Proteomic response of the biological control fungus Trichoderma atroviride to growth on the cell walls of Rhizoctonia solani

Insights into the ecological generalist lifestyle of Clonostachys fungi through analysis of their predicted secretomes

Introduction

The fungal secretome comprise diverse proteins that are involved in various aspects of fungal lifestyles, including adaptation to ecological niches and environmental interactions. The aim of this study was to investigate the composition and activity of fungal secretomes in mycoparasitic and beneficial fungal-plant interactions.

Methods

We used six Clonostachys spp. that exhibit saprotrophic, mycotrophic and plant endophytic lifestyles. Genome-wide analyses was performed to investigate the composition, diversity, evolution and gene expression of Clonostachys secretomes in relation to their potential role in mycoparasitic and endophytic lifestyles.

Results and discussion

Our analyses showed that the predicted secretomes of the analyzed species comprised between 7 and 8% of the respective proteomes. Mining of transcriptome data collected during previous studies showed that 18% of the genes encoding predicted secreted proteins were upregulated during the interactions with the mycohosts Fusarium graminearum and Helminthosporium solani. Functional annotation of the predicted secretomes revealed that the most represented protease family was subclass S8A (11-14% of the total), which include members that are shown to be involved in the response to nematodes and mycohosts. Conversely, the most numerous lipases and carbohydrate-active enzyme (CAZyme) groups appeared to be potentially involved in eliciting defense responses in the plants. For example, analysis of gene family evolution identified nine CAZyme orthogroups evolving for gene gains (p ≤ 0.05), predicted to be involved in hemicellulose degradation, potentially producing plant defense-inducing oligomers. Moreover, 8-10% of the secretomes was composed of cysteine-enriched proteins, including hydrophobins, important for root colonization. Effectors were more numerous, comprising 35-37% of the secretomes, where certain members belonged to seven orthogroups evolving for gene gains and were induced during the C. rosea response to F. graminearum or H. solani. Furthermore, the considered Clonostachys spp. possessed high numbers of proteins containing Common in Fungal Extracellular Membranes (CFEM) modules, known for their role in fungal virulence. Overall, this study improves our understanding of Clonostachys spp. adaptation to diverse ecological niches and establishes a basis for future investigation aiming at sustainable biocontrol of plant diseases.

Assessing the Various Antagonistic Mechanisms of Trichoderma Strains against the Brown Root Rot Pathogen Pyrrhoderma noxium Infecting Heritage Fig Trees

A wide range of phytopathogenic fungi exist causing various plant diseases, which can lead to devastating economic, environmental, and social impacts on a global scale. One such fungus is Pyrrhoderma noxium, causing brown root rot disease in over 200 plant species of a variety of life forms mostly in the tropical and subtropical regions of the globe. The aim of this study was to discover the antagonistic abilities of two Trichoderma strains (#5001 and #5029) found to be closely related to Trichoderma reesei against P. noxium. The mycoparasitic mechanism of these Trichoderma strains against P. noxium involved coiling around the hyphae of the pathogen and producing appressorium like structures. Furthermore, a gene expression study identified an induced expression of the biological control activity associated genes in Trichoderma strains during the interaction with the pathogen. In addition, volatile and diffusible antifungal compounds produced by the Trichoderma strains were also effective in inhibiting the growth of the pathogen. The ability to produce Indole-3-acetic acid (IAA), siderophores and the volatile compounds related to plant growth promotion were also identified as added benefits to the performance of these Trichoderma strains as biological control agents. Overall, these results show promise for the possibility of using the Trichoderma strains as potential biological control agents to protect P. noxium infected trees as well as preventing new infections.

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.

