Botrytis cinerea manipulates the antagonistic effects between immune pathways to promote disease development in tomato

Antimicrobial activity of sophorolipids produced by Starmerella bombicola against phytopathogens from cherry tomato

BACKGROUND

Phytopathogenic microorganisms are the main cause of plant diseases, generating significant economic losses for the agricultural and food supply chain. Cherry tomatoes (Solanum lycopersicum var. cerasiforme) are very perishable plants and highly demanding in the use of pesticides; therefore, alternative solutions such as biosurfactants have aroused as a potent substituent. The main objective of the present study was to investigate the antimicrobial activity of sophorolipids against the phytopathogens Botrytis cinerea, Sclerotium rolfsii, Rhizoctonia solani and Pythium ultimum.

RESULTS

The biosurfactant inhibited the mycelial growth in vitro with a minimum concentration of 2 mg mL^-1 . The application of sophorolipids at 1, 2 and 4 mg mL^-1 in detached leaves of tomato before the inoculation of the fungus B. cinerea was the best treatment, reducing leaf necrosis by up to 76.90%. The use of sophorolipids for washing tomato fruits before the inoculation of B. cinerea was able to inhibit the development of gray mold by up to 96.27%.

CONCLUSION

The results for tomato leaves and fruits revealed that the biosurfactant acts more effectively when used preventively. Sophorolipids are stable molecules that show promising action for the potential replacement of pesticides in the field and the post-harvest process against the main tomato phytopathogens. © 2021 Society of Chemical Industry.

Pseudomonas syringae activates ZAT18 to inhibit salicylic acid accumulation by repressing EDS1 transcription for bacterial infection

Phytopathogens can manipulate plant hormone signaling to counteract immune responses; however, the underlying mechanism is mostly unclear. Here, we report that Pseudomonas syringae pv tomato (Pst) DC3000 induces expression of C2H2 zinc finger transcription factor ZAT18 in a jasmonic acid (JA)-signaling-dependent manner. Biochemical assays further confirmed that ZAT18 is a direct target of MYC2, which is a very important regulator in JA signaling. CRISPR/Cas9-generated zat18-cr mutants exhibited enhanced resistance to Pst DC3000, while overexpression of ZAT18 resulted in impaired disease resistance. Genetic characterization of ZAT18 mutants demonstrated that ZAT18 represses defense responses by inhibiting the accumulation of the key plant immune signaling molecule salicylic acid (SA), which is dependent on its EAR motif. ZAT18 exerted this inhibitory effect by directly repressing the transcription of Enhanced Disease Susceptibility 1 (EDS1), which is the key signaling component of pathogen-induced SA accumulation. Overexpression of ZAT18 resulted in decreased SA content, while loss of function of ZAT18 showed enhanced SA accumulation upon pathogen infection. Furthermore, enhanced resistance and SA content in zat18-cr mutants was abolished by the mutation in EDS1. Our data indicate that pathogens induce ZAT18 expression to repress the transcription of EDS1, further antagonising SA accumulation for bacterial infection.

Tomato Prosystemin Is Much More than a Simple Systemin Precursor

Simple Summary

Prosystemin is a 200 amino acid precursor that releases, upon wounding and biotic attacks, an 18 amino acid peptide called Systemin. This peptide was traditionally considered as the principal actor of the resistance of tomato plants induced by triggering multiple defense pathways in response to a wide range of biotic/abiotic stress agents. Recent findings from our group discovered the disordered structure of Prosystemin that promotes the binding of different molecular partners and the possible activation of multiple stress-related pathways. All of our recent findings suggest that Prosystemin could be more than a simple precursor of Systemin peptide. Indeed, we hypothesized that it contains other sequences able to activate multiple stress-related responses. To verify this hypothesis, we produced a truncated Prosystemin protein deprived of the Systemin peptide and the relative deleted gene. Experiments with transgenic tomato plants overexpressing the truncated Prosystemin and with plants exogenously treated with the recombinant truncated protein demonstrated that both transgenic and treated plants modulated the expression of defense-related genes and were protected against a noctuid moth and a fungal pathogen. Taken together, our results demonstrated that Prosystemin is not a mere scaffold of Systemin, but itself contains other biologically active regions.

Abstract

Systemin (Sys) is an octadecapeptide, which upon wounding, is released from the carboxy terminus of its precursor, Prosystemin (ProSys), to promote plant defenses. Recent findings on the disordered structure of ProSys prompted us to investigate a putative biological role of the whole precursor deprived of the Sys peptide. We produced transgenic tomato plants expressing a truncated ProSys gene in which the exon coding for Sys was removed and compared their defense response with that induced by the exogenous application of the recombinant truncated ProSys (ProSys_(1-178), the Prosystemin sequence devoid of Sys region). By combining protein structure analyses, transcriptomic analysis, gene expression profiling and bioassays with different pests, we demonstrate that truncated ProSys promotes defense barriers in tomato plants through a hormone-independent defense pathway, likely associated with the production of oligogalacturonides (OGs). Both transgenic and plants treated with the recombinant protein showed the modulation of the expression of genes linked with defense responses and resulted in protection against the lepidopteran pest Spodoptera littoralis and the fungus Botrytis cinerea. Our results suggest that the overall function of the wild-type ProSys is more complex than previously shown, as it might activate at least two tomato defense pathways: the well-known Sys-dependent pathway connected with the induction of jasmonic acid biosynthesis and the successive activation of a set of defense-related genes, and the ProSys_(1-178)-dependent pathway associated with OGs production leading to the OGs mediate plant immunity.

Mechanisms of far-red light-mediated dampening of defense against Botrytis cinerea in tomato leaves

Plants detect neighboring competitors through a decrease in the ratio between red and far-red light (R:FR). This decreased R:FR is perceived by phytochrome photoreceptors and triggers shade avoidance responses such as shoot elongation and upward leaf movement (hyponasty). In addition to promoting elongation growth, low R:FR perception enhances plant susceptibility to pathogens: the growth-defense tradeoff. Although increased susceptibility in low R:FR has been studied for over a decade, the associated timing of molecular events is still unknown. Here, we studied the chronology of FR-induced susceptibility events in tomato (Solanum lycopersicum) plants pre-exposed to either white light (WL) or WL supplemented with FR light (WL+FR) prior to inoculation with the necrotrophic fungus Botrytis cinerea (B.c.). We monitored the leaf transcriptional changes over a 30-h time course upon infection and followed up with functional studies to identify mechanisms. We found that FR-induced susceptibility in tomato is linked to a general dampening of B.c.-responsive gene expression, and a delay in both pathogen recognition and jasmonic acid-mediated defense gene expression. In addition, we found that the supplemental FR-induced ethylene emissions affected plant immune responses under the WL+FR condition. This study improves our understanding of the growth-immunity tradeoff, while simultaneously providing leads to improve tomato resistance against pathogens in dense cropping systems.

The tomato Mediator subunit MED8 positively regulates plant response to Botrytis cinerea

The Mediator complex acts as a bridge between specific transcription factors and the RNA polymerase II transcriptional machinery and plays a central role in plant immunity. Biological induction of plant resistance against pathogens requires endogenous hormone jasmonic acid (JA) and involves profound transcriptional changes controlled by the key transcription factor MYC2. Arabidopsis thaliana Mediator subunit 25 (AtMED25) regulates JA-dependent defense response through interacting with MYC2. Here, we report that the tomato (Solanum lycopersicum, Sl) Mediator subunit 8 (SlMED8) is another essential component in JA-dependent defense response. The transcript levels of SlMED8 could not be affected by treatment with MeJA, SA, ABA, and mechanical wounding. Yeast two-hybrid assays showed that SlMED8 could interact with itself, SlMYC2, and SlMED25, respectively. In addition, ectopic overexpression of SlMED8 complemented the late flowering and pathogen hypersensitivity phenotypes of Arabidopsis med8 mutant. Overexpression of SlMED8 rendered transgenic plants higher tolerance to necrotrophic pathogen Botrytis cinerea. Meanwhile, SlMED8 antisense plants displayed compromised resistance to Botrytis cinerea. Consistent with this, differential expression levels of several JA-responsive genes were detected within the transgenic plants. Overall, our results identified an important control point in the regulation of the JA signaling pathway within the transcriptional machinery.

Transcriptional differentiation driving Cucumis sativus-Botrytis cinerea interactions based on the Skellam model and Bayesian networks

Robust statistical tools such as the Skellam model and Bayesian networks can capture the count properties of transcriptome sequencing data and clusters of genes among treatments, thereby improving our knowledge of gene functions and networks. In this study, we successfully implemented a model to analyze a transcriptome dataset of Cucumis sativus and Botrytis cinerea before and after their interaction. First, 4200 differentially expressed genes (DEGs) from C. sativus were clustered into 17 distinct groups, and 670 DEGs from B. cinerea were clustered into 12 groups. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were applied on these DEGs to assess the interactions between C. sativus and B. cinerea. In C. sativus, more DEGs were divided into terms in the molecular function and biological process domains than into cellular components, and 277 DEGs were allocated to 19 KEGG pathways. In B. cinerea, more DEGs were divided into terms in the biological process and cellular component domains than into molecular functions, and 150 DEGs were allocated to 26 KEGG pathways. In this study, we constructed networks of genes that interact with each other to screen hub genes based on a directed graphical model known as Bayesian networks. Through a detailed GO analysis, we excavated hub genes which were biologically meaningful. These results verify that availability of Skellam model and Bayesian networks in clustering gene expression data and sorting out hub genes. These models are instrumental in increasing our knowledge of gene functions and networks in plant–pathogen interaction.

