Proteomic analysis of secreted proteins from Trichoderma harzianum

Genome and transcriptome sequencing of Trichoderma harzianum T4, an important biocontrol fungus of Rhizoctonia solani, reveals genes related to mycoparasitism

Trichoderma harzianum is a well-known biological control strain and a mycoparasite of Rhizoctonia solani. To explore the mechanisms of mycoparasitism, the genome and transcriptome of T. harzianum T4 were both assembled and analyzed in this study. The genome of T. harzianum T4 was assembled into 106 scaffolds, sized 41.25 Mb, and annotated with a total of 8118 predicted genes. We analyzed the transcriptome of T. harzianum T4 against R. solani in a dual culture in three culture periods: before contact (BC), during contact (C), and after contact (AC). Transcriptome sequencing identified 1092, 1222, and 2046 differentially expressed genes (DEGs), respectively. These DEGs, which are involved in pathogen recognition and signal transduction, hydrolase, transporters, antibiosis, and defense-related functional genes, are significantly upregulated in the mycoparasitism process. The results of genome and transcriptome analysis indicated that the mycoparasitism process of T. harzianum T4 was very complex. T. harzianum successfully recognizes and invades host cells and kills plant pathogens by regulating various DEGs at different culture periods. The relative expression levels of the 26 upregulated DEGs were confirmed by RT-qPCR to validate the reliability of the transcriptome data. The results provide insight into the molecular mechanisms underlying T. harzianum T4's mycoparasitic processes, and they provide a potential molecular target for the biological control mechanism of T. harzianum T4.

Fungal Secretomics Through iTRAQ-Based Analysis

Our understanding of how fungi respond and adapt to external environments can be increased by the comprehensive data sets of fungal-secreted proteins. Fungi produce a variety of secreted proteins, and environmental conditions can easily influence the fungal secretome. However, the low abundance of secreted proteins and their post-translational modifications make protein extraction more challenging. Hence, the enrichment of secreted proteins is a crucial procedure for secretome analysis. This chapter illustrates a protocol for iTRAQ-based quantitative secretome analysis describing the example of fungi exposed to different environmental conditions. The fungal-secreted proteins can be extracted by combining ultrafiltration and TCA-acetone precipitation. Subsequently, the secreted proteins can be identified and quantified by the iTRAQ-based quantitative proteomics approach.

Identification of Mycoparasitism-Related Genes against the Phytopathogen Botrytis cinerea via Transcriptome Analysis of Trichoderma harzianum T4

Trichoderma harzianum is a well-known biological control agent (BCA) that is effective against a variety of plant pathogens. In previous studies, we found that T. harzianum T4 could effectively control the gray mold in tomatoes caused by Botrytis cinerea. However, the research on its biocontrol mechanism is not comprehensive, particularly regarding the mechanism of mycoparasitism. In this study, in order to further investigate the mycoparasitism mechanism of T. harzianum T4, transcriptomic sequencing and real-time fluorescence quantitative PCR (RT-qPCR) were used to identify the differentially expressed genes (DEGs) of T. harzianum T4 at 12, 24, 48 and 72 h of growth in the cell wall of B. cinerea (BCCW) or a sucrose medium. A total of 2871 DEGs and 2148 novel genes were detected using transcriptome sequencing. Through GO and KEGG enrichment analysis, we identified genes associated with mycoparasitism at specific time periods, such as encoding kinases, signal transduction proteins, carbohydrate active enzymes, hydrolytic enzymes, transporters, antioxidant enzymes, secondary metabolite synthesis, resistance proteins, detoxification genes and genes associated with extended hyphal longevity. To validate the transcriptome data, RT-qCPR was performed on the transcriptome samples. The RT-qPCR results show that the expression trend of the genes was consistent with the RNA-Seq data. In order to validate the screened genes associated with mycoparasitism, we performed a dual-culture antagonism test on T. harzianum and B. cinerea. The results of the dual-culture RT-qPCR showed that 15 of the 24 genes were upregulated during and after contact between T. harzianum T4 and B. cinerea (the same as BCCW), which further confirmed that these genes were involved in the mycoparasitism of T. harzianum T4. In conclusion, the transcriptome data provided in this study will not only improve the annotation information of gene models in T. harzianum T4 genome, but also provide important transcriptome information regarding the process of mycoparasitism at specific time periods, which can help us to further understand the mechanism of mycoparasitism, thus providing a potential molecular target for T. harzianum T4 as a biological control agent.

Strain improvement of Trichoderma harzianum for enhanced biocontrol capacity: Strategies and prospects

In the control of plant diseases, biocontrol has the advantages of being efficient and safe for human health and the environment. The filamentous fungus Trichoderma harzianum and its closely related species can inhibit the growth of many phytopathogenic fungi, and have been developed as commercial biocontrol agents for decades. In this review, we summarize studies on T. harzianum species complex from the perspective of strain improvement. To elevate the biocontrol ability, the production of extracellular proteins and compounds with antimicrobial or plant immunity-eliciting activities need to be enhanced. In addition, resistance to various environmental stressors should be strengthened. Engineering the gene regulatory system has the potential to modulate a variety of biological processes related to biocontrol. With the rapidly developing technologies for fungal genetic engineering, T. harzianum strains with increased biocontrol activities are expected to be constructed to promote the sustainable development of agriculture.

Protective effect of Bacillus species associated with Rumex dentatus against postharvest soil borne disease in potato tubers and GC-MS metabolite profile

Potato is constantly exposed to various kinds of phytopathogens which cause diseases during the developmental stage and post-harvest storage. This investigation was designed to assay the anti-phytopathogen activity of bacterial endophytes and their suppressive effects on rot disease in potato. The study also aimed to screen isolates for their plant growth-promoting traits and establish GC-MS-based metabolite profile of the potent isolate. Endophytes were isolated from Rumex dentatus and identified based on 16S rRNA gene. They were screened in dual culture assay against fungal phytopathogens and the potent isolate was tested for its capability to suppress Fusarium rot disease in potato tubers. The mechanism of action of endophytes on the phytopathogens was assessed using scanning electron microcopy. Isolates were also screened in vitro to assay their capability to produce phytohormones, hydrolytic enzymes, and to solubilize phosphates. Endophytic isolates produced proteases with a diameter of halo zone ranging from 7 to 32 mm. Bacillus sp. KL5 exhibited the highest production of indole acetic acid (IAA) with the amount of 104.28 µg/mL and was the most potent antagonist of Fusarium oxysporum and Verticillium dahliae with an inhibitory percentage of 61.53 and 100%, respectively. It showed a reduction of potato rot disease severity by more than 50%. GC-MS of active fractions of KL5 showed the presence of dibutylphthalate and 2,4-di-tert-butylphenol as major metabolites. From this study, it is evident that endophytic Bacillus species from R. dentatus are potent antagonists of F. oxysporum and V. dahliae. Bacillus sp. KL5 is a potent inhibitor of pathogenic F. oxysporum in potato tubers and can be developed as a biocontrol agent.

