Transcriptomic analysis towards identification of defence-responsive genes and pathways upon application of Sargassum seaweed extract on tomato plants infected with Macrophominaphaseolina

The charcoal-rot caused by Macrophomina phaseolina is one of the major disease in many economically important crop plants including tomato. The molecular responses of the host plant against the M. phaseolina are poorly stated. In the present study, for the first time the molecular insight of tomato-Macrophomina interaction and Sargassum tenerrimum extract (SE) toward managing disease through RNA-seq approach is established. A total of 449 million high-quality reads (HQRs) were obtained and aligned to the tomato genome with an average mapping of 89.12%. The differentially expressed genes (DEGs) regulated across the different treatment pairs were identified. Several DEGs, such as receptor-like kinases (SlRLKs), transcription factors including SlWRKY70, SlGRAS4, SlERF4, SlERF25, pathogenesis related-1 (SlPR1), SlPR2, endochitinase and peroxidase were significantly up-regulated in SE + Macrophomina treated sample as compared to only Macrophomina treated sample. The crosstalk between salicylic acid (SA), jasmonic acid (JA) and ethylene (ET) was a key factor to regulate resistance in tomato during SE + Macrophomina treatment. The KEGG pathway including plant hormone signal transduction, plant-pathogen interaction and mitogen-activated protein kinase (MAPK) signaling pathway were significantly enriched. The RNA-seq data were validated through qPCR using 12 disease-responsive genes and correlated significantly with R2 = 0.73. The present study suggests that SE act as an elicitor molecule and activate the defence-related pathways similar to PAMP-triggered immunity in tomato. The jasmonic acid (JA) mediated signaling pathway was identified as a key factor to induce resistance in tomato against Macrophomina infection. The present study depicts the beneficial effects of SE by regulating molecular mechanism towards defence responses in tomato against Macrophomina infection. The application of SE brings out new prospects to induce disease tolerance in the agricultural crops.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03565-4.

Land snails can trap trematode cercariae in their shell: Encapsulation as a general response against parasites?

Terrestrial gastropods are hosts of a wide variety of metazoan parasites and can respond to parasite exposure in various ways. One of these defence mechanisms, the ability to trap parasites in the host shell, was previously thought to apply only against nematodes. During a field survey along an urbanisation gradient, we found that the shell of Cornu aspersum and Cepaea nemoralis can contain encapsulated trematode cercariae, with prevalences of 7% and 1%, respectively over the entire sample, and up to 47% at the local population level. To our knowledge, this is the first case study unambiguously showing that land snails can trap non-nematode parasites in their shell at non-negligible prevalences. Shell-encapsulation could be a more general defence mechanism than previously described, and more studies are needed to understand its importance and variability.

Comparative transcriptome analysis reveals different defence responses during the early stage of wounding stress in Chi-Nan germplasm and ordinary Aquilaria sinensis

BACKGROUND

Agarwood is a valuable Chinese medicinal herb and spice that is produced from wounded Aquilaria spp., is widely used in Southeast Asia and is highly traded on the market. The lack of highly responsive Aquilaria lines has seriously restricted agarwood yield and the development of its industry. In this article, a comparative transcriptome analysis was carried out between ordinary A. sinensis and Chi-Nan germplasm, which is a kind of A. sinensis tree with high agarwood-producing capacity in response to wounding stress, to elucidate the molecular mechanism underlying wounding stress in different A. sinensis germplasm resources and to help identify and breed high agarwood-producing strains.

RESULTS

A total of 2427 and 1153 differentially expressed genes (DEGs) were detected in wounded ordinary A. sinensis and Chi-Nan germplasm compared with the control groups, respectively. KEGG enrichment analysis revealed that genes participating in starch metabolism, secondary metabolism and plant hormone signal transduction might play major roles in the early regulation of wound stress. 86 DEGs related to oxygen metabolism, JA pathway and sesquiterpene biosynthesis were identified. The majority of the expression of these genes was differentially induced between two germplasm resources under wounding stress. 13 candidate genes related to defence and sesquiterpene biosynthesis were obtained by WGCNA. Furthermore, the expression pattern of genes were verified by qRT-PCR. The candidate genes expression levels were higher in Chi-Nan germplasm than that in ordinary A. sinensis during early stage of wounding stress, which may play important roles in regulating high agarwood-producing capacity in Chi-Nan germplasm.

CONCLUSIONS

Compared with A. sinensis, Chi-Nan germplasm invoked different biological processes in response to wounding stress. The genes related to defence signals and sesquiterepene biosynthesis pathway were induced to expression differentially between two germplasm resources. A total of 13 candidate genes were identified, which may correlate with high agarwood-producting capacity in Chi-Nan germplasm during the early stage of wounding stress. These genes will contribute to the development of functional molecular markers and the rapid breeding highly of responsive Aquilaria lines.

Gene expression analysis of resistant and susceptible rice cultivars to sheath blight after inoculation with Rhizoctonia solani

BACKGROUND

Rice sheath blight, caused by Rhizoctonia solani Kühn (teleomorph: Thanatephorus cucumeris), is one of the most severe diseases in rice (Oryza sativa L.) worldwide. Studies on resistance genes and resistance mechanisms of rice sheath blight have mainly focused on indica rice. Rice sheath blight is a growing threat to rice production with the increasing planting area of japonica rice in Northeast China, and it is therefore essential to explore the mechanism of sheath blight resistance in this rice subspecies.