Pochonia chlamydosporia Isolate PC-170-Induced Expression of Marker Genes for Defense Pathways in Tomatoes Challenged by Different Pathogens

Pochonia chlamydosporia is a fungal parasite of nematode eggs. Studies have shown that some strains of Pochonia chlamydosporia can promote plant growth and induce plants’ systemic resistance to root-knot nematodes by colonizing in their roots. This study aimed to verify the effect of the PC-170 strain on tomato growth and systemic resistance. Split-root experiments were conducted to observe the systemic resistance induced by PC-170. To explore the defense pathway that was excited due to the colonization by PC-170, we tested the expression of marker genes for defense pathways, and used mutant lines to verify the role of plant defense pathways. Our results showed that PC-170 can colonize roots, and promotes growth. We found a role for jasmonic acid (JA) in modulating tomato colonization by PC-170. PC-170 can activate tomato defense responses to reduce susceptibility to infection by the root-knot nematode Meloidogyne incognita, and induced resistance to some pathogens in tomatoes. The marker genes of the defense pathway were significantly induced after PC-170 colonization. However, salicylic acid (SA)- and jasmonic acid (JA)-dependent defenses in roots were variable with the invasion of different pathogens. Defense pathways play different roles at different points in time. SA- and JA-dependent defense pathways were shown to cross-communicate. Different phytohormones have been involved in tomato plants’ responses against different pathogens. Our study confirmed that adaptive JA signaling is necessary to regulate PC-170 colonization and induce systemic resistance in tomatoes.

Over-expression of SlWRKY46 in tomato plants increases susceptibility to Botrytis cinerea by modulating ROS homeostasis and SA and JA signaling pathways

WRKY, as one of the largest families of transcription factors (TFs), binds to cis-acting elements of downstream genes to regulate biotic and abiotic stress. However, the role of SlWRKY46 in fungal disease response induced by Botrytis cinerea (B.cinerea) and potential mechanism remains obscure. To ascertain the role of SlWRKY46 in response to B.cinerea, we constructed SlWRKY46-overexpression plants, which were then inoculated with B.cinerea. SlWRKY46-overexpression plants were more susceptible to B.cinerea and accompanied by the inhibited activities of phenylalanine ammonialyase (PAL), polyphenol oxidase (PPO), chitinase (CHI), and β-1,3-glucanase (GLU). Additionally, SlWRKY46-overexpression plants showed the decreased activities of ascorbate peroxidase (APX), superoxide dismutase (SOD) and the content of H₂O₂, and the increased content of O₂^•-. Moreover, over-expression of SlWRKY46 suppressed the salicylic acid (SA) and jasmonic acid (JA) marker genes, pathogenesis related protein (PR1), and proteinase inhibitors (PI Ⅰ and PI Ⅱ) and consequently aggravated the disease symptoms. Therefore, we speculated that SlWRKY46 played negative regulatory roles in B. cinerea infection probably by inhibiting the activities of antioxidants and disease resistance enzymes, regulating SA and JA signaling pathways and modulating reactive oxygen (ROS) homeostasis.

Plant volatile organic compound (E)-2-hexenal facilitates Botrytis cinerea infection of fruits by inducing sulfate assimilation

Investigation into plant-fungal pathogen interactions is one of the most interesting fields in plant sciences. However, the roles of plant volatile organic compounds in the arms race are still largely unknown. Based on precise quantification of plant volatiles, we discovered that the plant volatile organic compound (E)-2-hexenal, at concentrations that were similar to or lower than those in tissues of strawberry and tomato fruits, upregulates sulfate assimilation in spores and hyphae of the phytopathogenic fungus Botrytis cinerea. This upregulation is independent of the types of sulfur sources in the plant and can be achieved in the presence of inorganic sulfate and organic sulfur sources. Using the fungal deletion mutants, we further found that sulfate assimilation is involved in the infection of tomato and strawberry fruits by B. cinerea, and that the severity of the disease is proportional to the sulfate content in the fruits. Both before and during the infection, (E)-2-hexenal induced utilisation of plant sulfate by B. cinerea facilitates its pathogenesis through enhancing its tolerance to oxidative stress. This work provides novel insights into the role of plant volatiles in plant-fungal pathogen interaction and highlights the importance of sulfur levels in the host in the prevention of grey mould disease.

Effectors of Plant Necrotrophic Fungi

Plant diseases caused by necrotrophic fungal pathogens result in large economic losses in field crop production worldwide. Effectors are important players of plant-pathogen interaction and deployed by pathogens to facilitate plant colonization and nutrient acquisition. Compared to biotrophic and hemibiotrophic fungal pathogens, effector biology is poorly understood for necrotrophic fungal pathogens. Recent bioinformatics advances have accelerated the prediction and discovery of effectors from necrotrophic fungi, and their functional context is currently being clarified. In this review we examine effectors utilized by necrotrophic fungi and hemibiotrophic fungi in the latter stages of disease development, including plant cell death manipulation. We define "effectors" as secreted proteins and other molecules that affect plant physiology in ways that contribute to disease establishment and progression. Studying and understanding the mechanisms of necrotrophic effectors is critical for identifying avenues of genetic intervention that could lead to improved resistance to these pathogens in plants.

Apparent inhibition of induced plant volatiles by a fungal pathogen prevents airborne communication between potato plants

Plant communication in response to insect herbivory has been increasingly studied, whereas that involving pathogen attack has received much less attention. We tested for communication between potato (Solanum tuberosum) plants in response to leaf infection by the fungal pathogen Sclerotinia sclerotiorum. To this end, we measured the total amount and composition of volatile organic compounds (VOCs) produced by control and infected emitter plants, as well as tested for induced resistance of receiver plants exposed to VOCs from emitters. We further tested for changes in the expression of defensive genes due to pathogen infection. Fungal infection did not significantly affect the total amount or composition of VOCs produced by emitter plants. Correspondingly, we found no evidence of higher resistance to the pathogen in receiver plants exposed to VOCs from infected emitters relative to control emitters. Molecular analyses indicated that pathogen infection drove a down-regulation of genes coding for VOC precursors, potentially explaining the absence of pathogen effects on VOC emissions and thus of communication. Overall, these results indicate no evidence of airborne communication between potato plants in response to fungal infection and point at pathogen inhibition of VOC emissions as a likely explanation for this result.

A Novel Role of Salt- and Drought-Induced RING 1 Protein in Modulating Plant Defense Against Hemibiotrophic and Necrotrophic Pathogens

Many plant-encoded E3 ligases are known to be involved in plant defense. Here, we report a novel role of E3 ligase SALT- AND DROUGHT-INDUCED RING FINGER1 (SDIR1) in plant immunity. Even though SDIR1 is reasonably well-characterized, its role in biotic stress response is not known. The silencing of SDIR1 in Nicotiana benthamiana reduced the multiplication of the virulent bacterial pathogen Pseudomonas syringae pv. tabaci. The Arabidopsis sdir1 mutant is resistant to virulent pathogens, whereas SDIR1 overexpression lines are susceptible to both host and nonhost hemibiotrophic bacterial pathogens. However, sdir1 mutant and SDIR1 overexpression lines showed hypersusceptibility and resistance, respectively, against the necrotrophic pathogen Erwinia carotovora. The mutant of SDIR1 target protein, i.e., SDIR-interacting protein 1 (SDIR1P1), also showed resistance to host and nonhost pathogens. In SDIR1 overexpression plants, transcripts of NAC transcription factors were less accumulated and the levels of jasmonic acid (JA) and abscisic acid were increased. In the sdir1 mutant, JA signaling genes JAZ7 and JAZ8 were downregulated. These data suggest that SDIR1 is a susceptibility factor and its activation or overexpression enhances disease caused by P. syringae pv. tomato DC3000 in Arabidopsis. Our results show a novel role of SDIR1 in modulating plant defense gene expression and plant immunity.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Pseudomonas fluorescens DN16 Enhances Cucumber Defense Responses Against the Necrotrophic Pathogen Botrytis cinerea by Regulating Thermospermine Catabolism

Plants can naturally interact with beneficial rhizobacteria to mediate defense responses against foliar pathogen infection. However, the mechanisms of rhizobacteria-mediated defense enhancement remain rarely clear. In this study, beneficial rhizobacterial strain Pseudomonas fluorescens DN16 greatly increased the resistance of cucumber plants against Botrytis cinerea infection. RNA-sequencing analyses showed that several polyamine-associated genes including a thermospermine (TSpm) synthase gene (CsACL5) and polyamine catabolic genes (CsPAO1, CsPAO5, and CsCuAO1) were notably induced by DN16. The associations of TSpm metabolic pathways with the DN16-mediated cucumber defense responses were further investigated. The inoculated plants exhibited the increased leaf TSpm levels compared with the controls. Accordantly, overexpression of CsACL5 in cucumber plants markedly increased leaf TSpm levels and enhanced defense against B. cinerea infection. The functions of TSpm catabolism in the DN16-mediated defense responses of cucumber plants to B. cinerea were further investigated by pharmacological approaches. Upon exposure to pathogen infection, the changes of leaf TSpm levels were positively related to the enhanced activities of polyamine catabolic enzymes including polyamine oxidases (PAOs) and copper amine oxidases (CuAOs), which paralleled the transcription of several defense-related genes such as pathogenesis-related protein 1 (CsPR1) and defensin-like protein 1 (CsDLP1). However, the inhibited activities of polyamine catabolic enzymes abolished the DN16-induced cucumber defense against B. cinerea infection. This was in line with the impaired expression of defense-related genes in the inoculated plants challenged by B. cinerea. Collectively, our findings unraveled a pivotal role of TSpm catabolism in the regulation of the rhizobacteria-primed defense states by mediating the immune responses in cucumber plants after B. cinerea infection.