Trichoderma spp. Genes Involved in the Biocontrol Activity Against Rhizoctonia solani

Rhizoctonia solani is a pathogen that causes considerable harm to plants worldwide. In the absence of hosts, R. solani survives in the soil by forming sclerotia, and management methods, such as cultivar breeding, crop rotations, and fungicide sprays, are insufficient and/or inefficient in controlling R. solani. One of the most challenging problems facing agriculture in the twenty-first century besides with the impact of global warming. Environmentally friendly techniques of crop production and improved agricultural practices are essential for long-term food security. Trichoderma spp. could serve as an excellent example of a model fungus to enhance crop productivity in a sustainable way. Among biocontrol mechanisms, mycoparasitism, competition, and antibiosis are the fundamental mechanisms by which Trichoderma spp. defend against R. solani, thereby preventing or obstructing its proliferation. Additionally, Trichoderma spp. induce a mixed induced systemic resistance (ISR) or systemic acquired resistance (SAR) in plants against R. solani, known as Trichoderma-ISR. Stimulation of every biocontrol mechanism involves Trichoderma spp. genes responsible for encoding secondary metabolites, siderophores, signaling molecules, enzymes for cell wall degradation, and plant growth regulators. Rhizoctonia solani biological control through genes of Trichoderma spp. is summarized in this paper. It also gives information on the Trichoderma-ISR in plants against R. solani. Nonetheless, fast-paced current research on Trichoderma spp. is required to properly utilize their true potential against diseases caused by R. solani.

Isolation and identification of Arbutus unedo L. fungi endophytes and biological control of Phytophthora cinnamomi in vitro

Strawberry tree (Arbutus unedo, Ericaceae) is an evergreen tree with a circum-Mediterranean distribution. It has a great ecological and economic importance as a source of bioactive compounds with industrial applications and for fruit production. This study aims to characterize the fungi microbiome of this forestry species in order to develop biological control strategies in the increasing orchard production area. For this purpose, fungi endophytes were isolated from wild strawberry tree plants, and a molecular identification was carried out. In vitro assays were carried out to evaluate and characterize the antagonism of some endophytes. Among the several fungi endophytes isolated from strawberry tree (a total of 53 from 20 genera), a Trichoderma atroviride strain proved to have antagonism effect against several phytopathogens, including Alternaria alternata, Botrytis cinerea, Glomerella cingulata, and Mycosphaerella aurantia. This antagonism was particularly effective against Phytophthora cinnamomi, causing a reduction in growth of about 80% on this invasive oomycete. An enzymatic assay revealed the production of several enzymes by T. atroviride, such as cellulases, chitinases, glucosidases, alkaline phosphatases, and proteases, which is one of the several mechanisms known to be involved on Trichoderma biological control ability. The enzymatic activity, in particular that of cell wall-degrading enzymes, was accentuated when in a dual culture with P. cinnamomi. The production of serine proteases, aspartyl proteases, metalloproteases, and cysteine proteases was also detected in an experiment carried out in liquid medium, suggesting the involvement of these proteases on Trichoderma mycoparasitism mechanisms. Finally, in a three-way interaction with in vitro strawberry tree plants, the T. atroviride strain identified on this study (Au50) was able to protect the plants against P. cinnamomi, thus proving its potential as a biological control agent.

Deciphering Trichoderma-Plant-Pathogen Interactions for Better Development of Biocontrol Applications

Members of the fungal genus Trichoderma (Ascomycota, Hypocreales, Hypocreaceae) are ubiquitous and commonly encountered as soil inhabitants, plant symbionts, saprotrophs, and mycoparasites. Certain species have been used to control diverse plant diseases and mitigate negative growth conditions. The versatility of Trichoderma’s interactions mainly relies on their ability to engage in inter- and cross-kingdom interactions. Although Trichoderma is by far the most extensively studied fungal biocontrol agent (BCA), with a few species already having been commercialized as bio-pesticides or bio-fertilizers, their wide application has been hampered by an unpredictable efficacy under field conditions. Deciphering the dialogues within and across Trichoderma ecological interactions by identification of involved effectors and their underlying effect is of great value in order to be able to eventually harness Trichoderma’s full potential for plant growth promotion and protection. In this review, we focus on the nature of Trichoderma interactions with plants and pathogens. Better understanding how Trichoderma interacts with plants, other microorganisms, and the environment is essential for developing and deploying Trichoderma-based strategies that increase crop production and protection.

Understanding sheath blight resistance in rice: the road behind and the road ahead

Rice sheath blight disease, caused by the basidiomycetous necrotroph Rhizoctonia solani, became one of the major threats to the rice cultivation worldwide, especially after the adoption of high-yielding varieties. The pathogen is challenging to manage because of its extensively broad host range and high genetic variability and also due to the inability to find any satisfactory level of natural resistance from the available rice germplasm. It is high time to find remedies to combat the pathogen for reducing rice yield losses and subsequently to minimize the threat to global food security. The development of genetic resistance is one of the alternative means to avoid the use of hazardous chemical fungicides. This review mainly focuses on the effort of better understanding the host-pathogen relationship, finding the gene loci/markers imparting resistance response and modifying the host genome through transgenic development. The latest development and trend in the R. solani-rice pathosystem research with gap analysis are provided.