RESULTS

In this study, RNA-seq technology was used to analyse the gene expression changes of leaf sheath at 12, 24, 36, 48, and 72 h after inoculation of the resistant cultivar 'Shennong 9819' and susceptible cultivar 'Koshihikari' with R. solani. In the early stage of R. solani infection of rice leaf sheaths, the number of differentially expressed genes (DEGs) in the inoculated leaf sheaths of resistant and susceptible cultivars showed different regularity. After inoculation, the number of DEGs in the resistant cultivar fluctuated, while the number of DEGs in the susceptible cultivar increased first and then decreased. In addition, the number of DEGs in the susceptible cultivar was always higher than that in the resistant cultivar. After inoculation with R. solani, the overall transcriptome changes corresponding to multiple biological processes, molecular functions, and cell components were observed in both resistant and susceptible cultivars. These included metabolic process, stimulus response, biological regulation, catalytic activity, binding and membrane, and they were differentially regulated. The phenylalanine metabolic pathway; tropane, piperidine, and pyridine alkaloid biosynthesis pathways; and plant hormone signal transduction were significantly enriched in the early stage of inoculation of the resistant cultivar Shennong 9819, but not in the susceptible cultivar Koshihikari. This indicates that the response of the resistant cultivar Shennong 9819 to pathogen stress was faster than that of the susceptible cultivar. The expression of plant defense response marker PR1b gene, transcription factor OsWRKY30 and OsPAL1 and OsPAL6 genes that induce plant resistance were upregulated in the resistant cultivar. These data suggest that in the early stage of rice infection by R. solani, there is a pathogen-induced defence system in resistant rice cultivars, involving the expression of PR genes, key transcription factors, PAL genes, and the enrichment of defence-related pathways.

CONCLUSION

The transcriptome data revealed the molecular and biochemical differences between resistant and susceptible cultivars of rice after inoculation with R. solani, indicating that resistant cultivars have an immune response mechanism in the early stage of pathogen infection. Disease resistance is related to the overexpression of PR genes, key transcriptome factors, and PAL genes, which are potential targets for crop improvement.

Transcriptome and plant hormone analyses provide new insight into the molecular regulatory networks underlying hybrid lethality in cabbage (Brassica oleracea)

Comparative morphological, transcriptomic and phytohormone analyses reveal a defence network leading to PCD involved in cabbage hybrid lethality. Hybrid lethality (HL) plays an essential role in the stability of a population by blocking gene exchange between species, but the molecular mechanism remains largely undetermined. In this study, we performed phenotype, transcriptome and plant hormone analyses of HL in cabbage. Phenotype analysis confirmed that HL is characterised by a typical programmed cell death (PCD) process. A time-resolved RNA-Seq identified 2724 differentially expressed genes (DEGs), and functional annotations analyses revealed that HL was closely associated with the defence response. A defence regulation network was constructed based on the plant-pathogen interaction pathway and MAPK signalling pathway, which comprised DEGs related to Ca²⁺ and hydrogen peroxide (H₂O₂) leading to PCD. Moreover, important DEGs involved in hormone signal transduction pathways including salicylic acid (SA) and jasmonic acid (JA) were identified, which were further confirmed by endogenous and exogenous SA and JA measurements. Our results identified key genes and pathways in the regulating network of HL in cabbage, and might open the gate for revealing the molecular mechanism of HL in plants.

Mechanostimulation: a promising alternative for sustainable agriculture practices

Plants memorize events associated with environmental fluctuations. The integration of environmental signals into molecular memory allows plants to cope with future stressors more efficiently-a phenomenon that is known as 'priming'. Primed plants are more resilient to environmental stresses than non-primed plants, as they are capable of triggering more robust and faster defence responses. Interestingly, exposure to various forms of mechanical stimuli (e.g. touch, wind, or sound vibration) enhances plants' basal defence responses and stress tolerance. Thus, mechanostimulation appears to be a potential priming method and a promising alternative to chemical-based priming for sustainable agriculture. According to the currently available method, mechanical treatment needs to be repeated over a month to alter plant growth and defence responses. Such a long treatment protocol restricts its applicability to fast-growing crops. To optimize the protocol for a broad range of crops, we need to understand the molecular mechanisms behind plant mechanoresponses, which are complex and depend on the frequency, intervals, and duration of the mechanical treatment. In this review, we synthesize the molecular underpinnings of plant mechanoperception and signal transduction to gain a mechanistic understanding of the process of mechanostimulated priming.

ABCG transporter proteins with beneficial activity on plants

Among the several subfamilies of ABC transporters the ABC-G subfamily is very significant. In the model plant Arabidopsis thaliana itself, ABCG subfamily houses highest number of transporters with mostly half-size transporters (called WBC) and fewer full-size transporters (called PDR). During drought stress the stress hormone abscisic acid (ABA) is exported from the root xylem and imported by the leaf stomatal cells by ABCG transporter proteins to reduce the transpiration of water from leaves. Moreover, the ABCG transporters play a chief role in export of prime biotic stress induced hormones like jasmonic acid and salicylic acid among other secondary metabolites. In this way they protect the plant as the first line of defense against pathogenic damages. The ABCG transporters help the plant in becoming kanamycin resistant which help in plant growth. ABCG transporters of Nicotiana plumbaginifolia provide resistance to pathogens like Pseudomonas syringae. Furthermore several ABCG transporters of A. thaliana are efficient in transporting cuticular lipids like cutin to help development of cuticle. Pollen exine wall formation is also aided by one ABCG transporter itself. Some important ABCG transporters like ABCG36 and ABCG40 have been suggested to contribute hugely towards heavy metal resistance and cellular detoxification in Arabidopsis thaliana.

