Proteomic Studies to Understand the Mechanisms of Peach Tissue Degradation by Monilinia laxa

Monilinia fructicola genes involved in the cell wall-degrading process in early nectarine infection

Brown rot symptoms may be linked to alterations in the gene expression pattern of genes associated with cell wall degradation. In this study, we identify key carbohydrate-active enzymes (CAZymes) involved in cell wall degradation by Monilinia fructicola, including pme2 and pme3 (pectin methylesterases), cut1 (cutinase) and nep2 (necrosis-inducing factor). The expression of these genes is significantly modulated by red and blue light during early nectarine infection. The polygalacturonase gene pg1 and the cellulase gene cel1 also exhibit photoinduction albeit to a lesser extent. Red and blue light cause an acceleration in the initial stages of brown rot development caused by M. fructicola on nectarines. Disease symptoms like tissue maceration were evident after an incubation period of 24 h followed by 14 h of light exposition, in contrast to the usual incubation period of 48 to 72 h. Furthermore, the culture media exerts an impact on gene regulation, suggesting a complex interplay between light and nutrient signalling pathways in M. fructicola. In addition, we observe that red light promotes colony growth on a 12 h photoperiod and consistently reduces conidiation. In contrast, blue light hampers growth rate on both the 12 h and the 8 h photoperiod but only diminishes conidiation on the 12 h photoperiod. These findings enhance our comprehension of genes associated with cell wall degradation and the environmental factors influencing brown rot development.

Global Transcriptome Analysis of the Peach (Prunus persica) in the Interaction System of Fruit-Chitosan-Monilinia fructicola

The peach (Prunus persica L.) is one of the most important stone-fruit crops worldwide. Nevertheless, successful peach fruit production is seriously reduced by losses due to Monilinia fructicola the causal agent of brown rot. Chitosan has a broad spectrum of antimicrobial properties and may also act as an elicitor that activate defense responses in plants. As little is known about the elicitation potential of chitosan in peach fruits and its impact at their transcriptional-level profiles, the aim of this study was to uncover using RNA-seq the induced responses regulated by the action of chitosan in fruit-chitosan-M. fructicola interaction. Samples were obtained from fruits treated with chitosan or inoculated with M. fructicola, as well from fruits pre-treated with chitosan and thereafter inoculated with the fungus. Chitosan was found to delay the postharvest decay of fruits, and expression profiles showed that its defense-priming effects were mainly evident after the pathogen challenge, driven particularly by modulations of differentially expressed genes (DEGs) related to cell-wall modifications, pathogen perception, and signal transduction, preventing the spread of fungus. In contrast, as the compatible interaction of fruits with M. fructicola was challenged, a shift towards defense responses was triggered with a delay, which was insufficient to limit fungal expansion, whereas DEGs involved in particular processes have facilitated early pathogen colonization. Physiological indicators of peach fruits were also measured. Additionally, expression profiles of particular M. fructicola genes highlight the direct antimicrobial activity of chitosan against the fungus. Overall, the results clarify the possible mechanisms of chitosan-mediated tolerance to M. fructicola and set new foundations for the potential employment of chitosan in the control of brown rot in peaches.

Monilinia fructicola Response to White Light

Light represents a powerful signal for the regulation of virulence in many microbial pathogens. Monilinia fructicola is the most virulent species causing brown rot in stone fruit crops. To understand the influence of light on M. fructicola, we measured the effect of white light and photoperiods on the colonial growth and sporulation of the model M. fructicola strain 38C on solid cultures. Searches in the M. fructicola 38C genome predicted a complete set of genes coding for photoreceptors possibly involved in the perception of all ranges of wavelengths. Since white light had an obvious negative effect on vegetative growth and the asexual development of M. fructicola 38C on potato dextrose agar, we studied how light influences photoresponse genes in M. fructicola during early peach infection and in liquid culture. The transcriptomes were analyzed in "Red Jim" nectarines infected by M. fructicola 38C and subjected to light pulses for 5 min and 14 h after 24 h of incubation in darkness. Specific light-induced genes were identified. Among these, we confirmed in samples from infected fruit or synthetic media that blue light photoreceptor vvd1 was among the highest expressed genes. An unknown gene, far1, coding for a small protein conserved in many families of Ascomycota phylum, was also highly induced by light. In contrast, a range of well-known photoreceptors displayed a low transcriptional response to light in M. fructicola from nectarines but not on the pathogen mycelium growing in liquid culture media for 6 days.