Identification of Differentially Expressed Genes in Trichoderma koningii IABT1252 During Its Interaction with Sclerotium rolfsii

Sclerotium rolfsii, a soil-borne fungal pathogen, infects more than 500 crop species and causes stem rot/collar rot/seed rot/southern blight/wilt in a wide variety of crops which results in significant yield loses. Presently, antagonistic microbes are gaining more importance in managing plant pathogens because they control the pathogen in an environment-friendly manner. Trichoderma is an antagonistic fungi and most popularly used biocontrol agent against phytopathogenic fungi. It is predominantly used to treat soil and seed for the control of Sclerotium rolfsii infestation. In this study, the Trichoderma koningii IABT1252 that performed better in controlling groundnut seed/ seedling rot caused by S. rolfsii in pot experiments were selected to know the molecular basis for the control. Differentially expressed genes in Trichoderma at two different stages of interaction (prior to contact and after contact with S. rolfsii) were identified. In both the stages, some of the differentially expressed genes included ones coding for hydrolytic enzymes, secondary metabolite biosynthesis, transcription factors, signaling proteins, transporter proteins, and proteins involved in mycoparasitic process of Trichoderma.

Trichoderma/pathogen/plant interaction in pre-harvest food security

Large losses before crop harvesting are caused by plant pathogens, such as viruses, bacteria, oomycetes, fungi, and nematodes. Among these, fungi are the major cause of losses in agriculture worldwide. Plant pathogens are still controlled through application of agrochemicals, causing human disease and impacting environmental and food security. Biological control provides a safe alternative for the control of fungal plant pathogens, because of the ability of biocontrol agents to establish in the ecosystem. Some Trichoderma spp. are considered potential agents in the control of fungal plant diseases. They can interact directly with roots, increasing plant growth, resistance to diseases, and tolerance to abiotic stress. Furthermore, Trichoderma can directly kill fungal plant pathogens by antibiosis, as well as via mycoparasitism strategies. In this review, we will discuss the interactions between Trichoderma/fungal pathogens/plants during the pre-harvest of crops. In addition, we will highlight how these interactions can influence crop production and food security. Finally, we will describe the future of crop production using antimicrobial peptides, plants carrying pathogen-derived resistance, and plantibodies.

Transcriptomic Analysis of Trichoderma atroviride Overgrowing Plant-Wilting Verticillium dahliae Reveals the Role of a New M14 Metallocarboxypeptidase CPA1 in Biocontrol

Verticillium dahliae, a vascular-colonizing fungus, causes economically important wilt diseases in many crops, including olive trees. Trichoderma spp. have demonstrated an effective contribution as biocontrol agents against this pathogen through a variety of mechanisms that may involve direct mycoparasitism and antibiosis. However, molecular aspects underlaying Trichoderma–V. dahliae interactions are not well known yet due to the few studies in which this pathogen has been used as a target for Trichoderma. In the present study, Trichoderma atroviride T11 overgrew colonies of V. dahliae on agar plates and inhibited growth of highly virulent defoliating (D) V. dahliae V-138I through diffusible molecules and volatile organic compounds produced before contact. A Trichoderma microarray approach of T11 growing alone (CON), and before contact (NV) or overgrowing (OV) colonies of V-138I, helped to identify 143 genes that differed significantly in their expression level by more than twofold between OV and CON or NV. Functional annotation of these genes indicated a marked up-regulation of hydrolytic, catalytic and transporter activities, and secondary metabolic processes when T11 overgrew V-138I. This transcriptomic analysis identified peptidases as enzymatic activity overrepresented in the OV condition, and the cpa1 gene encoding a putative carboxypeptidase (ID number 301733) was selected to validate this study. The role of cpa1 in strain T11 on antagonism of V-138I was analyzed by a cpa1-overexpression approach. The increased levels of cpa1 expression and protease activity in the cpa1-overexpressed transformants compared to those in wild-type or transformation control strains were followed by significantly higher antifungal activity against V-138I in in vitro assays. The use of Trichoderma spp. for the integrated management of plant diseases caused by V. dahliae requires a better understanding of the molecular mechanisms underlying this interaction that might provide an increase on its efficiency.

The study of intracellular and secreted high-molecular-mass protease(s) of Trichoderma spp., and their responses to conidiation stimuli

We continued our study of high-molecular-mass proteases (HMMPs) using several strains of the genus Trichoderma, and other filamentous fungi (Botrytis cinerea, Aspergillus niger, Fusarium culmorum, and Penicillium purpurogenum). We found that five Trichoderma strains secreted HMMPs into the media after induction with bovine serum albumin. Botrytis cinerea and F. culmorum secreted proteases in the absence of inducer, while A. niger or P. purpurogenum did not secrete proteolytic activity (PA). The activity of HMMPs secreted by or intracellularly located in Trichoderma spp. represents the predominant part of cellular PA, according to zymogram patterns. This observation allowed the study of HMMPs' physiological role(s) independent from the secretion. In studying conidiation, we found that illumination significantly stimulated PA in Trichoderma strains. In the T. atroviride IMI 206040 strain, we demonstrated that this stimulation is dependent on the BLR1 and BLR2 receptors. No stimulation of PA was observed when mechanical injury was used as an elicitor of conidiation. Compounds used as inhibitors or activators of conidiation exerted no congruent effects on both PA and conidiation. These results do not favour a direct role of HMMPs in conidiation. Probably, HMMP activity may be involved in the process of the activation of metabolism during vegetative growth, differentiation, and aging-related processes.

Genomic characterization of Trichoderma atrobrunneum (T. harzianum species complex) ITEM 908: insight into the genetic endowment of a multi-target biocontrol strain

BACKGROUND

So far, biocontrol agent selection has been performed mainly by time consuming in vitro confrontation tests followed by extensive trials in greenhouse and field. An alternative approach is offered by application of high-throughput techniques, which allow extensive screening and comparison among strains for desired genetic traits. In the genus Trichoderma, the past assignments of particular features or strains to one species need to be reconsidered according to the recent taxonomic revisions. Here we present the genome of a biocontrol strain formerly known as Trichoderma harzianum ITEM 908, which exhibits both growth promoting capabilities and antagonism against different fungal pathogens, including Fusarium graminearum, Rhizoctonia solani, and the root-knot nematode Meloidogyne incognita. By genomic analysis of ITEM 908 we investigated the occurrence and the relevance of genes associated to biocontrol and stress tolerance, providing a basis for future investigation aiming to unravel the complex relationships between genomic endowment and exhibited activities of this strain.