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.

Enhancement of adaptive response in peanut hairy root by exogenous signalling molecules under cadmium stress

Plants counteract Cd toxicity by activating cellular stress responses. The simultaneous exogenous application of methyl jasmonate (MeJA) and methyl-β-cyclodextrin (CD) before Cd exposure improved the response of Arachis hypogaea hairy root culture to the unfavourable effects of Cd toxicity. At 24 h after elicitation, genes that encode key enzymes in the phenylpropanoid biosynthesis pathway (i.e., PAL and RS3) were up-regulated to 3.2- and 5.4-fold changes respectively, thereby inducing stilbene production. The up-regulation of genes that encode transcription factors (i.e., ERF1 and ERF6) significantly increased the expression of several genes (PR4A, PR5, PR10, and chitinase) that encode the pathogenesis-related (PR) proteins to 25.8-, 45-, 5- and 12.6-fold changes, respectively. The more dramatic up-regulation of PR protein-encoding genes demonstrated the significant role of defence proteins in plant protective mechanisms. The prolonged (i.e., 72-h) treatment with MeJA + CD_Cd triggered adaptive responses by substantially increasing the levels of antioxidants, stilbenes, and other phenolic substances. These findings suggest that the interaction between signalling elicitors (MeJA and CD) and Cd modulates a complex signalling network for plant defence system.

Lasiodiplodia theobromae-induced alteration in ROS metabolism and its relation to gummosis development in Prunus persica

Peach gummosis caused by Lasiodiplodia theobromae is one of the most detrimental diseases to peaches in southern China. Reactive oxygen species (ROS) play major roles in plant-pathogen interactions, however, their roles in the pathogenesis of peach gummosis, especially shoot disease in perennials, are largely unknown. In this study, the effects of L. theobromae on ROS production-scavenging systems and on signalling transduction during L. theobromae-induced gummosis in current-year peach shoots were investigated. The infection by L. theobromae led to a ROS burst and activated the plant antioxidant enzyme-dependent scavenging system. With disease progression, the capacity of the plant antioxidant machinery declined, and allowed for ROS accumulation and eventual malondialdehyde production. As for the fungus L. theobromae, the transcripts of genes related to ROS production were significantly repressed, and concomitantly the expression of genes related to antioxidant systems and oxidative stress resistance was markedly upregulated, perhaps to alleviate oxidative stress for successful colonisation. Moreover, genes involved in phytohormones biosynthesis and pathogenesis-related proteins were all markedly promoted, which could contribute to the restriction of disease development in peach shoots. Overall, the results showed that the ROS production-scavenging system in P. persica might affect disease development during peach-L. theobromae interaction. Our findings lay the foundations for future in-depth investigations of the molecular mechanisms and regulatory networks underlying L. theobromae-mediated shoot diseases in terms of ROS production-scavenging systems.

Defensins: Transcriptional regulation and function beyond antimicrobial activity

Defensins are one the largest group of antimicrobial peptides and are part of the innate defence. Defensins are produced by animals, plants and fungi. In animals and plants, defensins can be constitutively or differentially expressed both locally or systemically which confer defence before and a stronger response after infection. Immune signalling pathways regulate the gene expression of defensins. These pathways include cellular receptors, which recognise pathogen-associated molecular patterns and are found both in plants and animals. After recognition, signalling pathways and, subsequently, transcriptional factors are activated. There is an increasing number of novel functions in defensins, such as immunomodulators and immune cell attractors. Identification of defensin triggers could help us to elucidate other new functions. The present article reviews the different elicitors of defensins with a main focus on human, fish and marine invertebrate defensins.

Colletotrichum acutatum M11 can suppress the defence response in strawberry plants

Colletotrichum acutatum M11 produces a diffusible compound that suppresses the biochemical, physiological, molecular and anatomical events associated with the defence response induced by the plant defence elicitor AsES. The fungal pathogen Colletotrichum acutatum, the causal agent of anthracnose disease, causes important economical losses in strawberry crop worldwide and synthetic agrochemicals are used to control it. In this context, the control of the disease using bioproducts is gaining reputation as an alternative of those toxic and pollutant agrochemicals. However, the success of the strategies using bioproducts can be seriously jeopardized in the presence of biological agents exerting a defence suppression effect. In this report, we show that the response defence induced in plant by the elicitor AsES from the fungus Acremonium strictum can be suppressed by a diffusible compound produced by isolate M11 of C. acutatum. Results revealed that strawberry plants treated with conidia of the isolated M11 or the culture supernatant of the isolate M11 suppress: ROS accumulation (e.g., H₂O₂, O₂^·- and NO), cell wall reinforcement (e.g., lignin and callose), and the up-regulation of defence-related genes (e.g., FaPR1, FaCHI23, FaPDF1.2, FaCAT, FaCDPK, FaCML39) induced by the elicitor AsES. Additionally, we show that the defence suppressing effect causes a systemic sensitization of plants. Results presented here highlights the necessity to make an integral study of the microbiome present in soils and plant biosphere before applying defence activation bioproducts to control crop diseases.