Stone fruit phenolic and triterpenoid compounds modulate gene expression of Monilinia spp. in culture media

Phenolic and triterpenoid compounds are essential components in stone fruit skin and flesh tissues. They are thought to possess general antimicrobial activity. However, regarding brown rot disease, investigations were only confined to a limited number of phenolics, especially chlorogenic acid. The activity of triterpenoids against Monilinia spp., as an essential part of the peach cuticular wax, has not been studied before. In this work, the anti-fungal effect of some phenolics, triterpenoids, and fruit surface compound (FSC) extracts of peach fruit at two developmental stages were investigated on Monilinia fructicola and Monilinia laxa characteristics during in vitro growth. A new procedure for assaying anti-fungal activity of triterpenoids, which are notoriously difficult to assess in vitro because of their hydrophobicity, has been developed. Measurements of colony diameter, sporulation, and germination of second-generation conidia were recorded. Furthermore, the expression of twelve genes of M. fructicola associated with germination and/or appressorium formation and virulence-related genes was studied relative to the presence of the compounds. The study revealed that certain phenolics and triterpenoids showed modest anti-fungal activity while dramatically modulating gene expression in mycelium of M. fructicola on culture medium. MfRGAE1 gene was overexpressed by chlorogenic and ferulic acids and MfCUT1 by betulinic acid, at 4- and 7- days of mycelium incubation. The stage II FSC extract, corresponding to the period when the fruit is resistant to Monilinia spp., considerably up-regulated the MfLAE1 gene. These findings effectively contribute to the knowledge of biochemical compounds effects on fungi on in vitro conditions.

Secretome analysis of the phytopathogen Macrophomina phaseolina cultivated in liquid medium supplemented with and without soybean leaf infusion

Macrophomina phaseolina (Tassi) Goid. is a fungal pathogen that causes root and stem rot in several economically important crops. However, most of disease control strategies have shown limited effectiveness. Despite its impact on agriculture, molecular mechanisms involved in the interaction with host plant remains poorly understood. Nevertheless, it has been proven that fungal pathogens secrete a variety of proteins and metabolites to successfully infect their host plants. In this study, a proteomic analysis of proteins secreted by M. phaseolina in culture media supplemented with soybean leaf infusion was performed. A total of 250 proteins were identified with a predominance of hydrolytic enzymes. Plant cell wall degrading enzymes together peptidases were found, probably involved in the infection process. Predicted effector proteins were also found that could induce plant cell death or suppress plant immune response. Some of the putative effectors presented similarities to known fungal virulence factors. Expression analysis of ten selected protein-coding genes showed that these genes are induced during host tissue infection and suggested their participation in the infection process. The identification of secreted proteins of M. phaseolina could be used to improve the understanding of the biology and pathogenesis of this fungus. Although leaf infusion was able to induce changes at the proteome level, it is necessary to study the changes induced under conditions that mimic the natural infection process of the soil-borne pathogen M. phaseolina to identify virulence factors.

A Secondary Metabolism Pathway Involved in the Production of a Putative Toxin Is Expressed at Early Stage of Monilinia laxa Infection

The necrotrophic pathogenic fungus Monilinia laxa causes brown rot disease on stone fruit generating significant yield losses. So far, a limited number of pathogenesis-related virulence factors, such as cell wall degrading enzymes and potential phytotoxins, have been described in Monilinia spp. Using RNA-sequencing data from highly virulent M. laxa ML8L strain at early stages of the infection process (6, 14, 24, and 48 h post-inoculation, hpi) on nectarine and the Pathogen-Host-Interactions (PHI) database, we selected a number of genes for further study and ranked them according to their transcription levels. We identified a class of genes highly expressed at 6 hpi and that their expression decreased to almost undetectable levels at 14 to 48 hpi. Among these genes we found Monilinia__061040 encoding a non-ribosomal peptide synthase (NRPS). Monilinia__061040 together with other five co-regulated genes, forms a secondary metabolism cluster potentially involved in the production of epipolythiodioxopiperazine (ETP) toxin. Quantitative-PCR data confirmed previous RNA sequencing results from the virulent ML8L strain. Interestingly, in a less virulent M. laxa ML5L strain the expression levels of this pathway were reduced compared to the ML8L strain during nectarine infection. In vitro experiments showed that liquid medium containing peach extract mimicked the results observed using nectarines. In fact, upregulation of the NRPS coding gene was also observed in minimal medium suggesting the existence of a fruit-independent mechanism of regulation for this putative toxin biosynthetic pathway that is also downregulated in the less virulent strain. These results emphasize the role of this secondary metabolism pathway during the early stage of brown rot disease development and show alternative models to study the induction of virulence genes in this fungus.