RESULTS

The MLST analysis of ITS-TEF1 concatenated datasets reclassified ITEM 908 as T. atrobrunneum, a species recently described within the T. harzianum species complex and phylogenetically close to T. afroharzianum and T. guizhouense. Genomic analysis revealed the presence of a broad range of genes encoding for carbohydrate active enzymes (CAZYmes), proteins involved in secondary metabolites production, peptaboils, epidithiodioxopiperazines and siderophores potentially involved in parasitism, saprophytic degradation as well as in biocontrol and antagonistic activities. This abundance is comparable to other Trichoderma spp. in the T. harzianum species complex, but broader than in other biocontrol species and in the species T. reesei, known for its industrial application in cellulase production. Comparative analysis also demonstrated similar genomic organization of major secondary metabolites clusters, as in other Trichoderma species.

CONCLUSIONS

Reported data provide a contribution to a deeper understanding of the mode of action and identification of activity-specific genetic markers useful for selection and improvement of biocontrol strains. This work will also enlarge the availability of genomic data to perform comparative studies with the aim to correlate phenotypic differences with genetic diversity of Trichoderma species.

Biocontrol activity of recombinant aspartic protease from Trichoderma harzianum against pathogenic fungi

The use of cell wall degrading enzymes of Trichoderma is a promising alternative for improving food storage. The aspartic protease P6281 secreted by the fungus Trichoderma harzianum plays an important role in mycoparasitism on phytopathogenic fungi. In this study, recombinant P6281 (rP6281) expressed in Pichia pastoris showed high activity of 321.8 U/mL. Maximum activity was observed at pH 2.5 and 40 °C, and the enzyme was stable in the pH range of 2.5-6.0. rP6281 significantly inhibited spore germination and growth of plant and animal pathogenic fungi such as Botrytis cinerea, Mucor circinelloides, Aspergillus fumigatus, Aspergillus flavus, Rhizoctonia solani, and Candida albicans. Transmission electron microscopy revealed that rP6281 efficiently damages the cell wall of Botrytis cinerea. In addition, the protease significantly inhibited the development of grey mold that causes rotting of apple, orange, and cucumber, indicating that rP6281 may be developed as an effective anti-mold agent for fruit storage.

Fungal lifestyle reflected in serine protease repertoire

Fungi are able to switch between different lifestyles in order to adapt to environmental changes. Their ecological strategy is connected to their secretome as fungi obtain nutrients by secreting hydrolytic enzymes to their surrounding and acquiring the digested molecules. We focus on fungal serine proteases (SPs), the phylogenetic distribution of which is barely described so far. In order to collect a complete set of fungal proteases, we searched over 600 fungal proteomes. Obtained results suggest that serine proteases are more ubiquitous than expected. From 54 SP families described in MEROPS Peptidase Database, 21 are present in fungi. Interestingly, 14 of them are also present in Metazoa and Viridiplantae - this suggests that, except one (S64), all fungal SP families evolved before plants and fungi diverged. Most representatives of sequenced eukaryotic lineages encode a set of 13-16 SP families. The number of SPs from each family varies among the analysed taxa. The most abundant are S8 proteases. In order to verify hypotheses linking lifestyle and expansions of particular SP, we performed statistical analyses and revealed previously undescribed associations. Here, we present a comprehensive evolutionary history of fungal SP families in the context of fungal ecology and fungal tree of life.

Secretome analysis of rice suspension-cultured cells infected by Xanthomonas oryzae pv.oryza (Xoo)

BACKGROUND

Rice bacterial blight (BB) caused by Xanthomonas oryzae pv.oryzae (Xoo) is one of the most devastating bacterial diseases in rice-growing regions worldwide. The rice-Xoo interaction is a classical model for studying the interaction between plants and pathogens. Secreted proteins play important roles in plant-bacterial interactions, but are poorly studied in the rice-Xoo system. Rice cv. Nipponbare is highly susceptible to Xoo. Here, we used two-dimensional difference gel electrophoresis (2D-DIGE) coupled with MALDI-TOF/TOF mass spectrometry (MS), to investigate secreted proteins in Nipponbare embryo cell suspension culture infected by Xoo.

RESULTS

A total of 32 protein spots changed significantly (p < 0.05) by more than 1.5 fold in gel intensity after Xoo inoculation, and were identified by MS. They represent protein products of 11 unique genes, seven from rice and four from Xoo. Of the rice proteins, six up-regulated proteins are involved in cell wall modification, the TCA cycle, glycolysis and redox, while a down-regulated protein, CHIT16, is involved in plant defense. Quantitative Real-Time PCR showed that transcript levels were not correlated with secreted protein levels. Of the Xoo proteins, three of them were possibly located in the extracellular space as shown by transient expression assays in rice protoplasts. Two of the Xoo proteins were previously reported to be likely involved in pathogenicity, and the third gene, Xoo3654, is likely a negative regulator of Xoo virulence as its overexpression reduced Xoo pathogenicity in our study.

CONCLUSION

Among the secreted proteins that responded to Xoo inoculation, we identified rice proteins involved in cell defense and Xoo proteins involved in pathogenicity. Our study also showed that Xoo3654 (X2) protein is likely a novel negative regulator of Xoo virulence. These results not only help us better understand the interaction between susceptible rice and Xoo, but also serve as a reference for studying the interaction between other plants and their pathogens.

Secretome analysis of the mycoparasitic fungus Trichoderma harzianum ALL 42 cultivated in different media supplemented with Fusarium solani cell wall or glucose

Trichoderma harzianum is a fungus well known for its potential as a biocontrol agent against many fungal phytopathogens. The aim of this study was to characterize the proteins secreted by T. harzianum ALL42 when its spores were inoculated and incubated for 48 h in culture media supplemented with glucose (GLU) or with cell walls from Fusarium solani (FSCW), a phytopathogen that causes severe losses in common bean and soy crops in Brazil, as well as other crop diseases around the world. Trichoderma harzianum was able to grow in Trichoderma Liquid Enzyme Production medium (TLE) and Minimal medium (MM) supplemented with FSCW and in TLE+GLU, but was unable to grow in MM+GLU medium. Protein quantification showed that TLE+FSCW and MM+FSCW had 45- and 30- fold, respectively, higher protein concentration on supernatant when compared to TLE+GLU, and this difference was observable on 2D gel electrophoresis (2DE). A total of 94 out of 105 proteins excised from 2DE maps were identified. The only protein observed in all three conditions was epl1. In the media supplemented with FSCW, different hydrolases such as chitinases, β-1,3-glucanases, glucoamylases, α-1,3-glucanases and proteases were identified, along with other proteins with no known functions in mycoparasitism, such as npp1 and cys. Trichoderma harzianum showed a complex and diverse arsenal of proteins that are secreted in response to the presence of FSCW, with novel proteins not previously described in mycoparasitic-related studies.