Comparative analysis of remodelling of the plant-microbe interface in Pisum sativum and Medicago truncatula symbiotic nodules

Infection of host cells by nitrogen-fixing soil bacteria, known as rhizobia, involves the progressive remodelling of the plant-microbe interface. This process was examined by using monoclonal antibodies to study the subcellular localisation of pectins and arabinogalactan proteins (AGPs) in wild-type and ineffective nodules of Pisum sativum and Medicago truncatula. The highly methylesterified homogalacturonan (HG), detected by monoclonal antibody JIM7, showed a uniform localisation in the cell wall, regardless of the cell type in nodules of P. sativum and M. truncatula. Low methylesterified HG, recognised by JIM5, was detected mainly in the walls of infection threads in nodules of both species. The galactan side chain of rhamnogalacturonan I (RG-I), recognised by LM5, was present in the nodule meristem in both species and in the infection thread walls in P. sativum, but not in M. truncatula. The membrane-anchored AGP recognised by JIM1 was observed on the plasma membrane in nodules of P. sativum and M. truncatula. In P. sativum, the AGP epitope recognised by JIM1 was present on mature symbiosome membranes of wild-type nodules, but JIM1 labelling was absent from symbiosome membranes in the mutant Sprint-2Fix- (sym31) with undifferentiated bacteroids, suggesting a possible involvement of AGP in the maturation of symbiosomes. Thus, the common and species-specific traits of cell wall remodelling during nodule differentiation were demonstrated.

Cell division and turgor mediate enhanced plant growth in Arabidopsis plants treated with the bacterial signalling molecule lumichrome

Transcriptomic analysis indicates that the bacterial signalling molecule lumichrome enhances plant growth through a combination of enhanced cell division and cell enlargement, and possibly enhances photosynthesis. Lumichrome (7,8 dimethylalloxazine), a novel multitrophic signal molecule produced by Sinorhizobium meliloti bacteria, has previously been shown to elicit growth promotion in different plant species (Phillips et al. in Proc Natl Acad Sci USA 96:12275-12280, https://doi.org/10.1073/pnas.96.22.12275 , 1999). However, the molecular mechanisms that underlie this plant growth promotion remain obscure. Global transcript profiling using RNA-seq suggests that lumichrome enhances growth by inducing genes impacting on turgor driven growth and mitotic cell cycle that ensures the integration of cell division and expansion of developing leaves. The abundance of XTH9 and XPA4 transcripts was attributed to improved mediation of cell-wall loosening to allow turgor-driven cell enlargement. Mitotic CYCD3.3, CYCA1.1, SP1L3, RSW7 and PDF1 transcripts were increased in lumichrome-treated Arabidopsis thaliana plants, suggesting enhanced growth was underpinned by increased cell differentiation and expansion with a consequential increase in biomass. Synergistic ethylene-auxin cross-talk was also observed through reciprocal over-expression of ACO1 and SAUR54, in which ethylene activates the auxin signalling pathway and regulates Arabidopsis growth by both stimulating auxin biosynthesis and modulating the auxin transport machinery to the leaves. Decreased transcription of jasmonate biosynthesis and responsive-related transcripts (LOX2; LOX3; LOX6; JAL34; JR1) might contribute towards suppression of the negative effects of methyl jasmonate (MeJa) such as chlorophyll loss and decreases in RuBisCO and photosynthesis. This work contributes towards a deeper understanding of how lumichrome enhances plant growth and development.

Transcriptome profiling of lentil (Lens culinaris) through the first 24 hours of Ascochyta lentis infection reveals key defence response genes

Background

Ascochyta blight, caused by the fungus Ascochyta lentis, is one of the most destructive lentil diseases worldwide, resulting in over $16 million AUD annual loss in Australia alone. The use of resistant cultivars is currently considered the most effective and environmentally sustainable strategy to control this disease. However, little is known about the genes and molecular mechanisms underlying lentil resistance against A. lentis.

Results

To uncover the genetic basis of lentil resistance to A. lentis, differentially expressed genes were profiled in lentil plants during the early stages of A. lentis infection. The resistant ‘ILL7537’ and susceptible ‘ILL6002’ lentil genotypes were examined at 2, 6, and 24 h post inoculation utilising high throughput RNA-Sequencing. Genotype and time-dependent differential expression analysis identified genes which play key roles in several functions of the defence response: fungal elicitors recognition and early signalling; structural response; biochemical response; transcription regulators; hypersensitive reaction and cell death; and systemic acquired resistance. Overall, the resistant genotype displayed an earlier and faster detection and signalling response to the A. lentis infection and demonstrated higher expression levels of structural defence-related genes.

Conclusions

This study presents a first-time defence-related transcriptome of lentil to A. lentis, including a comprehensive characterisation of the molecular mechanism through which defence against A. lentis is induced in the resistant lentil genotype.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4488-1) contains supplementary material, which is available to authorized users.

Enhanced Arabidopsis disease resistance against Botrytis cinerea induced by sulfur dioxide

Sulfur dioxide (SO₂) is a common air pollutant that has complex impacts on plants. The effect of prior exposure to 30mgm^-3 SO₂ on defence against Botrytis cinerea (B. cinerea) in Arabidopsis thaliana and the possible mechanisms of action were investigated. The results indicated that pre-exposure to 30mgm^-3 SO₂ resulted in significantly enhanced resistance to B. cinerea infection. SO₂ pre-treatment significantly enhanced the activities of defence-related enzymes including phenylalanine ammonia-lyase (PAL), polyphenol oxidase (PPO), β-1,3-glucanase (BGL) and chitinase (CHI). Transcripts of the defence-related genes PAL, PPO, PR2, and PR3, encoding PAL, PPO, BGL and CHI, respectively, were markedly elevated in Arabidopsis plants pre-exposed to SO₂ and subsequently inoculated with B. cinerea (SO₂+ treatment group) compared with those that were only treated with SO₂ (SO₂) or inoculated with B. cinerea (CK+). Moreover, SO₂ pre-exposure also led to significant increases in the expression levels of MIR393, MIR160 and MIR167 in Arabidopsis. Meanwhile, the expression of known targets involved in the auxin signalling pathway, was negatively correlated with their corresponding miRNAs. Additionally, the transcript levels of the primary auxin-response genes GH3-like, BDL/IAA12, and AXR3/IAA17 were markedly repressed. Our findings indicate that 30mgm^-3 SO₂ pre-exposure enhances disease resistance against B. cinerea in Arabidopsis by priming defence responses through enhancement of defence-related gene expression and enzyme activity, and miRNA-mediated suppression of the auxin signalling pathway.