Trichoderma as biological control agent: scope and prospects to improve efficacy

A major current challenge is to increase the food production while preserving natural resources. Agricultural practices that enhance the productivity and progressively improve the soil quality are relevant to face this challenge. Trichoderma species are widely used in agriculture to stimulate the plant growth and to control different pathogens affecting crops, representing useful tools for sustainable food production. This mini-review summarizes applications of Trichoderma strains in agriculture to control fungal pathogens, nematodes and insects, the involved biocontrol mechanisms, efficacy and inoculation forms in greenhouse, field and post-harvest conditions. Aspects of Trichoderma handling that influence on biocontrol efficacy such as preventive treatments, frequency of applications and delivery methods are discussed. Strategies useful to improve the antagonistic performance such as the use of native strains, protoplast fusion, formulation, growth on pathogen cell wall medium and combination with other antagonists in integrated treatments are discussed. This mini-review provides practical knowledge to design safe and optimal biocontrol strategies based on Trichoderma and pose challenges to expand its antagonist performance.

An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota

Fungi are among the most successful eukaryotes on Earth: they have evolved strategies to survive in the most diverse environments and stressful conditions and have been selected and exploited for multiple aims by humans. The characteristic features intrinsic of Fungi have required evolutionary changes and adaptations at deep molecular levels. Omics approaches, nowadays including genomics, metagenomics, phylogenomics, transcriptomics, metabolomics, and proteomics have enormously advanced the way to understand fungal diversity at diverse taxonomic levels, under changeable conditions and in still under-investigated environments. These approaches can be applied both on environmental communities and on individual organisms, either in nature or in axenic culture and have led the traditional morphology-based fungal systematic to increasingly implement molecular-based approaches. The advent of next-generation sequencing technologies was key to boost advances in fungal genomics and proteomics research. Much effort has also been directed towards the development of methodologies for optimal genomic DNA and protein extraction and separation. To date, the amount of proteomics investigations in Ascomycetes exceeds those carried out in any other fungal group. This is primarily due to the preponderance of their involvement in plant and animal diseases and multiple industrial applications, and therefore the need to understand the biological basis of the infectious process to develop mechanisms for biologic control, as well as to detect key proteins with roles in stress survival. Here we chose to present an overview as much comprehensive as possible of the major advances, mainly of the past decade, in the fields of genomics (including phylogenomics) and proteomics of Ascomycota, focusing particularly on those reporting on opportunistic pathogenic, extremophilic, polyextremotolerant and lichenized fungi. We also present a review of the mostly used genome sequencing technologies and methods for DNA sequence and protein analyses applied so far for fungi.

Exploring the Extracellular Macromolecular Composition of Crude Extracts of Penicillium rubens Strain 212 for Elucidation Its Mode of Action as a Biocontrol Agent

Penicillium rubens strain 212 (PO212) acts as an inducer of systemic resistance in tomato plants. The effect of crude extracellular extracts of PO212 on the soil-borne pathogen Fusarium oxysporum f. sp. lycopersici has been evaluated. Evidence of the involvement of soluble, thermo-labile, and proteinase-inactivated macromolecules present in PO212 crude extracts in the control of Fusarium vascular disease in tomato plants was found. Proteomic techniques and the availability of the access to the PO212 genome database have allowed the identification of glycosyl hydrolases, oxidases, and peptidases in these extracellular extracts. Furthermore, a bioassay-guided fractionation of PO212 crude extracellular extracts using an integrated membrane/solid phase extraction process was set up. This method enabled the separation of a PO212 crude extracellular extract of seven days of growth into four fractions of different molecular sizes and polarities: high molecular mass protein fraction >5 kDa, middle molecular mass protein fraction 5-1 kDa, low molecular mass metabolite fraction, and nutrients from culture medium (mainly glucose and minerals). The high and middle molecular mass protein fractions retained disease control activity in a way similar to that of the control extracts. Proteomic techniques have allowed the identification of nine putatively secreted proteins in the high molecular mass protein fraction matching those identified in the total crude extracts. Therefore, these enzymes are considered to be potentially responsible of the crude extracellular extract-induced resistance in tomato plants against F. oxysporum f. sp. lycopersici. Further studies are required to establish which of the identified proteins participate in the PO212's action mode as a biocontrol agent.