Unraveling Aspects of Bacillus amyloliquefaciens Mediated Enhanced Production of Rice under Biotic Stress of Rhizoctonia solani

Rhizoctonia solani is a necrotrophic fungi causing sheath blight in rice leading to substantial loss in yield. Excessive and persistent use of preventive chemicals raises human health and environment safety concerns. As an alternative, use of biocontrol agents is highly recommended. In the present study, an abiotic stress tolerant, plant growth promoting rhizobacteria Bacillus amyloliquefaciens (SN13) is demonstrated to act as a biocontrol agent and enhance immune response against R. solani in rice by modulating various physiological, metabolic, and molecular functions. A sustained tolerance by SN13 primed plant over a longer period of time, post R. solani infection may be attributed to several unconventional aspects of the plants' physiological status. The prolonged stress tolerance observed in presence of SN13 is characterized by (a) involvement of bacterial mycolytic enzymes, (b) sustained maintenance of elicitors to keep the immune system induced involving non-metabolizable sugars such as turanose besides the known elicitors, (c) a delicate balance of ROS and ROS scavengers through production of proline, mannitol, and arabitol and rare sugars like fructopyranose, β-D-glucopyranose and myoinositol and expression of ferric reductases and hypoxia induced proteins, (d) production of metabolites like quinazoline and expression of terpene synthase, and (e) hormonal cross talk. As the novel aspect of biological control this study highlights the role of rare sugars, maintenance of hypoxic conditions, and sucrose and starch metabolism in B. amyloliquefaciens (SN13) mediated sustained biotic stress tolerance in rice.

Fungal biomolecules assisted biosynthesis of Au-Ag alloy nanoparticles and evaluation of their catalytic property

The catalytic reduction of methylene blue was studied using biosynthesised gold-silver (Au-Ag) alloy nanoparticles (NPs). The fungal biomass of Trichoderma harzianum was used as a reducing and stabilising agent in the synthesis of Au-Ag alloy NPs. The synthesised NPs were well characterised by UV-vis spectroscopy, dynamic light scattering, X-ray diffraction, transmission electron microscopy, energy dispersive X-ray spectroscopy and Fourier transform infrared spectroscopy. The plausible synthesis mechanism involved in the formation of Au-Ag alloy NPs was also discussed with diagrammatic representation. A series of experiments was performed to investigate the catalytic activity of the as-prepared Au-Ag alloy NPs and found that the alloy NPs show excellent catalytic activity.

The platelet-activating factor acetylhydrolase gene derived from Trichoderma harzianum induces maize resistance to Curvularia lunata through the jasmonic acid signaling pathway

Platelet-activating factor acetylhydrolase (PAF-AH) derived from Trichoderma harzianum was upregulated by the interaction of T. harzianum with maize roots or the foliar pathogen Curvularia lunata. PAF-AH was associated with chitinase and cellulase expressions, but especially with chitinase, because its activity in the KO40 transformant (PAF-AH disruption transformant) was lower, compared with the wild-type strain T28. The result demonstrated that the colonization of maize roots by T. harzianum induced systemic protection of leaves inoculated with C. lunata. Such protection was associated with the expression of inducible jasmonic acid pathway-related genes. Moreover, the data from liquid chromatography-mass spectrometry confirmed that the concentration of jasmonic acid in maize leaves was associated with the expression level of defense-related genes, suggesting that PAF-AH induced resistance to the foliar pathogen. Our findings showed that PAF-AH had an important function in inducing systemic resistance to maize leaf spot pathogen.

Evaluation of hollocelulase production by Lentinula edodes (Berk.) Pegler during the submerged fermentation growth using RSM

The cellulase proteins have a great importance in the enzymatic hydrolysis of woody biomass. Despite of costs being a major concern, it has been a stimulus to study basidiomycetes biochemical properties which degrade lignocellulosic material and have prompted the processes' study for obtaining cellulolytic enzymes in fungi. The objective of this research was to evaluate the effects of the initial nitrogen content on (ammonium sulfate) and on sugar cane bagasse, which hereby, acts as an inducer of hydrolytic enzymes to produce cellulases and xylanases, using three Lentinula edodes (Berk.) Pegler strains as a transformation agent. A factorial design with 22 replications in the central point was conducted, varying concentrations of ammonium sulfate and sugar cane bagasse. The submerged cultures carried out in synthetic culture medium and incubated at 25°C for 7 days on an orbital shaker at 150 rpm. The total protein and cellulase activity as endoglucanase, exoglucanase and β-glucosidase and the xylanase was also determined. The results showed that the production of hydrolytic enzymes was stimulated by the presence of high concentrations of sugar cane bagasse (30g/L), characterizing it as an inducer due to the demonstrated proportional relationship. Thus, ammonium sulfate acted as a reducing agent in the synthesis of enzymes, being the low concentrations (0.1g/L) indicated for the enzyme production system under study. Among the studied strains, the EF52 showed higher activity for xylanase, endoglucanases, β-glucosidase and also protein.

Global protein-protein interaction network of rice sheath blight pathogen

Rhizoctonia solani is the major pathogenic fungi of rice sheath blight. It is responsible for the most serious disease of rice (Oryza sativa L.) and causes significant yield losses in rice-growing countries. Identifying the protein-protein interaction (PPI) maps of R. solani can provide insights into the potential pathogenic mechanisms and assign putative functions to unknown genes. Here, we exploited a PPI map of R. solani anastomosis group 1 IA (AG-1 IA) based on the interolog and domain-domain interaction methods. We constructed a core subset of high-confidence protein networks consisting of 6705 interactions among 1773 proteins. The high quality of the network was revealed by comprehensive methods, including yeast two-hybrid experiments. Pathogenic interaction subnetwork, secreted proteins subnetwork, and mitogen-activated protein kinase (MAPK) cascade subnetwork and their interacting partners were constructed and analyzed. Moreover, to exactly predict the pathogenic factors, the expression levels of the interaction proteins were investigated by analyzing RNA sequences that consisted of samples from the entire infection progress. The PPIs offer an exceptionally rich source of data that can be used to understand the gene functions and biological processes of this serious disease at the system level.