De novo assembly of Phlomis purpurea after challenging with Phytophthora cinnamomi

BACKGROUND

Phlomis plants are a source of biological active substances with potential applications in the control of phytopathogens. Phlomis purpurea (Lamiaceae) is autochthonous of southern Iberian Peninsula and Morocco and was found to be resistant to Phytophthora cinnamomi. Phlomis purpurea has revealed antagonistic effect in the rhizosphere of Quercus suber and Q. ilex against P. cinnamomi. Phlomis purpurea roots produce bioactive compounds exhibiting antitumor and anti-Phytophthora activities with potential to protect susceptible plants. Although these important capacities of P. purpurea have been demonstrated, there is no transcriptomic or genomic information available in public databases that could bring insights on the genes underlying this anti-oomycete activity.

RESULTS

Using Illumina technology we obtained a de novo assembly of P. purpurea transcriptome and differential transcript abundance to identify putative defence related genes in challenged versus non-challenged plants. A total of 1,272,600,000 reads from 18 cDNA libraries were merged and assembled into 215,739 transcript contigs. BLASTX alignment to Nr NCBI database identified 124,386 unique annotated transcripts (57.7%) with significant hits. Functional annotation identified 83,550 out of 124,386 unique transcripts, which were mapped to 141 pathways. 39% of unigenes were assigned GO terms. Their functions cover biological processes, cellular component and molecular functions. Genes associated with response to stimuli, cellular and primary metabolic processes, catalytic and transporter functions were among those identified. Differential transcript abundance analysis using DESeq revealed significant differences among libraries depending on post-challenge times. Comparative cyto-histological studies of P. purpurea roots challenged with P. cinnamomi zoospores and controls revealed specific morphological features (exodermal strips and epi-cuticular layer), that may provide a constitutive efficient barrier against pathogen penetration. Genes involved in cutin biosynthesis and in exodermal Casparian strips formation were up-regulated.

CONCLUSIONS

The de novo assembly of transcriptome using short reads for a non-model plant, P. purpurea, revealed many unique transcripts useful for further gene expression, biological function, genomics and functional genomics studies. The data presented suggest a combination of a constitutive resistance and an increased transcriptional response from P. purpurea when challenged with the pathogen. This knowledge opens new perspectives for the understanding of defence responses underlying pathogenic oomycete/plant interaction upon challenge with P. cinnamomi.

Functional characterization of a novel jasmonate ZIM-domain interactor (NINJA) from upland cotton (Gossypium hirsutum)

The jasmonic acid (JA) signalling pathway plays roles in plant development and defence against biotic and abiotic stresses. We isolated a cotton NINJA (novel interactor of JA ZIM-domain) gene, designated GhNINJA, which contains a 1305 bp open read frame. The GhNINJA gene encodes a 434 amino acid peptide. According to quantitative real-time PCR analysis, GhNINJA is preferentially expressed in roots, and its expression level is greatly induced by Verticillium dahliae infection. Through a virus-induced gene silencing technique, we developed GhNINJA-silenced cotton plants, which had significantly decreased expression of the target gene with an average expression of 6% of the control. The regenerating lateral root growth of silenced plants was largely inhibited compared to the control. Analysis by microscopy demonstrated that the cell length of the root differentiation zone in GhNINJA-silenced plants is significantly shorter than those of the control. Moreover, the silenced plants exhibited higher tolerance to V. dahliae infection compared to the control, which was linked to the increased expression of the defence marker genes PDF1.2 and PR4. Together, these data indicated that knockdown of GhNINJA represses the root growth and enhances the tolerance to V. dahliae. Therefore, GhNINJA gene can be used as a candidate gene to breed the new cultivars for improving cotton yield and disease resistance.

iTRAQ-based proteomic analysis of defence responses triggered by the necrotrophic pathogen Rhizoctonia solani in cotton

The soil-borne necrotrophic pathogen fungus Rhizoctonia solani is destructive, causing disease in various important crops. To date, little is known about the host defence mechanism in response to invasion of R. solani. Here, an iTRAQ-based proteomic analysis was employed to investigate pathogen-responsive proteins in the disease tolerant/resistant cotton cultivar CRI35. A total of 174 differentially accumulated proteins (DAPs) were identified after inoculation of cotton plants with R. solani. Functional categorization analysis indicated that these DAPs can be divided into 12 subclasses. Notably, a large portion of DAPs are known to function in reactive oxygen species (ROS) metabolism and the expression of several histone-modifying and DNA methylating proteins were significantly induced upon challenge with the fungus, indicating that the redox homeostasis and epigenetic regulation are important for cotton defence against the pathogen. Additionally, the expression of proteins involved in phenylpropanoid biosynthesis was markedly changed in response to pathogen invasion, which may reflect a particular contribution of secondary metabolism in protection against the fungal attack in cotton. Together, our results indicate that the defence response of cotton plants to R. solani infection is active and multifaceted and involves the induction of proteins from various innate immunity-related pathways.