Diversified Regulation of Cytokinin Levels and Signaling During Botrytis cinerea Infection in Arabidopsis

Cytokinins (CKs) can modulate plant immunity to various pathogens, but how CKs are involved in plant defense responses to the necrotrophic pathogen Botrytis cinerea is still unknown. Here, we found that B. cinerea infection induced transcriptional changes in multiple genes involved in the biosynthesis, degradation, and signaling of CKs, as well as their contents, in pathogen-infected Arabidopsis leaves. Among the CKs, the gene expression of CYTOKININ OXIDASE/DEHYDROGENASE 5 (CKX5) was remarkably induced in the local infected leaves and the distant leaves of the same plant without pathogen inoculation. Cis-zeatin (cZ) and its riboside (cZR) accumulated considerably in infected leaves, suggesting an important role of the cis-zeatin type of CKs in the plant response to B. cinerea. Cytokinin double-receptor mutants were more susceptible to B. cinerea infection, whereas an exogenous CK treatment enhanced the expression levels of defense-related genes and of jasmonic acid (JA) and ethylene (ET), but not salicylic acid (SA), resulting in higher resistance of Arabidopsis to B. cinerea. Investigation of CK responses to B. cinerea infection in the JA biosynthesis mutant, jar1-1, and ET-insensitive mutant, ein2-1, showed that CK signaling and levels of CKs, namely, those of isopentenyladenine (iP), isopentenyladenine riboside (iPR), and trans-zeatin (tZ), were enhanced in jar1-1-infected leaves. By contrast, reductions in iP, iPR, tZ, and tZ riboside (tZR) as well as cZR contents occurred in ein2-1-infected leaves, whose transcript levels of CK signaling genes were likewise differentially regulated. The Arabidopsis Response Regulator 5 (ARR5) gene was upregulated in infected leaves of ein2-1 whereas another type-A response regulator, ARR16, was significantly downregulated, suggesting the existence of a complex regulation of CK signaling via the ET pathway. Accumulation of the cis-zeatin type of CKs in B. cinerea-infected leaves depended on ET but not JA pathways. Collectively, our findings provide evidence that CK responds to B. cinerea infection in a variety of ways that are differently modulated by JA and ET pathways in Arabidopsis.

Arabidopsis Defense against the Pathogenic Fungus Drechslera gigantea Is Dependent on the Integrity of the Unfolded Protein Response

Drechslera gigantea Heald & Wolf is a worldwide-spread necrotrophic fungus closely related to the Bipolaris genus, well-known because many member species provoke severe diseases in cereal crops and studied because they produce sesterpenoid phytoxins named ophiobolins which possess interesting biological properties. The unfolded protein response (UPR) is a conserved mechanism protecting eukaryotic cells from the accumulation of unfolded/misfolded proteins in the endoplasmic reticulum (ER). In plants, consolidated evidence supports the role of UPR in the tolerance to abiotic stress, whereas much less information is available concerning the induction of ER stress by pathogen infection and consequent UPR elicitation as part of the defense response. In this study, the infection process of D. gigantea in Arabidopsis thaliana wild type and UPR-defective bzip28 bzip60 double mutant plants was comparatively investigated, with the aim to address the role of UPR in the expression of resistance to the fungal pathogen. The results of confocal microscopy, as well as of qRT-PCR transcript level analysis of UPR genes, proteomics, microRNAs expression profile and HPLC-based hormone analyses demonstrated that ophiobolin produced by the fungus during infection compromised ER integrity and that impairment of the IRE1/bZIP60 pathway of UPR hampered the full expression of resistance, thereby enhancing plant susceptibility to the pathogen.

Bacillus subtilis SL18r Induces Tomato Resistance Against Botrytis cinerea, Involving Activation of Long Non-coding RNA, MSTRG18363, to Decoy miR1918

Mounting evidence has indicated that beneficial rhizobacteria can suppress foliar pathogen invasion via elicitation of induced systemic resistance (ISR). However, it remains elusive whether long non-coding RNAs (lncRNAs) are involved in the mediation of the rhizobacteria-primed ISR processes in plants. Herein, we demonstrated the ability of the rhizobacterial strain Bacillus subtilis SL18r to trigger ISR in tomato plants against the foliar pathogen Botrytis cinerea. Comparative transcriptome analysis was conducted to screen differentially expressed lncRNAs (DELs) between the non-inoculated and SL18r-inoculated plants. Among these DELs, four variants of MSTRG18363 possessed conserved binding sites for miR1918, which negatively regulates immune systems in tomato plants. The expression of MSTRG18363 in tomato leaves was significantly induced by SL18r inoculation. The transcription of MSTRG18363 was negatively correlated with the expression of miR1918, but displayed a positive correlation with the transcription of the RING-H2 finger gene SlATL20 (a target gene of miR1918). Moreover, MSTRG18363-overexpressing plants exhibited the enhanced disease resistance, reduction of miR1918 transcripts, and marked increases of SlATL20 expression. However, the SL18r-induced disease resistance was largely impaired in the MSTRG18363-silenced plants. VIGS-mediated SlATL20 silencing also greatly weakened the SL18r-induced disease resistance. Collectively, our results suggested that induction of MSTRG18363 expression in tomato plants by SL18r was conducive to promoting the decoy of miR1918 and regulating the expression of SlATL20, thereby provoking the ISR responses against foliar pathogen infection.

Solution Structure, Dynamics, and New Antifungal Aspects of the Cysteine-Rich Miniprotein PAFC

The genome of Penicillium chrysogenum Q176 contains a gene coding for the 88-amino-acid (aa)-long glycine- and cysteine-rich P. chrysogenum antifungal protein C (PAFC). After maturation, the secreted antifungal miniprotein (MP) comprises 64 aa and shares 80% aa identity with the bubble protein (BP) from Penicillium brevicompactum, which has a published X-ray structure. Our team expressed isotope (15N, 13C)-labeled, recombinant PAFC in high yields, which allowed us to determine the solution structure and molecular dynamics by nuclear magnetic resonance (NMR) experiments. The primary structure of PAFC is dominated by 14 glycines, and therefore, whether the four disulfide bonds can stabilize the fold is challenging. Indeed, unlike the few published solution structures of other antifungal MPs from filamentous ascomycetes, the NMR data indicate that PAFC has shorter secondary structure elements and lacks the typical β-barrel structure, though it has a positively charged cavity and a hydrophobic core around the disulfide bonds. Some parts within the two putative γ-core motifs exhibited enhanced dynamics according to a new disorder index presentation of 15N-NMR relaxation data. Furthermore, we also provided a more detailed insight into the antifungal spectrum of PAFC, with specific emphasis on fungal plant pathogens. Our results suggest that PAFC could be an effective candidate for the development of new antifungal strategies in agriculture.

Unraveling the sugar code: the role of microbial extracellular glycans in plant-microbe interactions

To defend against microbial invaders but also to establish symbiotic programs, plants need to detect the presence of microbes through the perception of molecular signatures characteristic of a whole class of microbes. Among these molecular signatures, extracellular glycans represent a structurally complex and diverse group of biomolecules that has a pivotal role in the molecular dialog between plants and microbes. Secreted glycans and glycoconjugates such as symbiotic lipochitooligosaccharides or immunosuppressive cyclic β-glucans act as microbial messengers that prepare the ground for host colonization. On the other hand, microbial cell surface glycans are important indicators of microbial presence. They are conserved structures normally exposed and thus accessible for plant hydrolytic enzymes and cell surface receptor proteins. While the immunogenic potential of bacterial cell surface glycoconjugates such as lipopolysaccharides and peptidoglycan has been intensively studied in the past years, perception of cell surface glycans from filamentous microbes such as fungi or oomycetes is still largely unexplored. To date, only few studies have focused on the role of fungal-derived cell surface glycans other than chitin, highlighting a knowledge gap that needs to be addressed. The objective of this review is to give an overview on the biological functions and perception of microbial extracellular glycans, primarily focusing on their recognition and their contribution to plant-microbe interactions.

Antimicrobial activity screening of rhizosphere soil bacteria from tomato and genome-based analysis of their antimicrobial biosynthetic potential

Background

Tomato plant growth is frequently hampered by a high susceptibility to pests and diseases. Traditional chemical control causes a serious impact on both the environment and human health. Therefore, seeking environment-friendly and cost-effective green methods in agricultural production becomes crucial nowadays. Plant Growth Promoting Rhizobacteria (PGPR) can promote plant growth through biological activity. Their use is considered to be a promising sustainable approach for crop growth. Moreover, a vast number of biosynthetic gene clusters (BGCs) for secondary metabolite production are being revealed in PGPR, which helps to find potential anti-microbial activities for tomato disease control.