Biological role of Trichoderma harzianum-derived platelet-activating factor acetylhydrolase (PAF-AH) on stress response and antagonism

We investigated the properties of platelet-activating factor acetylhydrolase (PAF-AH) derived from Trichoderma harzianum. The enzyme, comprised of 572 amino acids, shares high homology with PAF-AH proteins from T. koningii and other microbial species. The optimum enzymatic activity of PAF-AH occurred at pH 6 in the absence of Ca²⁺ and it localized in the cytoplasm, and we observed the upregulation of PAF-AH expression in response to carbon starvation and strong heat shock. Furthermore, PAF-AH knockout transformant growth occurred more slowly than wild type cells and over-expression strains grown in SM medium at 37°C and 42°C. In addition, PAF-AH expression significantly increased under a series of maize root induction assay. Eicosanoic acid and ergosterol levels decreased in the PAF-AH knockouts compared to wild type cells, as revealed by GC/MS analysis. We also determined stress responses mediated by PAF-AH were related to proteins HEX1, Cu/Zn superoxide dismutase, and cytochrome c. Finally, PAF-AH exhibited antagonistic activity against Rhizoctonia solani in plate confrontation assays. Our results indicate PAF-AH may play an important role in T. harzianum stress response and antagonism under diverse environmental conditions.

Secretome of the biocontrol agent metarhizium anisopliae induced by the cuticle of the cotton pest Dysdercus peruvianus reveals new insights into infection

Metarhizium anisopliae is an entomopathogenic fungus that has evolved specialized strategies to infect insect hosts. Here we analyzed secreted proteins related to Dysdercus peruvianus infection. Using shotgun proteomics, abundance changes in 71 proteins were identified after exposure to host cuticle. Among these proteins were classical fungal effectors secreted by pathogens to degrade physical barriers and alter host physiology. These include lipolytic enzymes, Pr1A, B, C, I, and J proteases, ROS-related proteins, oxidorreductases, and signaling proteins. Protein interaction networks were generated postulating interesting candidates for further studies, including Pr1C, based on possible functional interactions. On the basis of these results, we propose that M. anisopliae is degrading host components and actively secreting proteins to manage the physiology of the host. Interestingly, the secretion of these factors occurs in the absence of a host response. The findings presented here are an important step in understanding the host–pathogen interaction and developing more efficient biocontrol of D. peruvianus by M. anisopliae.

Secretomic survey of Trichoderma harzianum grown on plant biomass substrates

The present work aims at characterizing T. harzianum secretome when the fungus is grown in synthetic medium supplemented with one of the four substrates: glucose, cellulose, xylan, and sugarcane bagasse (SB). The characterization was done by enzymatic assays and proteomic analysis using 2-DE/MALDI-TOF and gel-free shotgun LC-MS/MS. The results showed that SB induced the highest cellulolytic and xylanolytic activities when compared with the other substrates, while remarkable differences in terms of number and distribution of protein spots in 2-DE gels were also observed among the samples. Additionally, treatment of the secretomes with PNGase F revealed that most spot trails in 2-DE gels corresponded to N-glycosylated proteoforms. The LC-MS/MS analysis of the samples identified 626 different protein groups, including carbohydrate-active enzymes and accessory, noncatalytic, and cell-wall-associated proteins. Although the SB-induced secretome displayed the highest cellulolytic and xylanolytic activities, it did not correspond to a higher proteome complexity because CM-cellulose-induced secretome was significantly more diverse. Among the identified proteins, 73% were exclusive to one condition, while only 5% were present in all samples. Therefore, this study disclosed the variation of T. harzianum secretome in response to different substrates and revealed the diversity of the fungus enzymatic toolbox.

Functional analysis of a subtilisin-like serine protease gene from biocontrol fungus Trichoderma harzianum

The subtilisin-like serine protease gene ThSS45 has been cloned from Trichoderma harzianum ACCC30371. Its coding region is 1302 bp in length, encoding 433 amino acids, with a predicted protein molecular weight of 44.9 kDa and pI of 5.91. ThSS45 was shown by RT-qPCR analysis to be differentially transcribed in response to eight different treatments. The transcription of ThSS45 was up-regulated when grown in mineral medium, under carbon starvation, and nitrogen starvation, and in the presence of 1% root powder, 1% stem powder, and 1% leaf powder derived from Populus davidiana × P. bolleana (Shanxin poplar) aseptic seedlings. The highest increase in transcription approached 3.5-fold that of the control at 6 h under induction with 1% poplar root powder. The transcription of ThSS45 was also slightly up-regulated by 1% Alternaria alternata cell wall and 5% A. alternata fermentation liquid. Moreover, the analyses of coding and promoter regions of ThSS45 homologs indicated that serine protease may be involved in both mycoparasitism and antibiotic secretion. ThSS45 was cloned into the pGEX-4T-2 vector and then expressed in Escherichia coli BL21. The recombinant protein, with an expected molecular weight of approximately 69 kDa, was then purified. When transformant BL21-ss was induced with 1 mM IPTG for 6 h, the purified protease activity reached a peak of 18.25 U/ml at pH 7.0 and 40°C. In antifungal assays the purified protease obviously inhibited the growth of A. alternata mycelia.