SIGNIFICANCE

Cotton damping-off is a destructive disease caused by the necrotrophic fungus Rhizoctonia solani. To date, the host defence mechanism involved in the disease protection remains largely unknown. Here, we reported the first proteomic analysis on cotton immune responses against R. solani infection. Employing iTRAQ technique, we obtained a total of 174 differentially accumulated proteins (DAPs) that can be classified into 12 functional groups. Further analysis indicated that ROS homeostasis, epigenetic regulation and phenylpropanoid biosynthesis were tightly associated with the innate immune responses against R. solani infection in cotton. The obtained data provide not only important information for understanding the molecular mechanism involved in plant-R. solani interaction but also application clues for genetic breeding of crops with improved R. solani resistance.

The arabidopsis cyclic nucleotide interactome

BACKGROUND

Cyclic nucleotides have been shown to play important signaling roles in many physiological processes in plants including photosynthesis and defence. Despite this, little is known about cyclic nucleotide-dependent signaling mechanisms in plants since the downstream target proteins remain unknown. This is largely due to the fact that bioinformatics searches fail to identify plant homologs of protein kinases and phosphodiesterases that are the main targets of cyclic nucleotides in animals.

METHODS

An affinity purification technique was used to identify cyclic nucleotide binding proteins in Arabidopsis thaliana. The identified proteins were subjected to a computational analysis that included a sequence, transcriptional co-expression and functional annotation analysis in order to assess their potential role in plant cyclic nucleotide signaling.

RESULTS

A total of twelve cyclic nucleotide binding proteins were identified experimentally including key enzymes in the Calvin cycle and photorespiration pathway. Importantly, eight of the twelve proteins were shown to contain putative cyclic nucleotide binding domains. Moreover, the identified proteins are post-translationally modified by nitric oxide, transcriptionally co-expressed and annotated to function in hydrogen peroxide signaling and the defence response. The activity of one of these proteins, GLYGOLATE OXIDASE 1, a photorespiratory enzyme that produces hydrogen peroxide in response to Pseudomonas, was shown to be repressed by a combination of cGMP and nitric oxide treatment.

CONCLUSIONS

We propose that the identified proteins function together as points of cross-talk between cyclic nucleotide, nitric oxide and reactive oxygen species signaling during the defence response.

Biochemical characterization of the tomato phosphatidylinositol-specific phospholipase C (PI-PLC) family and its role in plant immunity

Plants possess effective mechanisms to quickly respond to biotic and abiotic stresses. The rapid activation of phosphatidylinositol-specific phospholipase C (PLC) enzymes occurs early after the stimulation of plant immune-receptors. Genomes of different plant species encode multiple PLC homologs belonging to one class, PLCζ. Here we determined whether all tomato homologs encode active enzymes and whether they can generate signals that are distinct from one another. We searched the recently completed tomato (Solanum lycopersicum) genome sequence and identified a total of seven PLCs. Recombinant proteins were produced for all tomato PLCs, except for SlPLC7. The purified proteins showed typical PLC activity, as different PLC substrates were hydrolysed to produce diacylglycerol. We studied SlPLC2, SlPLC4 and SlPLC5 enzymes in more detail and observed distinct requirements for Ca(2+) ions and pH, for both their optimum activity and substrate preference. This indicates that each enzyme could be differentially and specifically regulated in vivo, leading to the generation of PLC homolog-specific signals in response to different stimuli. PLC overexpression and specific inhibition of PLC activity revealed that PLC is required for both specific effector- and more general "pattern"-triggered immunity. For the latter, we found that both the flagellin-triggered response and the internalization of the corresponding receptor, Flagellin Sensing 2 (FLS2) of Arabidopsis thaliana, are suppressed by inhibition of PLC activity. Altogether, our data support an important role for PLC enzymes in plant defence signalling downstream of immune receptors. This article is part of a Special Issue entitled: Plant Lipid Biology edited by Kent D. Chapman and Ivo Feussner.

Induction of host defences by Rhizobium during ineffective nodulation of pea (Pisum sativum L.) carrying symbiotically defective mutations sym40 (PsEFD), sym33 (PsIPD3/PsCYCLOPS) and sym42

Rhizobia are able to establish a beneficial interaction with legumes by forming a new organ, called the symbiotic root nodule, which is a unique ecological niche for rhizobial nitrogen fixation. Rhizobial infection has many similarities with pathogenic infection and induction of defence responses accompanies both interactions, but defence responses are induced to a lesser extent during rhizobial infection. However, strong defence responses may result from incompatible interactions between legumes and rhizobia due to a mutation in either macro- or microsymbiont. The aim of this research was to analyse different plant defence reactions in response to Rhizobium infection for several pea (Pisum sativum) mutants that result in ineffective symbiosis. Pea mutants were examined by histochemical and immunocytochemical analyses, light, fluorescence and transmission electron microscopy and quantitative real-time PCR gene expression analysis. It was observed that mutations in pea symbiotic genes sym33 (PsIPD3/PsCYCLOPS encoding a transcriptional factor) and sym40 (PsEFD encoding a putative negative regulator of the cytokinin response) led to suberin depositions in ineffective nodules, and in the sym42 there were callose depositions in infection thread (IT) and host cell walls. The increase in deposition of unesterified pectin in IT walls was observed for mutants in the sym33 and sym42; for mutant in the sym42, unesterified pectin was also found around degrading bacteroids. In mutants in the genes sym33 and sym40, an increase in the expression level of a gene encoding peroxidase was observed. In the genes sym40 and sym42, an increase in the expression levels of genes encoding a marker of hypersensitive reaction and PR10 protein was demonstrated. Thus, a range of plant defence responses like suberisation, callose and unesterified pectin deposition as well as activation of defence genes can be triggered by different pea single mutations that cause perception of an otherwise beneficial strain of Rhizobium as a pathogen.