Results

We isolated 181 Bacillus-like strains from healthy tomato, rhizosphere soil, and tomato tissues. In vitro antagonistic assays revealed that 34 Bacillus strains have antimicrobial activity against Erwinia carotovora, Pseudomonas syringae; Rhizoctonia solani; Botrytis cinerea; Verticillium dahliae and Phytophthora infestans. The genomes of 10 Bacillus and Paenibacillus strains with good antagonistic activity were sequenced. Via genome mining approaches, we identified 120 BGCs encoding NRPs, PKs-NRPs, PKs, terpenes and bacteriocins, including known compounds such as fengycin, surfactin, bacillibactin, subtilin, etc. In addition, several novel BGCs were identified. We discovered that the NRPs and PKs-NRPs BGCs in Bacillus species are encoding highly conserved known compounds as well as various novel variants.

Conclusions

This study highlights the great number of varieties of BGCs in Bacillus strains. These findings pave the road for future usage of Bacillus strains as biocontrol agents for tomato disease control and are a resource arsenal for novel antimicrobial discovery.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07346-8.

Chitosan primes plant defence mechanisms against Botrytis cinerea, including expression of Avr9/Cf-9 rapidly elicited genes

Current crop protection strategies against the fungal pathogen Botrytis cinerea rely on a combination of conventional fungicides and host genetic resistance. However, due to pathogen evolution and legislation in the use of fungicides, these strategies are not sufficient to protect plants against this pathogen. Defence elicitors can stimulate plant defence mechanisms through a phenomenon known as defence priming. Priming results in a faster and/or stronger expression of resistance upon pathogen recognition by the host. This work aims to study defence priming by a commercial formulation of the elicitor chitosan. Treatments with chitosan result in induced resistance (IR) in solanaceous and brassicaceous plants. In tomato plants, enhanced resistance has been linked with priming of callose deposition and accumulation of the plant hormone jasmonic acid (JA). Large-scale transcriptomic analysis revealed that chitosan primes gene expression at early time-points after infection. In addition, two novel tomato genes with a characteristic priming profile were identified, Avr9/Cf-9 rapidly elicited protein 75 (ACRE75) and 180 (ACRE180). Transient and stable over-expression of ACRE75, ACRE180 and their Nicotiana benthamiana homologs, revealed that they are positive regulators of plant resistance against B. cinerea. This provides valuable information in the search for strategies to protect Solanaceae plants against B. cinerea.

Overexpression of SlMYB75 enhances resistance to Botrytis cinerea and prolongs fruit storage life in tomato

SlMYB75 increased the accumulation of JA and improved the scavenging of excess H₂O₂ to resist B. cinerea. Overexpression of SlMYB75 greatly prolongs tomato fruit storage life. Botrytis cinerea (B. cinerea) is a major threat to the production and storage life of tomato (Solanum lycopersicum) fruit around the world. SlMYB75 is an R2R3MYB transcription factor associated with the biosynthesis of anthocyanidin, but little is known about its function in the resistance of tomato to B. cinerea. In this study, we found that the overexpression of SlMYB75 regulated the accumulation of jasmonic acid (JA) and promoted the JA-mediated signaling pathway to resist B. cinerea infection. Moreover, the activities of peroxidase and superoxide dismutase, which were activated to scavenge hydrogen peroxide produced as a result of the B. cinerea infection, were enhanced in the transgenic tomato plants. Scanning electron microscopy images showed that the wax on the fruit skin surface was significantly decreased in the transgenic tomatoes compared with the wild type. However, SlMYB75 prolonged fruit storage life by both enhancing resistance to B. cinerea and directly downregulating the fruit shelf life-related gene SlFSR. Collectively, this study provides a good candidate gene for breeding high-quality tomatoes with a long storage life and high disease resistance.

Ciboria carunculoides Suppresses Mulberry Immune Responses Through Regulation of Salicylic Acid Signaling

Ciboria carunculoides is the dominant causal agent of mulberry sclerotial disease, and it is a necrotrophic fungal pathogen with a narrow host range that causes devastating diseases in mulberry fruit. However, little is known about the interaction between C. carunculoides and mulberry. Here, our transcriptome sequencing results showed that the transcription of genes in the secondary metabolism and defense-related hormone pathways were significantly altered in infected mulberry fruit. Due to the antimicrobial properties of proanthocyanidins (PAs), the activation of PA biosynthetic pathways contributes to defense against pathogens. Salicylic acid (SA) and jasmonic acid (JA) are major plant defense hormones. However, SA signaling and JA signaling are antagonistic to each other. Our results showed that SA signaling was activated, while JA signaling was inhibited, in mulberry fruit infected with C. carunculoides. Yet SA mediated responses are double-edged sword against necrotrophic pathogens, as SA not only activates systemic acquired resistance (SAR) but also suppresses JA signaling. We also show here that the small secreted protein CcSSP1 of C. carunculoides activates SA signaling by targeting pathogenesis-related protein 1 (PR1). These findings reveal that the infection strategy of C. carunculoides functions by regulating SA signaling to inhibit host defense responses.

Roots drive oligogalacturonide-induced systemic immunity in tomato

Oligogalacturonides (OGs) are fragments of pectin released from the plant cell wall during insect or pathogen attack. They can be perceived by the plant as damage signals, triggering local and systemic defence responses. Here, we analyse the dynamics of local and systemic responses to OG perception in tomato roots or shoots, exploring their impact across the plant and their relevance in pathogen resistance. Targeted and untargeted metabolomics and gene expression analysis in plants treated with purified OGs revealed that local responses were transient, while distal responses were stronger and more sustained. Remarkably, changes were more conspicuous in roots, even upon foliar application of the OGs. The treatments differentially activated the synthesis of defence-related hormones and secondary metabolites including flavonoids, alkaloids and lignans, some of them exclusively synthetized in roots. Finally, the biological relevance of the systemic defence responses activated upon OG perception was confirmed, as the treatment induced systemic resistance to Botrytis cinerea. Overall, this study shows the differential regulation of tomato defences upon OGs perception in roots and shoots and reveals the key role of roots in the coordination of the plant responses to damage sensing.

Colonization of Solanum melongena and Vitis vinifera Plants by Botrytis cinerea Is Strongly Reduced by the Exogenous Application of Tomato Systemin

Plant defense peptides are able to control immune barriers and represent a potential novel resource for crop protection. One of the best-characterized plant peptides is tomato Systemin (Sys) an octadecapeptide synthesized as part of a larger precursor protein. Upon pest attack, Sys interacts with a leucine-rich repeat receptor kinase, systemin receptor SYR, activating a complex intracellular signaling pathway that leads to the wound response. Here, we demonstrated, for the first time, that the direct delivery of the peptide to Solanum melongena and Vitis vinifera plants protects from the agent of Grey mould (Botrytis cinerea). The observed disease tolerance is associated with the increase of total soluble phenolic content, the activation of antioxidant enzymes, and the up-regulation of defense-related genes in plants treated with the peptide. Our results suggest that in treated plants, the biotic defense system is triggered by the Sys signaling pathway as a consequence of Sys interaction with a SYR-like receptor recently found in several plant species, including those under investigation. We propose that this biotechnological use of Sys, promoting defense responses against invaders, represents a useful tool to integrate into pest management programs for the development of novel strategies of crop protection.

Knockout of SlNPR1 enhances tomato plants resistance against Botrytis cinerea by modulating ROS homeostasis and JA/ET signaling pathways

Tomato is one of the most popular horticultural crops, and many commercial tomato cultivars are particularly susceptible to Botrytis cinerea. Non-expressor of pathogenesis-related gene 1 (NPR1) is a critical component of the plant defense mechanisms. However, our understanding of how SlNPR1 influences disease resistance in tomato is still limited. In this study, two independent slnpr1 mutants were used to study the role of SlNPR1 in tomato resistance against B. cinerea. Compared to (WT), slnpr1 leaves exhibited enhanced resistance against B. cinerea with smaller lesion sizes, higher activities of chitinase (CHI), β-1, 3-glucanases (GLU) and phenylalanine ammonia-lyase (PAL), and significantly increased expressions of pathogenesis-related genes (PRs). The increased activities of peroxidase (POD), ascorbate peroxidase (APX) and decreased catalase (CAT) activities collectively regulated reactive oxygen species (ROS) homeostasis in slnpr1 mutants. The integrity of the cell wall in slnpr1 mutants was maintained. Moreover, the enhanced resistance was further reflected by induction of defense genes involved in jasmonic acid (JA) and ethylene (ET) signaling pathways. Taken together, these findings revealed that knocking out SlNPR1 resulted in increased activities of defense enzymes, changes in ROS homeostasis and integrity of cell walls, and activation of JA and ET pathways, which confers resistance against B. cinerea in tomato plants.