Proteins differentially expressed in conidia and mycelia of the entomopathogenic fungus Metarhizium anisopliae sensu stricto

Metarhizium anisopliae is a well-characterized entomopathogenic fungus that attacks a variety of insects. Its conidia are involved in its propagation and also in its infection of host insects. To investigate the protein expression profiles and to identify the proteins related to development and pathogenesis, we performed a comparative proteomic analysis of the conidia and mycelia of an M. anisopliae strain (Ma1291). The analysis used 2-dimensional gel electrophoresis and matrix-assisted laser desorption ionization time-of-flight mass spectrometry. We detected 898 ± 37 protein spots in conidia and 1072 ± 24 in mycelia of strain Ma1291. A comparison of the 2 protein-expression profiles indicated that only 28% of protein spots were common to both developmental stages. Finally, we identified 30 proteins (19 from conidia and 11 from mycelia). The identified proteins exclusive to conidia were those involved in protective processes, appressorium formation, and degradation of the host cuticle (protease PR1H). The identified proteins exclusive to mycelia included major proteins participating in biosynthetic and energy metabolism, such as UTP-glucose-1-phosphate uridylyltransferase and heat shock protein 70. This research provides the first proteomic analysis of different developmental stages of M. anisopliae, and the results should facilitate clarification of the molecular basis of these epigenetic variations.

Antagonism of Trichoderma harzianum ETS 323 on Botrytis cinerea mycelium in culture conditions

ABSTRACT Previous studies have shown that the extracellular proteins of Trichoderma harzianum ETS 323 grown in the presence of deactivated Botrytis cinerea in culture include a putative l-amino acid oxidase and have suggested the involvement of this enzyme in the antagonistic mechanism. Here, we hypothesized that the mycoparasitic process of Trichoderma spp. against B. cinerea involves two steps; that is, an initial hyphal coiling stage and a subsequent hyphal coiling stage, with different coiling rates. The two-step antagonism of T. harzianum ETS 323 against B. cinerea during the mycoparasitic process in culture was evaluated using a biexponential equation. In addition, an l-amino acid oxidase (Th-l-AAO) was identified from T. harzianum ETS 323. The secretion of Th-l-AAO was increased when T. harzianum ETS 323 was grown with deactivated hyphae of B. cinerea. Moreover, in vitro assays indicated that Th-l-AAO effectively inhibited B. cinerea hyphal growth, caused cytosolic vacuolization in the hyphae, and led to hyphal lysis. Th-l-AAO also showed disease control against the development of B. cinerea on postharvest apple fruit and tobacco leaves. Furthermore, an apoptosis-like response, including the generation of reactive oxygen species, was observed in B. cinerea after treatment with Th-l-AAO, suggesting that Th-l-AAO triggers programmed cell death in B. cinerea. This may be associated with the two-step antagonism of T. harzianum ETS 323 against B. cinerea.

A yeast secretion trap assay for identification of secreted proteins from eukaryotic phytopathogens and their plant hosts

Secreted proteins from plants and phytopathogens play important roles in their interactions and contribute to elaborate mechanisms of attack, defense, and counter-defense, as well as surveillance and signaling. There is therefore considerable interest in developing techniques to characterize "secretomes." Here, we describe the use of the yeast secretion trap (YST) functional screen to isolate and identify secreted proteins that are accumulated and detected in the extracellular matrix of eukaryotes. This method involves fusing cDNAs generated or derived from plants, pathogens, or infected tissue to a yeast (Saccharomyces cerevisiae) invertase (suc2) reporter gene lacking its signal peptide, transforming the resulting fusion library into an invertase-deficient yeast strain, and plating the transformants on a sucrose selection medium. A yeast transformant containing a cDNA that encodes a secreted protein can rescue the mutant and the plasmid DNA can then be sequenced to identify the secreted protein. The YST screen can be a very powerful tool in the study of dynamics of plant host-pathogen interactions.

Elevated activity of dolichyl phosphate mannose synthase enhances biocontrol abilities of Trichoderma atroviride

Antagonism of Trichoderma spp. against phytopathogenic fungi is widely exploited for biocontrol of plant diseases. A crucial role in the biocontrol mechanism is attributed to cell-wall-degrading enzymes secreted by Trichoderma spp. Therefore, more efficient production and secretion of the enzymes should elevate the biocontrol abilities of Trichoderma spp. Because the majority of secretory hydrolases are glycoproteins, it has been postulated that the posttranslational modification of these proteins could constitute a bottleneck in their production and secretion. Our previous study showed that improvement of O-glycosylation elevated protein secretion by Trichoderma reesei. In this study, we enhanced the biocontrol abilities of T. atroviride P1 against plant pathogens by overexpressing the Saccharomyces cerevisiae DPM1 gene coding for dolichyl phosphate mannose (DPM) synthase, a key enzyme in the O-glycosylation pathway. The transformants we obtained showed doubled DPM synthase activity and, at the same time, significantly elevated cellulolytic activity. They also revealed an improved antifungal activity against the plant pathogen Pythium ultimum.

Properties of secreted protease from vegetative Trichoderma atroviride mycelia cultivated with protein inducer reveal a complex protein-recognition mechanism

In this study, the submerged cultivation of Trichoderma atroviride with protein substrate (bovine serum albumin, casein, ovalbumin, etc.) led to the secretion of protease activity (PA) into the medium. The secretion started within 30 h and rose to the maximum after 72-h cultivation. It continued upon the prolonged cultivation (up to 8 days) with lower secreted PA. Zymography of the secreted protease (SDS-PAGE with 0.2% gelatine), revealing high molecular weight (m.w.) protease(s) (~200 kDa) with high autolytic activity as the only secretory product. Enzymological characteristics of high m.w. proteases elicited by different inducer proteins were surprisingly different, suggesting that mycelia can recognize not only the presence of inducer proteins but also some qualitative characteristics. Low m.w. protease(s), as found from other studies was(were) seen after prolonged cultivation only, as a band with m.w. about 36 kDa. Expression of known Trichoderma spp. genes encoding secreted proteases, prb1 and proA, showed that only prb1 was expressed after 3-4 days of cultivation, i.e., after the early-secretion phase. The secretory activity of the earlier phase was impaired by tunicamycin and brefeldin A and was significantly stimulated by uncoupler. The existence of a biphasic fungal secretory response and the protein quality recognition represent previously unrecognized processes.