Comparative Genomics Used to Predict Virulence Factors and Metabolic Genes among Monilinia Species

Brown rot, caused by Monilinia spp., is among the most important diseases in stone fruits, and some pome fruits (mainly apples). This disease is responsible for significant yield losses, particularly in stone fruits, when weather conditions favorable for disease development appear. To achieve future sustainable strategies to control brown rot on fruit, one potential approach will be to characterize genomic variation among Monilinia spp. to define, among others, the capacity to infect fruit in this genus. In the present work, we performed genomic and phylogenomic comparisons of five Monilinia species and inferred differences in numbers of secreted proteins, including CAZy proteins and other proteins important for virulence. Duplications specific to Monilinia were sparse and, overall, more genes have been lost than gained. Among Monilinia spp., low variability in the CAZome was observed. Interestingly, we identified several secondary metabolism clusters based on similarity to known clusters, and among them was a cluster with homology to pyriculol that could be responsible for the synthesis of chloromonilicin. Furthermore, we compared sequences of all strains available from NCBI of these species to assess their MAT loci and heterokaryon compatibility systems. Our comparative analyses provide the basis for future studies into understanding how these genomic differences underlie common or differential abilities to interact with the host plant.

Deciphering the Monilinia fructicola Genome to Discover Effector Genes Possibly Involved in Virulence

Brown rot is the most economically important fungal disease of stone fruits and is primarily caused by Monilinia laxa and Monlinia fructicola. Both species co-occur in European orchards although M. fructicola is considered to cause the most severe yield losses in stone fruit. This study aimed to generate a high-quality genome of M. fructicola and to exploit it to identify genes that may contribute to pathogen virulence. PacBio sequencing technology was used to assemble the genome of M. fructicola. Manual structural curation of gene models, supported by RNA-Seq, and functional annotation of the proteome yielded 10,086 trustworthy gene models. The genome was examined for the presence of genes that encode secreted proteins and more specifically effector proteins. A set of 134 putative effectors was defined. Several effector genes were cloned into Agrobacterium tumefaciens for transient expression in Nicotiana benthamiana plants, and some of them triggered necrotic lesions. Studying effectors and their biological properties will help to better understand the interaction between M. fructicola and its stone fruit host plants.

Transcriptomic Profiling of Populus Roots Challenged with Fusarium Reveals Differential Responsive Patterns of Invertase and Invertase Inhibitor-Like Families within Carbohydrate Metabolism

Fusarium solani (Fs) is one of the notorious necrotrophic fungal pathogens that cause root rot and vascular wilt, accounting for the severe loss of Populus production worldwide. The plant-pathogen interactions have a strong molecular basis. As yet, the genomic information and transcriptomic profiling on the attempted infection of Fs remain unavailable in a woody model species, Populus trichocarpa. We used a full RNA-seq transcriptome to investigate the molecular interactions in the roots with a time-course infection at 0, 24, 48, and 72 h post-inoculation (hpi) of Fs. Concomitantly, the invertase and invertase inhibitor-like gene families were further analyzed, followed by the experimental evaluation of their expression patterns using quantitative PCR (qPCR) and enzyme assay. The magnitude profiles of the differentially expressed genes (DEGs) were observed at 72 hpi inoculation. Approximately 839 genes evidenced a reception and transduction of pathogen signals, a large transcriptional reprogramming, induction of hormone signaling, activation of pathogenesis-related genes, and secondary and carbohydrate metabolism changes. Among these, a total of 63 critical genes that consistently appear during the entire interactions of plant-pathogen had substantially altered transcript abundance and potentially constituted suitable candidates as resistant genes in genetic engineering. These data provide essential clues in the developing new strategies of broadening resistance to Fs through transcriptional or translational modifications of the critical responsive genes within various analyzed categories (e.g., carbohydrate metabolism) in Populus.

Light-Photoreceptors and Proteins Related to Monilinia laxa Photoresponses

Light represents a ubiquitous source of information for organisms to evaluate their environment. The influence of light on colony growth and conidiation was determined for three Monilinia laxa isolates. The highest mycelial growth rate was observed under red light for the three M. laxa isolates, followed by green light, daylight or darkness. However, reduced sporulation levels were observed in darkness and red light, but conidiation enhancement was found under daylight, black and green light with more hours of exposure to light. Putative photoreceptors for blue (white-collar and cryptochromes), green (opsins), and red light (phytochromes) were identified, and the photoresponse-related regulatory family of velvet proteins. A unique ortholog for each photoreceptor was found, and their respective domain architecture was highly conserved. Transcriptional analyses of uncovered sets of genes were performed under daylight or specific color light, and both in time course illumination, finding light-dependent triggered gene expression of MlVEL2, MlPHY2, MlOPS2, and MlCRY2, and color light as a positive inductor of MlVEL3, MlVEL4, MlPHY1, and MlCRY1 expression. M. laxa has a highly conserved set of photoreceptors with other light-responsive fungi. Our phenotypic analyses and the existence of this light-sensing machinery suggest transcriptional regulatory systems dedicated to modulating the development and dispersion of this pathogen.