in the leaves of the soybean, particularly in the lower part of a leaf. The expression started at 2h after initiation of the stress and was highly induced between 18-72h. Gene expression of P21e (protein homologous to P21) was transiently induced by high-salt stress, but took place earlier than the gene expressions of GmOLPa and GmOLPb. Such differential expression was observed also under investigation with methyl jasmonate and salicylic acid. These results suggested that each soybean PR-5 might play a distinctive role in the defensive system protecting the soybean plant against high-salt stress, particularly in the leaves of the soybean.

MicroRNAs in loblolly pine (Pinus taeda L.) and their association with fusiform rust gall development

MicroRNAs (miRNAs) are endogenous small RNAs that can have large-scale regulatory effects on development and on stress responses in plants. The endemic rust fungus Cronartium quercuum f. sp. fusiforme causes fusiform rust disease in pines, resulting in the development of spindle-shaped galls (cankers) on branches or stems. This disease is the most destructive disease of pines in the southern USA. To test whether miRNAs play roles in fusiform rust gall development, we cloned and identified 26 miRNAs from stem xylem of loblolly pine (Pinus taeda), which belong to four conserved and seven loblolly pine-specific miRNA families. Forty-three targets for nine of these 11 families were experimentally validated in vivo. Sequence analysis suggested that the target cleavage site may be determined not only by the miRNA sequence but also by the target sequence. Members of three loblolly pine-specific miRNA families target a large number of non-protein coding transcripts, and one of these families could also initiate secondary phased production from its target of a putative trans-acting short interfering RNA (ta-siRNA). Expression of 10 of these 11 miRNA families was significantly repressed in the galled stem. PCR-based transcript quantification showed complex expression patterns of these miRNAs and their targets in the galled tissues and in tissues surrounding the gall. We further predict 82 plant disease-related transcripts that may also response to miRNA regulation in pine. These results reveal a new genetic basis for host-pathogen interactions in the development of fusiform rust gall.

Induction of a grapevine germin-like protein (VvGLP3) gene is closely linked to the site of Erysiphe necator infection: a possible role in defense?

Germin-like proteins (GLP) have various proposed roles in plant development and defense. Seven novel GLP cDNA clones were isolated from grapevine (Vitis vinifera cv. Chardonnay). Reverse transcriptase-polymerase chain reaction expression analysis revealed that the VvGLP genes exhibit diverse and highly specific patterns of expression in response to a variety of abiotic and biotic treatments, including challenge by Erysiphe necator, Plasmopara viticola, and Botrytis cinerea, suggesting a diversity of roles for each of the GLP family members. Significantly, one of the grapevine GLP genes, VvGLP3, is induced specifically by E. necator infection and expression is closely linked to the site of infection. Subcellular localization of VvGLP3 determined by transient expression of a VvGLP3:GFP fusion construct in onion cells indicated that the recombinant protein was targeted to the cell wall. Recombinant VvGLP3 was successfully expressed in Arabidopsis thaliana and the partially purified recombinant protein was demonstrated to have superoxide dismutase activity. This data has provided an insight into the diverse nature of the GLP family in grapevine and suggests that VvGLP3 may be involved in the defense response against E. necator.

Transcriptional response of Citrus aurantifolia to infection by Citrus tristeza virus

Changes in gene expression of Mexican lime plants in response to infection with a severe (T305) or a mild (T385) isolate of Citrus tristeza virus (CTV) were analyzed using a cDNA microarray containing 12,672 probes to 6875 different citrus genes. Statistically significant (P<0.01) expression changes of 334 genes were detected in response to infection with isolate T305, whereas infection with T385 induced no significant change. Induced genes included 145 without significant similarity with known sequences and 189 that were classified in seven functional categories. Genes related with response to stress and defense were the main category and included 28% of the genes induced. Selected transcription changes detected by microarray analysis were confirmed by quantitative real-time RT-PCR. Changes detected in the transcriptome upon infecting lime with T305 may be associated either with symptom expression, with a strain-specific defense mechanism, or with a general response to stress.