Potential fungal inhibition by immobilized hydrolytic enzymes from Trichoderma asperellum

The use of cell wall degrading enzymes from Trichoderma asperellum immobilized on biodegradable support is an alternative for food packaging. In this study, hydrolytic enzymes produced by T. asperellum were tested as a fungal growth inhibitor, in free form or immobilized on a biodegradable film composed of cassava starch and poly(butylene adipate-co-terephtalate) (PBAT). The inhibitory activity was tested against Aspergillus niger , Penicillium sp., and Sclerotinia sclerotiorum , microorganisms that frequently degrade food packaging. The use of chitin as carbon source in liquid medium induced T. asperellun to produce N-acetylglucosaminidase, β-1,3-glucanase, chitinase, and protease. The presence of T. asperellun cell wall degradating enzymes (T-CWD) immobilized by adsorption or covalent attachment resulted in effective inhibition of fungal growth. The enzymatic activity of T-CWD was stronger on S. sclerotiorum than on the Aspergillus or Penicillum isolates tested. These results suggest that T-CWD can be used in a free or immobilized form to suppress fungi that degrade food packaging.

Functional analysis of the Trichoderma harzianum nox1 gene, encoding an NADPH oxidase, relates production of reactive oxygen species to specific biocontrol activity against Pythium ultimum

The synthesis of reactive oxygen species (ROS) is one of the first events following pathogenic interactions in eukaryotic cells, and NADPH oxidases are involved in the formation of such ROS. The nox1 gene of Trichoderma harzianum was cloned, and its role in antagonism against phytopathogens was analyzed in nox1-overexpressed transformants. The increased levels of nox1 expression in these transformants were accompanied by an increase in ROS production during their direct confrontation with Pythium ultimum. The transformants displayed an increased hydrolytic pattern, as determined by comparing protease, cellulase, and chitinase activities with those for the wild type. In confrontation assays against P. ultimum the nox1-overexpressed transformants were more effective than the wild type, but not in assays against Botrytis cinerea or Rhizoctonia solani. A transcriptomic analysis using a Trichoderma high-density oligonucleotide (HDO) microarray also showed that, compared to gene expression for the interaction of wild-type T. harzianum and P. ultimum, genes related to protease, cellulase, and chitinase activities were differentially upregulated in the interaction of a nox1-overexpressed transformant with this pathogen. Our results show that nox1 is involved in T. harzianum ROS production and antagonism against P. ultimum.

Differential proteomic analysis of temperature-induced autolysis in mycelium of Pleurotus tuber-regium

Autolysis is an important physiological process found in fungal cultivation. However, there is hitherto no report on the autolysis of Pleurotus tuber-regium. We have investigated the enzymes secreted by temperature-induced (40°C as treatment versus 10°C as control) autolysis of the mycelium of P. tuber-regium grown in submerged cultivation. A comparison between the intracellular proteins (inside the mycelium) and the extracellular proteins (in the culture medium) of the treatment and control by proteomic analysis involving 2D PAGE and MALDI-TOF-MS was made. Twenty-two up-regulated protein spots were detected and eight proteins were identified. They included proteasome which participates in the ubiquitin-proteasome pathway; β-1,3-glucanosyltransferase and tubulin which are involved in the renewal and repair of cell wall; protease and endoglucanase which promote the natural degradation of cell wall and cytoplasm; 14-3-3 protein which takes part in cell signal transduction; and two putative proteins presumably relate to the autolysis process. These identified proteins suggest partially the metabolic processes of the autolysis in the P. tuber-regium mycelium.

The Botrytis cinerea early secretome

The extracellular proteome, or secretome, of phytopathogenic fungi is presumed to be a key element of their infection strategy. Especially interesting constituents of this set are those proteins secreted at the beginning of the infection, during the germination of conidia on the plant surfaces or wounds, since they may play essential roles in the establishment of a successful infection. We have germinated Botrytis cinerea conidia in conditions that resemble the plant environment, a synthetic medium enriched with low molecular weight plant compounds, and we have collected the proteins secreted during the first 16 h by a double precipitation protocol. 2-D electrophoresis of the precipitated secretome showed a spot pattern similar for all conditions evaluated and for the control medium without plant extract. The proteins in 16 of these spots were identified by PMF and corresponded to 11 different polypeptides. Alternative determination of secretome composition by LC-MS/MS of tryptic fragments rendered a much larger number, 105 proteins, which included all previously identified by PMF. All proteins were functionally classified according to their putative function in the infection process. Key features of the early secretome include a large number of proteases, the abundance of proteins involved in the degradation of plant defensive barriers, and plenty of proteins with unknown function.

Cytoplasmic- and extracellular-proteome analysis of Diplodia seriata: a phytopathogenic fungus involved in grapevine decline

BACKGROUND

The phytopathogenic fungus Diplodia seriata, whose genome remains unsequenced, produces severe infections in fruit trees (fruit blight) and grapevines. In this crop is recognized as one of the most prominent pathogens involved in grapevine trunk disease (or grapevine decline). This pathology can result in the death of adult plants and therefore it produces severe economical losses all around the world. To date no genes or proteins have been characterized in D. seriata that are involved in the pathogenicity process. In an effort to help identify potential gene products associated with pathogenicity and to gain a better understanding of the biology of D. seriata, we initiated a proteome-level study of the fungal mycelia and secretome.

RESULTS

Intracellular and secreted proteins from D. seriata collected from liquid cultures were separated using two-dimensional gel electrophoresis. About 550 cytoplasmic proteins were reproducibly present in 3 independent extractions, being 53 identified by peptide mass fingerprinting and tandem mass spectrometry. The secretome analysis showed 75 secreted proteins reproducibly present in 3 biological replicates, being 16 identified. Several of the proteins had been previously identified as virulence factors in other fungal strains, although their contribution to pathogenicity in D. seriata remained to be analyzed. When D. seriata was grown in a medium supplemented with carboxymethylcellulose, 3 proteins were up-regulated and 30 down-regulated. Within the up-regulated proteins, two were identified as alcohol dehydrogenase and mitochondrial peroxyrredoxin-1, suggesting that they could play a significant role in the pathogenicity process. As for the 30 down-regulated proteins, 9 were identified being several of them involved in carbohydrate metabolism.

CONCLUSIONS

This study is the first report on proteomics on D. seriata. The proteomic data obtained will be important to understand the pathogenicity process. In fact, several of the identified proteins have been reported as pathogenicity factors in other phytopathogenic fungi. Moreover, this proteomic analysis supposes a useful basis for deepening into D. seriata knowledge and will contribute to the development of the molecular biology of this fungal strain as it has been demonstrated by cloning the gene Prx1 encoding mitochondrial peroxiredoxin-1 of D. seriata (the first gene to be cloned in this microorganism; data not shown).