Cytokinin response induces immunity and fungal pathogen resistance, and modulates trafficking of the PRR LeEIX2 in tomato

Plant immunity is often defined by the immunity hormones: salicylic acid (SA), jasmonic acid (JA), and ethylene (ET). These hormones are well known for differentially regulating defence responses against pathogens. In recent years, the involvement of other plant growth hormones such as auxin, gibberellic acid, abscisic acid, and cytokinins (CKs) in biotic stresses has been recognized. Previous reports have indicated that endogenous and exogenous CK treatment can result in pathogen resistance. We show here that CK induces systemic immunity in tomato (Solanum lycopersicum), modulating cellular trafficking of the pattern recognition receptor (PRR) LeEIX2, which mediates immune responses to Xyn11 family xylanases, and promoting resistance to Botrytis cinerea and Oidium neolycopersici in an SA- and ET-dependent mechanism. CK perception within the host underlies its protective effect. Our results support the notion that CK promotes pathogen resistance by inducing immunity in the host.

Transcriptome Analysis of Early Defenses in Rice against Fusarium fujikuroi

BACKGROUND

Bakanae is a seedborne disease caused by Fusarium fujikuroi. Rice seedlings emerging from infected seeds can show diverse symptoms such as elongated and slender stem and leaves, pale coloring, a large leaf angle, stunted growth and even death. Little is known about rice defense mechanisms at early stages of disease development.

RESULTS

This study focused on investigating early defenses against F. fujikuroi in a susceptible cultivar, Zerawchanica karatals (ZK), and a resistant cultivar, Tainung 67 (TNG67). Quantitative PCR revealed that F. fujikuroi colonizes the root and stem but not leaf tissues. Illumina sequencing was conducted to analyze the stem transcriptomes of F. fujikuroi-inoculated and mock-inoculated ZK and TNG67 plants collected at 7 days post inoculation (dpi). More differentially expressed genes (DEGs) were identified in ZK (n = 169) than TNG67 (n = 118), and gene ontology terms related to transcription factor activity and phosphorylation were specifically enriched in ZK DEGs. Among the complex phytohormone biosynthesis and signaling pathways, only DEGs involved in the jasmonic acid (JA) signaling pathway were identified. Fourteen DEGs encoding pattern-recognition receptors, transcription factors, and JA signaling pathway components were validated by performing quantitative reverse transcription PCR analysis of individual plants. Significant repression of jasmonate ZIM-domain (JAZ) genes (OsJAZ9, OsJAZ10, and OsJAZ13) at 3 dpi and 7 dpi in both cultivars, indicated the activation of JA signaling during early interactions between rice and F. fujikuroi. Differential expression was not detected for salicylic acid marker genes encoding phenylalanine ammonia-lyase 1 and non-expressor of pathogenesis-related genes 1. Moreover, while MeJA did not affect the viability of F. fujikuroi, MeJA treatment of rice seeds (prior to or after inoculation) alleviated and delayed bakanae disease development in susceptible ZK.

CONCLUSIONS

Different from previous transcriptome studies, which analyzed the leaves of infected plants, this study provides insights into defense-related gene expression patterns in F. fujikuroi-colonized rice stem tissues. Twelve out of the 14 selected DEGs were for the first time shown to be associated with disease resistance, and JA-mediated resistance was identified as a crucial component of rice defense against F. fujikuroi. Detailed mechanisms underlying the JA-mediated bakanae resistance and the novel defense-related DEGs are worthy of further investigation.

The potential use of the Penicillium chrysogenum antifungal protein PAF, the designed variant PAFopt and its γ-core peptide Pγopt in plant protection

The prevention of enormous crop losses caused by pesticide-resistant fungi is a serious challenge in agriculture. Application of alternative fungicides, such as antifungal proteins and peptides, provides a promising basis to overcome this problem; however, their direct use in fields suffers limitations, such as high cost of production, low stability, narrow antifungal spectrum and toxicity on plant or mammalian cells. Recently, we demonstrated that a Penicillium chrysogenum-based expression system provides a feasible tool for economic production of P. chrysogenum antifungal protein (PAF) and a rational designed variant (PAFopt ), in which the evolutionary conserved γ-core motif was modified to increase antifungal activity. In the present study, we report for the first time that γ-core modulation influences the antifungal spectrum and efficacy of PAF against important plant pathogenic ascomycetes, and the synthetic γ-core peptide Pγopt , a derivative of PAFopt , is antifungal active against these pathogens in vitro. Finally, we proved the protective potential of PAF against Botrytis cinerea infection in tomato plant leaves. The lack of any toxic effects on mammalian cells and plant seedlings, as well as the high tolerance to harsh environmental conditions and proteolytic degradation further strengthen our concept for applicability of these proteins and peptide in agriculture.

Genomic and transcriptomic insights into Raffaelea lauricola pathogenesis

BACKGROUND

Laurel wilt caused by Raffaelea lauricola is a lethal vascular disease of North American members of the Lauraceae plant family. This fungus and its primary ambrosia beetle vector Xyleborus glabratus originated from Asia; however, there is no report of laurel wilt causing widespread mortality on native Lauraceae trees in Asia. To gain insight into why R. lauricola is a tree-killing plant pathogen in North America, we generated and compared high quality draft genome assemblies of R. lauricola and its closely related non-pathogenic species R. aguacate.

RESULTS

Relative to R. aguacate, the R. lauricola genome uniquely encodes several small-secreted proteins that are associated with virulence in other pathogens and is enriched in secondary metabolite biosynthetic clusters, particularly polyketide synthase (PKS), non-ribosomal peptide synthetase (NRPS) and PKS-NRPS anchored gene clusters. The two species also exhibit significant differences in secreted proteins including CAZymes that are associated with polysaccharide binding including the chitin binding CBM50 (LysM) domain. Transcriptomic comparisons of inoculated redbay trees and in vitro-grown fungal cultures further revealed a number of secreted protein genes, secondary metabolite clusters and alternative sulfur uptake and assimilation pathways that are coordinately up-regulated during infection.

CONCLUSIONS

Through these comparative analyses we have identified potential adaptations of R. lauricola that may enable it to colonize and cause disease on susceptible hosts. How these adaptations have interacted with co-evolved hosts in Asia, where little to no disease occurs, and non-co-evolved hosts in North America, where lethal wilt occurs, requires additional functional analysis of genes and pathways.

Menadione Sodium Bisulfite-Protected Tomato Leaves against Grey Mould via Antifungal Activity and Enhanced Plant Immunity

Tomato grey mould has been one of the destructive fungal diseases during tomato production. Ten mM of menadione sodium bisulfite (MSB) was applied to tomato plants for eco-friendly control of the grey mould. MSB-reduced tomato grey mould in the 3rd true leaves was prolonged at least 7 days prior to the fungal inoculation of two inoculum densities (2 × 10⁴ and 2 × 10⁵ conidia/ml) of Botrytis cinerea. Protection efficacy was significantly higher in the leaves inoculated with the lower disease pressure of conidial suspension compared to the higher one. MSB-pretreatment was not effective to arrest oxalic acid-triggered necrosis on tomato leaves. Plant cell death and hydrogen peroxide accumulation were restricted in necrotic lesions of the B. cinereainoculated leaves by the MSB-pretreatment. Decreased conidia number and germ-tube elongation of B. cinerea were found at 10 h, and mycelial growth was also impeded at 24 h on the MSB-pretreated leaves. MSBmediated disease suppressions were found in cotyledons and different positions (1st to 5th) of true leaves inoculated with the lower conidial suspension, but only 1st to 3rd true leaves showed decreases in lesion sizes by the higher inoculum density. Increasing MSB-pretreatment times more efficiently decreased the lesion size by the higher disease pressure. MSB led to inducible expressions of defence-related genes SlPR1a, SlPR1b, SlPIN2, SlACO1, SlChi3, and SlChi9 in tomato leaves prior to B. cinerea infection. These results suggest that MSB pretreatment can be a promising alternative to chemical fungicides for environment-friendly management of tomato grey mould.

Crop Protection against Botrytis cinerea by Rhizhosphere Biological Control Agent Bacillus velezensis XT1

This study aims to evaluate the use of Bacillus velezensis strain XT1 as a plant growth-promoting rhizobacterium (PGPR) and biocontrol agent against B. cinerea in tomato and strawberry plants. Foliar and radicular applications of strain XT1 increased plant total biomass as compared to the control and B. cinerea-infected plants, with root applications being, on the whole, the most effective mode of treatment. Applications of the bacterium were found to reduce infection parameters such as disease incidence and severity by 50% and 60%, respectively. We analyzed stress parameters and phytohormone content in order to evaluate the capacity of XT1 to activate the defense system through phytohormonal regulation. Overall, the application of XT1 reduced oxidative damage, while the H₂O₂ and malondialdehyde (MDA) content was lower in XT1-treated and B. cinerea-infected plants as compared to non-XT1-treated plants. Moreover, treatment with XT1 induced callose deposition, thus boosting the response to pathogenic infection. The results of this study suggest that the signaling and activation pathways involved in defense mechanisms are mediated by jasmonic acid (JA) and ethylene hormones, which are induced by preventive treatment with XT1. The study also highlights the potential of preventive applications of strain XT1 to activate defense mechanisms in strawberry and tomato plants through hormone regulation.