A cotton Raf-like MAP3K gene, GhMAP3K40, mediates reduced tolerance to biotic and abiotic stress in Nicotiana benthamiana by negatively regulating growth and development

Mitogen-activated protein kinase (MAPK) cascades mediate various responses in plants. As the top component, MAP3Ks deserve more attention; however, little is known about the role of MAP3Ks, especially in cotton, a worldwide economic crop. In this study, a gene encoding a putative Raf-like MAP3K, GhMAP3K40, was isolated. GhMAP3K40 expression was induced by stress and multiple signal molecules. The plants overexpressing GhMAP3K40 had an enhanced tolerance to drought and salt stress at the germination stage. However, at the seedling stage, the transgenic plants suffered more severe damage after drought, exposure to pathogens and oxidative stress. The defence-related genes and the antioxidant system were activated in transgenic palnts, suggesting that GhMAP3K40 positively regulate the defence response. The transgenic plants were less able to prevent pathogenic invasion, which was due to defects in the cell structure of the leaves. The root system of the control plants were stronger compared with the transgenic plants. These results indicated a negative role of GhMAP3K40 in growth and development and GhMAP3K40 possibly caused the defects by down-regulating the lignin biosynthesis. Overall, these results suggest that GhMAP3K40 may positively regulate defence response but cause reduced tolerance to biotic and abiotic stress by negatively regulating growth and development.

The Transcriptome and Terpene Profile of Eucalyptus grandis Reveals Mechanisms of Defense Against the Insect Pest, Leptocybe invasa

Plants have evolved complex defenses that allow them to protect themselves against pests and pathogens. However, there is relatively little information regarding the Eucalyptus defensome. Leptocybe invasa is one of the most damaging pests in global Eucalyptus forestry, and essentially nothing is known regarding the molecular mechanisms governing the interaction between the pest and host. The aim of the study was to investigate changes in the transcriptional landscape and terpene profile of a resistant and susceptible Eucalyptus genotype in an effort to improve our understanding of this interaction. We used RNA-seqencing to investigate transcriptional changes following L. invasa oviposition. Expression levels were validated using real-time quantitative PCR. Terpene profiles were investigated using gas chromatography coupled to mass spectometry on uninfested and oviposited leaves. We found 698 and 1,115 significantly differentially expressed genes from the resistant and susceptible interactions, respectively. Gene Ontology enrichment and Mapman analyses identified putative defense mechanisms including cell wall reinforcement, protease inhibitors, cell cycle suppression and regulatory hormone signaling pathways. There were significant differences in the mono- and sesquiterpene profiles between genotypes and between control and infested material. A model of the interaction between Eucalyptus and L. invasa was proposed from the transcriptomic and chemical data.

BcGs1, a glycoprotein from Botrytis cinerea, elicits defence response and improves disease resistance in host plants

In this study, a necrosis-inducing protein was purified from the culture filtrate of the necrotrophic fungus Botrytis cinerea BC-98 strain. Secreted proteins were collected and fractionated by liquid chromatography. The fraction with the highest necrosis-inducing activity was further purified. A glycoprotein named BcGs1 was identified by 2D electrophoresis and mass spectrometry. The BcGs1 protein consisted of 672 amino acids with a theoretical molecular weight of 70.487 kDa. Functional domain analysis indicated that BcGs1 was a glucan 1,4-alpha-glucosidase, a cell wall-degrading enzyme, with a Glyco_hydro_15 domain and a CBM20_glucoamylase domain. The BcGs1 protein caused necrotic lesions that mimicked a typical hypersensitive response and H2O2 production in tomato and tobacco leaves. BcGs1-treated plants exhibited resistance to B. cinerea, Pseudomonas syringae pv. tomato DC3000 and tobacco mosaic virus in systemic leaves. In addition, BcGs1 triggered elevation of the transcript levels of the defence-related genes PR-1a, TPK1b and Prosystemin. This is the first report of a Botrytis glucan 1,4-alpha-glucosidase triggering host plant immunity as an elicitor. These results lay a foundation for further study of the comprehensive interaction between plants and necrotrophic fungi.

Quantitative RT-PCR analysis of differentially expressed genes in Quercus suber in response to Phytophthora cinnamomi infection

cDNA-AFLP methodology was used to gain insight into gene fragments differentially present in the mRNA profiles of Quercus suber roots infected with zoospores of Phytophthora cinnamomi at different post challenge time points. Fifty-three transcript-derived fragments (TDFs) were identified and sequenced. Six candidate genes were selected based on their expression patterns and homology to genes known to play a role in defence. They encode a cinnamyl alcohol dehydrogenase2 (QsCAD2), a protein disulphide isomerase (QsPDI), a CC-NBS-LRR resistance protein (QsRPc), a thaumatin-like protein (QsTLP), a chitinase (QsCHI) and a 1,3-β-glucanase (QsGlu). Evaluation of the expression of these genes by quantitative polymerase chain reaction (qPCR) revealed that transcript levels of QsRPc, QsCHI, QsCAD2 and QsPDI increased during the first 24 h post-inoculation, while those of thaumatin-like protein decreased. No differential expression was observed for 1,3-β-glucanase (QsGlu). Four candidate reference genes, polymerase II (QsRPII), eukaryotic translation initiation factor 5A (QsEIF-5A), β-tubulin (QsTUB) and a medium subunit family protein of clathrin adaptor complexes (QsCACs) were assessed to determine the most stable internal references for qRT-PCR normalization in the Phytophthora-Q. suber pathosystem in root tissues. Those found to be more stable, QsRPII and QsCACs, were used as internal reference in the present work. Knowledge on the Quercus defence mechanisms against biotic stress is scarce. This study provides an insight into the gene profiling of a few important genes of Q. suber in response to P. cinnamomi infection contributing to the knowledge of the molecular interactions involving Quercus and root pathogens that can be useful in the future to understand the mechanisms underlying oak resistance to soil-borne oomycetes.

Photosynthetic and molecular responses of the marine diatom Thalassiosira pseudonana to triphenyltin exposure

This study aimed to investigate the responses of the marine diatom Thalassiosira pseudonana upon waterborne exposure to triphenyltin chloride (TPTCl) through determining their photosynthetic response, growth performance, and expressions of genes and proteins. Based on the growth inhibition test, the 96-h IC50 (i.e., median inhibition concentration) was found to be 1.09 μg/L (95% confidence interval (CI): 0.89-1.34 μg/L). According to photosynthetic parameters, the 96-h EC50s (i.e., median effect concentrations) were estimated at 1.54 μg/L (95% CI: 1.40-1.69 μg/L) and 1.51 μg/L (95% CI: 1.44-1.58 μg/L) for the maximum quantum yield of photosystem II (PSII) photochemistry (ΦPo) and the effective quantum yield of photochemical energy conversion in PSII (Φ2), respectively. Non-photochemical quenching in the algae was increased at low concentrations of TPTCl (0.5-1.0 μg/L) but it decreased gradually when the TPTCl concentration further increased from 1.0 to 2.5 μg/L. Results of gene expressions showed that lipid metabolism related genes were not influenced by TPTCl at 0.5 or 1.0 μg/L, while silica shell formation genes were down-regulated at 0.5 μg/L. Photosynthesis related genes were up-regulated at 0.5 μg/L TPTCl but were down-regulated at 1.0 μg/L TPTCl. Proteomics analysis revealed that relatively less proteins could be detected after exposure to 1.0 μg/L TPTCl (only about 50-60 spots) compared with that observed in the 0.5μg/L TPTCl treatment and two control groups (each with about 290-300 protein spots). At 0.5 μg/L TPTCl, five proteins were differentially expressed when compared with the seawater control and solvent control, and most of these proteins are involved in defence function to protect the biological systems from reactive oxygen species that generated by TPTCl. These proteins include oxygen-evolving enhancer protein 1 precursor, fucoxanthin chlorophyll a/c protein - LI818 clade, and mitochondrial manganese superoxide dismutase, which can function to maintain the capacity of PSII and stabilize the photosynthesis efficiency as reflected by the unchanged ΦPo and Φ2 values at 0.5 μg/L TPTCl. In contrast, the excess toxicity that caused by TPTCl at the high concentration (1.0 μg/L TPTCl) might directly damage the proteins, inhibit their expression, and/or cause the suppression of metabolism as indicated by the down-regulation of most studied proteins and genes, which could ultimately inhibit the photosynthesis and growth of the algae. Overall, this study comprehensively elucidated the toxicity effects of TPT on T. pseudonana, and partially revealed the molecular toxic mechanisms and corresponding defence responses in this model algal species.

Proteomic analysis of non-heading Chinese cabbage infected with Hyaloperonospora parasitica

Downy mildew is a serious fungal disease in non-heading Chinese cabbage (Brassica campestris ssp. chinensis Makino) that is caused by Hyaloperonospora parasitica, which infects members of the Brassicaceae family. For breeding improvement, researchers must understand the defence mechanisms employed by non-heading Chinese cabbage to combat H. parasitica infection. Using 2-DE protein analysis, we compared the proteomes from leaves of non-heading Chinese cabbage seedlings that were infected with H. parasitica or that were only treated with water at different time points post-infection. By MS analysis, 91 protein spots with significant differences in abundance (>2-fold, p<0.05) were identified in mock- and H. parasitica-inoculated leaves. Next, a resistance strategy for incompatible interactions was proposed. This network consisted of several functional components, including enhanced ethylene biosynthesis and energy supply, balanced ROS production and scavenging, accelerated protein metabolism and photorespiratory, reduced photosynthesis, and induced photosystem repair. These findings increase our knowledge of incompatible interactions between plants and pathogens and also provide new insight regarding the function of plant molecular processes, which should assist in the discovery of new strategies for pathogen control.

BIOLOGICAL SIGNIFICANCE

This study reported the proteomic analysis of the incompatible interactions between non-heading Chinese cabbage and downy mildew using 2-DE and MS. In total, 91 protein spots that were related to the resistance response were identified. These proteins were assigned to different functional categories, such as amino acid and carbohydrate metabolism, photosynthesis and photorespiration, protein metabolism, signal transduction, redox homeostasis, and ethylene biosynthesis. Meanwhile, several key proteins were determined to be associated with ethylene signalling, ROS scavenging and resistance-related proteins. Consistent with these results, the expression of ethylene biosynthesis genes and response genes, as well as the activity of antioxidant enzymes, increased after inoculation. These findings provide new insight for further understanding the molecular mechanisms of plant resistance.