Transcriptome analysis and functional validation reveal a novel gene, BcCGF1, that enhances fungal virulence by promoting infection-related development and host penetration

Simultaneous transcriptome analyses of both host plants and pathogens, and functional validation of the identified differentially expressed genes (DEGs) allow us to better understand the mechanisms underlying their interactions. Here, we analyse the mixed transcriptome derived from Botrytis cinerea (the causal agent of grey mould) infected tomato leaves at 24 hr after inoculation, a critical time point at which the pathogen has penetrated and developed in the leaf epidermis, whereas necrotic symptoms have not yet appeared. Our analyses identified a complex network of genes involved in the tomato-B. cinerea interaction. The expression of fungal transcripts encoding candidate effectors, enzymes for secondary metabolite biosynthesis, hormone and reactive oxygen species (ROS) production, and autophagy-related proteins was up-regulated, suggesting that these genes may be involved in the initial infection processes. Specifically, tomato genes involved in phytoalexin production, stress responses, ATP-binding cassette transporters, pathogenesis-related proteins, and WRKY DNA-binding transcription factors were up-regulated. We functionally investigated several B. cinerea DEGs via gene replacement and pathogenicity assays, and demonstrated that BcCGF1 was a novel virulence-associated factor that mediates fungal development and virulence via regulation of conidial germination, conidiation, infection structure formation, host penetration, and stress adaptation. The fungal infection-related development was controlled by BcCGF-mediated ROS production and exogenous cAMP restored the mutant infection-related development. Our findings provide new insights into the elucidation of the simultaneous tactics of pathogen attack and host defence. Our systematic elucidation of BcCGF1 in mediating fungal pathogenesis may open up new targets for fungal disease control.

Genome-wide identification of the NPR1-like gene family in Brassica napus and functional characterization of BnaNPR1 in resistance to Sclerotinia sclerotiorum

The BnaNPR1-like gene family was identified in B. napus, and it was revealed that repression of BnaNPR1 significantly reduces resistance toS. sclerotiorum, intensifies ROS accumulation, and changes the expression of genes associated with SA and JA/ET signaling in response to this pathogen. The NONEXPRESSOR OF PATHOGENESIS-RELATED GENES1 (NPR1) and related NPR1-like genes play an important role in regulating plant defense. Oilseed rape (Brassica napus L.) is an important oilseed crop; however, little is known about the B. napus (Bna) NPR1-like gene family. Here, a total of 19 BnaNPR1-like genes were identified in the B. napus genome, and then named according to their respective best match in Arabidopsis thaliana (At), which led to the determination of B. napus homologs of every AtNPR1-like gene. Analysis of important protein domains and functional motifs indicated the conservation and variation among these homologs. Phylogenetic analysis of these BnaNPR1-like proteins and their Arabidopsis homologs revealed six distinct sub-clades, consequently indicating that their name classification totally conformed to their phylogenetic relationships. Further, B. napus transcriptomic data showed that the expression of three BnaNPR1s was significantly down-regulated in response to infection with Sclerotinia sclerotiorum, the most important pathogen of this crop, whereas BnaNPR2/3/4/5/6s did not show the expression differences in general. Further, we generated B. napus BnaNPR1-RNAi lines to interpret the effect of the down-regulated expression of BnaNPR1s on resistance to S. sclerotiorum. The results showed that BnaNPR1-RNAi significantly decreased this resistance. Further experiments revealed that BnaNPR1-RNAi intensified ROS production and changed defense responses in the interaction of plants with this pathogen. These results indicated that S. sclerotiorum might use BnaNPR1 to regulate specific physiological processes of B. napus, such as ROS production and SA defense response, for the infection.

Phakopsora pachyrhizi triggers the jasmonate signaling pathway during compatible interaction in soybean and GmbZIP89 plays a role of major component in the pathway

The biotrophic fungus Phakopsora pachyrhizi is currently the major pathogen affecting soybean production worldwide. It has already been suggested for the non-host interaction between P. pachyrhizi and Arabidopsis thaliana that the fungus in early infection induces jasmonic acid (JA) pathway to the detriment of the salicylic acid (SA) pathway as a mechanism to the establishment of infection. In this study, we verified that this mechanism might also be occurring during the compatible interaction in soybean (Glycine max L. Merril). It was demonstrated that P. pachyrhizi triggers a JA pathway during the early and late stages of infection in a susceptible soybean cultivar. The expression of the GmbZIP89 was induced in a biphasic profile, similarly to other JA responsive genes, which indicates a new marker gene for this signaling pathway. Additionally, plants silenced for GmbZIP89 (iGmZIP89) by the virus-induced gene silencing (VIGS) approach present lower severity of infection and higher expression of pathogenesis related protein 1 (PR1). The lower disease severity showed that the iGmbZIP89 plants became more resistant to infection. These data corroborate the hypothesis that the GmbZIP89 may be a resistance negative regulator. In conclusion, we demonstrated that P. pachyrhizi mimics a necrotrophic fungus and activates the JA/ET pathway in soybean. It is possible to suppose that its direct penetration on epidermal cells or fungal effectors may modulate the expression of target genes aiming the activation of the JA pathway and inhibition of SA defense.

Natural variation in the Arabidopsis AGO2 gene is associated with susceptibility to potato virus X

RNA silencing functions as an anti-viral defence in plants through the action of DICER-like (DCL) and ARGONAUTE (AGO) proteins. Despite the importance of this mechanism, little is known about the functional consequences of variation in genes encoding RNA silencing components. The AGO2 protein has been shown to be important for defense against multiple viruses, and we investigated how naturally occurring differences in AGO2 between and within species affects its antiviral activities. We find that the AGO2 protein from Arabidopsis thaliana, but not Nicotiana benthamiana, effectively limits potato virus X (PVX). Consistent with this, we find that the A. thaliana AGO2 gene shows a high incidence of polymorphisms between accessions, with evidence of selective pressure. Using functional analyses, we identify polymorphisms that specifically affect AGO2 antiviral activity, without interfering with other AGO2-associated functions such as anti-bacterial resistance or DNA methylation. Our results suggest that viruses adapt to overcome RNA silencing in their hosts. Furthermore, they indicate that plant-virus interactions have influenced natural variation in RNA-silencing components and that the latter may be a source of genetically encoded virus resistance.

Communication of plants with microbial world: Exploring the regulatory networks for PGPR mediated defense signaling

Agricultural manipulation of potentially beneficial rhizosphere microbes is increasing rapidly due to their multi-functional plant-protective and growth related benefits. Plant growth promoting rhizobacteria (PGPR) are mostly non-pathogenic microbes which exert direct benefits on plants while there are rhizosphere bacteria which indirectly help plant by ameliorating the biotic and/or abiotic stress or induction of defense response in plant. Regulation of these direct or indirect effect takes place via highly specialized communication system induced at multiple levels of interaction i.e., inter-species, intra-species, and inter-kingdom. Studies have provided insights into the functioning of signaling molecules involved in communication and induction of defense responses. Activation of host immune responses upon bacterial infection or rhizobacteria perception requires comprehensive and precise gene expression reprogramming and communication between hosts and microbes. Majority of studies have focused on signaling of host pattern recognition receptors (PRR) and nod-like receptor (NLR) and microbial effector proteins under mining the role of other components such as mitogen activated protein kinase (MAPK), microRNA, histone deacytylases. The later ones are important regulators of gene expression reprogramming in plant immune responses, pathogen virulence and communications in plant-microbe interactions. During the past decade, inoculation of PGPR has emerged as potential strategy to induce biotic and abiotic stress tolerance in plants; hence, it is imperative to expose the basis of these interactions. This review discusses microbes and plants derived signaling molecules for their communication, regulatory and signaling networks of PGPR and their different products that are involved in inducing resistance and tolerance in plants against environmental stresses and the effect of defense signaling on root microbiome. We expect that it will lead to the development and exploitation of beneficial microbes as source of crop biofertilizers in climate changing scenario enabling more sustainable agriculture.

An effector of a necrotrophic fungal pathogen targets the calcium-sensing receptor in chloroplasts to inhibit host resistance

SsITL, a secretory protein of the necrotrophic phytopathogen Sclerotinia sclerotiorum, was previously reported to suppress host immunity at the early stages of infection. However, the molecular mechanism that SsITL uses to inhibit plant defence against S. sclerotiorum has not yet been elucidated. Here, we report that SsITL interacted with a chloroplast-localized calcium-sensing receptor, CAS, in chloroplasts. We found that CAS is a positive regulator of the salicylic acid signalling pathway in plant immunity to S. sclerotiorum and CAS-mediated resistance against S. sclerotiorum depends on Ca²⁺ signalling. Furthermore, we showed that SsITL could interfere with the plant salicylic acid (SA) signalling pathway and SsITL-expressing transgenic plants were more susceptible to S. sclerotiorum. However, truncated SsITLs (SsITL-NT1 or SsITL-CT1) that lost the ability to interact with CAS do not affect plant resistance to S. sclerotiorum. Taken together, our findings reveal that SsITL inhibits SA accumulation during the early stage of infection by interacting with CAS and then facilitating the infection by S. sclerotiorum.

Comparative N-glycoproteome analysis provides novel insights into the regulation mechanism in tomato (solanum lycopersicum L.) During fruit ripening process

Protein N-glycosylation plays key roles in protein folding, stability, solubility, biogenesis, and enzyme activity. Tomato (Solanum lycopersicum L.) is an important vegetable crop with abundant nutritional value, and the formation of tomato fruit qualities primarily occurs in the fruit ripening process. However, a large number of N-glycosylation-mediated mechanisms in regulating tomato fruit ripening have not been elucidated to date. In this study, western blot assays showed that the extents of mature N-glycoproteins were differentially expressed in mature green fruits (fruit start ripening) and ripe fruits (fruit stop ripening). Next, through performing a comparative N-glycoproteome analysis strategy, a total of 553 N-glycosites from 363 N-glycoproteins were identified in mature green fruits compared with ripe fruits. Among them, 252 N-glycosites from 191 N-glycoproteins were differentially expressed in mature green fruits compared with ripe fruits. The differentially expressed N-glycoproteins were mainly located in the chloroplast (30 %) and cytoplasm (16 %). Gene Ontology (GO) analysis showed that these N-glycoproteins were involved in various biological processes, cellular components and molecular functions. These N-glycoproteins participate in biological processes, such as metabolic processes, cellular processes and single-organism processes. These N-glycoproteins are also cellular components in biological process cells, membranes and organelles and have different molecular functions, such as catalytic activity and binding. Notably, these N-glycoproteins were enriched in starch and sucrose metabolism and galactose metabolism by KEGG pathway analysis. This community resource regarding N-glycoproteins is the first large-scale N-glycoproteome during plant fruit ripening. This study will contribute to understanding the function of N-glycosylation in regulating plant fruit ripening.

Exogenous sodium diethyldithiocarbamate, a Jasmonic acid biosynthesis inhibitor, induced resistance to powdery mildew in wheat

Jasmonic acid (JA) is an important plant hormone associated with plant-pathogen defense. To study the role of JA in plant-fungal interactions, we applied a JA biosynthesis inhibitor, sodium diethyldithiocarbamate (DIECA), on wheat leaves. Our results showed that application of 10 mM DIECA 0-2 days before inoculation effectively induced resistance to powdery mildew (Bgt) in wheat. Transcriptome analysis identified 364 up-regulated and 68 down-regulated differentially expressed genes (DEGs) in DIECA-treated leaves compared with water-treated leaves. Gene ontology (GO) enrichment analysis of the DEGs revealed important GO terms and pathways, in particular, response to growth hormones, activity of glutathione metabolism (e.g., glutathione transferase activity), oxalate oxidase, and chitinase activity. Gene annotaion revealed that some pathogenesis-related (PR) genes, such as PR1.1, PR1, PR10, PR4a, Chitinase 8, beta-1,3-glucanase, RPM1, RGA2, and HSP70, were induced by DIECA treatment. DIECA reduced JA and auxin (IAA) levels, while increased brassinosteroid, glutathione, and ROS lesions in wheat leaves, which corroborated with the transcriptional changes. Our results suggest that DIECA can be applied to increase plant immunity and reduce the severity of Bgt disease in wheat fields.

Salicylic Acid as a Safe Plant Protector and Growth Regulator

Since salicylic acid (SA) was discovered as an elicitor of tobacco plants inducing the resistance against Tobacco mosaic virus (TMV) in 1979, increasing reports suggest that SA indeed is a key plant hormone regulating plant immunity. In addition, recent studies indicate that SA can regulate many different responses, such as tolerance to abiotic stress, plant growth and development, and soil microbiome. In this review, we focused on the recent findings on SA's effects on resistance to biotic stresses in different plant-pathogen systems, tolerance to different abiotic stresses in different plants, plant growth and development, and soil microbiome. This allows us to discuss about the safe and practical use of SA as a plant defense activator and growth regulator. Crosstalk of SA with different plant hormones, such as abscisic acid, ethylene, jasmonic acid, and auxin in different stress and developmental conditions were also discussed.

Revealing Shared and Distinct Genes Responding to JA and SA Signaling in Arabidopsis by Meta-Analysis

Plant resistance against biotrophic and necrotrophic pathogens is mediated by mutually synergistic and antagonistic effects of salicylic acid (SA) and jasmonic acid (JA) signals. However, the unique and shared genes responding to the defense mediated by JA/SA signals were largely unclear. To reveal discrete, synergistic and antagonistic JA/SA responsive genes in Arabidopsis thaliana, Meta-Analysis was employed with 257 publicly available Arabidopsis thaliana RNA-Seq gene expression profiles following treatment of mock, JA or SA analogs. JA/SA signalings were found to co-induce broad-spectrum disease-response genes, co-repress the genes related to photosynthesis, auxin, and gibberellin, and reallocate resources of growth toward defense. JA might attenuate SA induced immune response by inhibiting the expression of resistance genes and receptor-like proteins/kinases. Strikingly, co-expression network analysis revealed that JA/SA uniquely regulated genes showing highly coordinated co-expression only in their respective treatment. Using principal component analysis, and hierarchical cluster analysis, JA/SA analogs were segregated into separate entities based on the global differential expression matrix rather than the expression matrix. To accurately classify JA/SA analogs with as few genes as possible, 87 genes, including the SA receptor NPR4, and JA biosynthesis gene AOC1 and JA response biomarkers VSP1/2, were identified by three feature selection algorithms as JA/SA markers. The results were confirmed by independent datasets and provided valuable resources for further functional analyses in JA- or SA- mediated plant defense. These methods would provide cues to build a promising approach for probing the mode of action of potential elicitors.

Role of Jasmonates in Beneficial Microbe-Root Interactions

The phytohormone jasmonate (JA) modulates various defense and developmental responses of plants, and is implied in the integration of multiple environmental signals. Given its centrality in regulating plant physiology according to external stimuli, JA influences the establishment of interactions between plant roots and beneficial bacteria or fungi. In many cases, moderate JA signaling promotes the onset of mutualism, while massive JA signaling inhibits it. The output also depends on the compatibility between microbe and host plant and on nutritional or environmental cues. Also, JA biosynthesis and perception participate in the systemic regulation of mutualistic interactions and in microbe-induced resistance to biotic and abiotic stress. Here, we review our current knowledge of the role of JA biosynthesis, signaling, and responses during mutualistic root-microbe interactions.

Heterologous Expression of the AtNPR1 Gene in Olive and Its Effects on Fungal Tolerance

The NPR1 gene encodes a key component of systemic acquired resistance (SAR) signaling mediated by salicylic acid (SA). Overexpression of NPR1 confers resistance to biotrophic and hemibiotrophic fungi in several plant species. The NPR1 gene has also been shown to be involved in the crosstalk between SAR signaling and the jasmonic acid-ethylene (JA/Et) pathway, which is involved in the response to necrotrophic fungi. The aim of this research was to generate transgenic olive plants expressing the NPR1 gene from Arabidopsis thaliana to evaluate their differential response to the hemibiotrophic fungus Verticillium dahliae and the necrotroph Rosellinia necatrix. Three transgenic lines expressing the AtNPR1 gene under the control of the constitutive promoter CaMV35S were obtained using an embryogenic line derived from a seed of cv. Picual. After maturation and germination of the transgenic somatic embryos, the plants were micropropagated and acclimated to ex vitro conditions. The level of AtNPR1 expression in the transgenic materials varied greatly among the different lines and was higher in the NPR1-780 line. The expression of AtNPR1 did not alter the growth of transgenic plants either in vitro or in the greenhouse. Different levels of transgene expression also did not affect basal endochitinase activity in the leaves, which was similar to that of control plants. Response to the hemibiotrophic pathogen V. dahliae varied with pathotype. All plants died by 50 days after inoculation with defoliating (D) pathotype V-138, but the response to non-defoliating (ND) strains differed by race: following inoculation with the V-1242 strain (ND, race 2), symptoms appeared after 44-55 days, with line NPR1-780 showing the lowest disease severity index. This line also showed good performance when inoculated with the V-1558 strain (ND, race 1), although the differences from the control were not statistically significant. In response to the necrotroph R. necatrix, all the transgenic lines showed a slight delay in disease development, with mean area under the disease progress curve (AUDPC) values 7-15% lower than that of the control.

Expression of Putative Defense Responses in Cannabis Primed by Pseudomonas and/or Bacillus Strains and Infected by Botrytis cinerea

Cannabis (Cannabis sativa L.) offers many industrial, agricultural, and medicinal applications, but is commonly threatened by the gray mold disease caused by the fungus Botrytis cinerea. With few effective control measures currently available, the use of beneficial rhizobacteria represents a promising biocontrol avenue for cannabis. To counter disease development, plants rely on a complex network of inducible defense pathways, allowing them to respond locally and systemically to pathogens attacks. In this study, we present the first attempt to control gray mold in cannabis using beneficial rhizobacteria, and the first investigation of cannabis defense responses at the molecular level. Four promising Pseudomonas (LBUM223 and WCS417r) and Bacillus strains (LBUM279 and LBUM979) were applied as single or combined root treatments to cannabis seedlings, which were subsequently infected by B. cinerea. Symptoms were recorded and the expression of eight putative defense genes was monitored in leaves by reverse transcription quantitative polymerase chain reaction. The rhizobacteria did not significantly control gray mold and all infected leaves were necrotic after a week, regardless of the treatment. Similarly, no systemic activation of putative cannabis defense genes was reported, neither triggered by the pathogen nor by the rhizobacteria. However, this work identified five putative defense genes (ERF1, HEL, PAL, PR1, and PR2) that were strongly and sustainably induced locally at B. cinerea's infection sites, as well as two stably expressed reference genes (TIP41 and APT1) in cannabis. These markers will be useful in future researches exploring cannabis defense pathways.

Comprehensive analysis of multiprotein bridging factor 1 family genes and SlMBF1c negatively regulate the resistance to Botrytis cinerea in tomato

BACKGROUND

Multiprotein bridging factor 1 s (MBF1s) are members of the transcriptional co-activator family that have involved in plant growth, development and stress responses. However, little is known about the Solanum lycopersicum MBF1 (SlMBF1) gene family.

RESULTS

In total, five SlMBF1 genes were identified based on the tomato reference genome, and these genes were mapped to five chromosomes. All of the SlMBF1 proteins were highly conserved, with a typical MBF1 domain and helix-turn-helix_3 domain. In addition, the promoter regions of the SlMBF1 genes have various stress and hormone responsive cis-regulatory elements. Encouragingly, the SlMBF1 genes were expressed with different expression profiles in different tissues and responded to various stress and hormone treatments. The biological function of SlMBF1c was further identified through its overexpression in tomato, and the transgenic tomato lines showed increased susceptibility to Botrytis cinerea (B. cinerea). Additionally, the expression patterns of salicylic acid (SA)-, jasmonic acid (JA)- and ethylene (ET)- mediated defense related genes were altered in the transgenic plants.

CONCLUSIONS

Our comprehensive analysis provides valuable information for clarifying the evolutionary relationship of the SlMBF1 members and their expression patterns in different tissues and under different stresses. The overexpression of SlMBF1c decreased the resistance of tomato to B. cinerea through enhancing the gene expression of the SA-mediated signaling pathway and depressing JA/ET-mediated signaling pathways. These results will facilitate future functional studies of the transcriptional co-activator family.

Tomato Plants Treated with Systemin Peptide Show Enhanced Levels of Direct and Indirect Defense Associated with Increased Expression of Defense-Related Genes

Plant defense peptides represent an important class of compounds active against pathogens and insects. These molecules controlling immune barriers can potentially be used as novel tools for plant protection, which mimic natural defense mechanisms against invaders. The constitutive expression in tomato plants of the precursor of the defense peptide systemin was previously demonstrated to increase tolerance against moth larvae and aphids and to hamper the colonization by phytopathogenic fungi, through the expression of a wealth of defense-related genes. In this work we studied the impact of the exogenous supply of systemin to tomato plants on pests to evaluate the use of the peptide as a tool for crop protection in non-transgenic approaches. By combining gene expression studies and bioassays with different pests we demonstrate that the exogenous supply of systemin to tomato plants enhances both direct and indirect defense barriers. Experimental plants, exposed to this peptide by foliar spotting or root uptake through hydroponic culture, impaired larval growth and development of the noctuid moth Spodoptera littoralis, even across generations, reduced the leaf colonization by the fungal pathogen Botrytis cinerea and were more attractive towards natural herbivore antagonists. The induction of these defense responses was found to be associated with molecular and biochemical changes under control of the systemin signalling cascade. Our results indicate that the direct delivery of systemin, likely characterized by a null effect on non-target organisms, represents an interesting tool for the sustainable protection of tomato plants.

Gene Expression Profiling Reveals Enhanced Defense Responses in an Invasive Weed Compared to Its Native Congener During Pathogenesis

Invasive plants are a huge burden on the environment, and modify local ecosystems by affecting the indigenous biodiversity. Invasive plants are generally less affected by pathogens, although the underlying molecular mechanisms responsible for their enhanced resistance are unknown. We investigated expression profiles of three defense hormones (salicylic acid, jasmonic acid, and ethylene) and their associated genes in the invasive weed, Alternanthera philoxeroides, and its native congener, A. sessilis, after inoculation with Rhizoctonia solani. Pathogenicity tests showed significantly slower disease progression in A. philoxeroides compared to A. sessilis. Expression analyses revealed jasmonic acid (JA) and ethylene (ET) expressions were differentially regulated between A. philoxeroides and A. sessilis, with the former having prominent antagonistic cross-talk between salicylic acid (SA) and JA, and the latter showing weak or no cross-talk during disease development. We also found that JA levels decreased and SA levels increased during disease development in A. philoxeroides. Variations in hormonal gene expression between the invasive and native species (including interspecific differences in the strength of antagonistic cross-talk) were identified during R. solani pathogenesis. Thus, plant hormones and their cross-talk signaling may improve the resistance of invasive A. philoxeroides to pathogens, which has implications for other invasive species during the invasion process.

Novel Cell Death-Inducing Elicitors from Phytophthora palmivora Promote Infection on Hevea brasiliensis

Elicitors play an important role in plant and pathogen interactions. The discovery of new elicitors and their effects on plant defense responses is significant and challenging. In this study, we investigated novel elicitors from Phytophthora palmivora and their effects on plant defenses. A crude elicitor isolated by ethanol precipitation from culture filtrates of P. palmivora induced cell death in tobacco leaves. When tobacco leaves were infiltrated with this cell death-inducing elicitor, the accumulations of H2O2, salicylic acid (SA), scopoletin (Scp), and abscisic acid (ABA) were detected. Accumulations of SA, Scp, and ABA were also induced in rubber tree leaves. P. palmivora infection significantly increased in rubber tree leaves pretreated with the elicitor and cotreated with the elicitor and zoospores of P. palmivora. This elicitor can be described as compound elicitor because Fourier-transform infrared spectroscopy revealed that it consisted of both polysaccharide and protein. We also found that the cell death effect caused by this compound elicitor was completely neutralized by Proteinase K. The compound elicitor was composed of four fractions which were beta-glucan, high-molecular-weight glycoprotein, broad-molecular-weight glycoprotein and 42-kDa protein. Interestingly, the broad-molecular-weight glycoprotein caused the highest level of cell death in tobacco leaves, while the beta-glucan had no effect. The high-molecular-weight glycoprotein, broad-molecular-weight glycoprotein and 42-kDa protein fractions not only caused cell death in tobacco leaves but also induced high levels of SA accumulation. Furthermore, these three fractions clearly promoted P. palmivora infection of rubber tree leaves.

Transcriptome Arofile of Brassica rapa L. Reveals the Involvement of Jasmonic Acid, Ethylene, and Brassinosteroid Signaling Pathways in Clubroot Resistance

Plasmodiophora brassicae is a protozoan pathogen that causes clubroot disease in cruciferous plants, particularly Chinese cabbage (Brassica rapa). A previous study identified a clubroot resistance gene (CRd) conferring race-specific resistance to P. brassicae. However, the defense mechanisms of B. rapa against virulent vs. avirulent P. brassicae are poorly understood. In this study, we carried out a global transcriptional analysis in the clubroot-resistant Chinese cabbage inbred line “85–74” carrying the CRd gene and inoculated with avirulent (LAB-4) or virulent (SCCD-52) P. brassicae. RNA sequencing showed that “85–74” responded most rapidly to SCCD-52 infection, and the number of differentially expressed genes was much higher in SCCD-52-treated as compared to LAB-4-treated plants (5552 vs. 304). Transcriptome profiling revealed that plant hormone signal transduction and plant–pathogen interaction pathways played key roles in the late stages of P. brassicae infection. Genes relating to the salicyclic acid (SA), jasmonic acid (JA)/ethylene (ET), and brassinosteroid (BR) signaling pathways were up-regulated relative to untreated plants in response to LAB-4 infection at 8, 16, and 32 days post-inoculation (dpi) whereas JA, ET, and BR signaling-related genes were not activated in response to SCCD-52, and SA signaling-related genes were up-regulated in both LAB-4 and SCCD-52, suggesting that SA signaling is not the key factor in host resistance to avirulent P. brassicae. In addition, genes associated with phosphorylation and Ca2+ signaling pathways were down-regulated to a greater degree following LAB-4 as compared to SCCD-52 infection at 8 dpi. These results indicate that effector-triggered immunity in “85–74” is more potently activated in response to infection with avirulent P. brassicae and that JA, ET, and BR signaling are important for the host response at the late stage of infection. These findings provide insight into P. brassicae pathotype-specific defense mechanisms in cruciferous crops.

The Effector AGLIP1 in Rhizoctonia solani AG1 IA Triggers Cell Death in Plants and Promotes Disease Development Through Inhibiting PAMP-Triggered Immunity in Arabidopsis thaliana

Rhizoctonia solani, one of the most detrimental necrotrophic pathogens, causes rice sheath blight and poses a severe threat to production. Focus on the function of effectors secreted by necrotrophic pathogens during infection has grown rapidly in recent years. However, little is known about the virulence and mechanisms of these proteins. In this study, we performed functional studies on putative effectors in R. solani and revealed that AGLIP1 out of 13 putative effectors induced cell death in Nicotiana benthamiana. AGLIP1 was also demonstrated to trigger cell death in rice protoplasts. The predicted lipase active sites and signal peptide (SP) of this protein were required for the cell death-inducing ability. AGLIP1 was greatly induced during R. solani infection in rice sheath. The AGLIP1's virulence function was further demonstrated by transgenic technology. The pathogenesis-related genes induced by pathogen-associated molecular pattern and bacteria were remarkably inhibited in AGLIP1-expressing transgenic Arabidopsis lines. Ectopic expression of AGLIP1 strongly facilitated disease progression in Arabidopsis caused by the type III secretion system-defective mutant from Pseudomonas syringae pv. tomato DC3000. Collectively, these results indicate that AGLIP1 is a possible effector that plays a significant role in pathogen virulence through inhibiting basal defenses and promoting disease development in plants.