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.

Differential Proteomic Profiles of Pleurotus ostreatus in Response to Lignocellulosic Components Provide Insights into Divergent Adaptive Mechanisms

Pleurotus ostreatus is a white rot fungus that grows on lignocellulosic biomass by metabolizing the main constituents. Extracellular enzymes play a key role in this process. During the hydrolysis of lignocellulose, potentially toxic molecules are released from lignin, and the molecules are derived from hemicellulose or cellulose that trigger various responses in fungus, thereby influencing mycelial growth. In order to characterize the mechanism underlying the response of P. ostreatus to lignin, we conducted a comparative proteomic analysis of P. ostreatus grown on different lignocellulose substrates. In this work, the mycelium proteome of P. ostreatus grown in liquid minimal medium with lignin, xylan, and carboxymethyl cellulose (CMC) was analyzed using the complementary two-dimensional gel electrophoresis (2-DE) approach; 115 proteins were identified, most of which were classified into five types according to their function. Proteins with an antioxidant function that play a role in the stress response were upregulated in response to lignin. Most proteins involving in carbohydrate and energy metabolism were less abundant in lignin. Xylan and CMC may enhanced the process of carbohydrate metabolism by regulating the level of expression of various carbohydrate metabolism-related proteins. The change of protein expression level was related to the adaptability of P. ostreatus to lignocellulose. These findings provide novel insights into the mechanisms underlying the response of white-rot fungus to lignocellulose.

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.

Methodologies and perspectives of proteomics applied to filamentous fungi: from sample preparation to secretome analysis

Filamentous fungi possess the extraordinary ability to digest complex biomasses and mineralize numerous xenobiotics, as consequence of their aptitude to sensing the environment and regulating their intra and extra cellular proteins, producing drastic changes in proteome and secretome composition. Recent advancement in proteomic technologies offers an exciting opportunity to reveal the fluctuations of fungal proteins and enzymes, responsible for their metabolic adaptation to a large variety of environmental conditions. Here, an overview of the most commonly used proteomic strategies will be provided; this paper will range from sample preparation to gel-free and gel-based proteomics, discussing pros and cons of each mentioned state-of-the-art technique. The main focus will be kept on filamentous fungi. Due to the biotechnological relevance of lignocellulose degrading fungi, special attention will be finally given to their extracellular proteome, or secretome. Secreted proteins and enzymes will be discussed in relation to their involvement in bio-based processes, such as biomass deconstruction and mycoremediation.

Transcriptional Reprogramming of the Mycoparasitic Fungus Ampelomyces quisqualis During the Powdery Mildew Host-Induced Germination

Ampelomyces quisqualis is a mycoparasite of a diverse range of phytopathogenic fungi associated with the powdery mildew disease. Among them are several Erysiphaceae species with great economic impact on high-value crops such as grape. Due to its ability to parasitize and prevent the spread of powdery mildews, A. quisqualis has received considerable attention for its biocontrol potential. However, and in sharp contrast to the extensively studied biocontrol species belonging to the genus Trichoderma, little is known about the biology of A. quisqualis at the molecular and genetic levels. We present the first genome-wide transcription profiling in A. quisqualis during host-induced germination. A total of 1,536 putative genes showed significant changes in transcription during the germination of A. quisqualis. This finding denotes an extensive transcriptional reprogramming of A. quisqualis induced by the presence of the host. Several upregulated genes were predicted to encode for putative mycoparasitism-related proteins such as secreted proteases, virulence factors, and proteins related to toxin biosynthesis. Our data provide the most comprehensive sequence resource currently available for A. quisqualis in addition to offering valuable insights into the biology of A. quisqualis and its mycoparasitic lifestyle. Eventually, this may improve the biocontrol capacity of this mycoparasite.

Identification of metabolic pathways expressed by Pichia anomala Kh6 in the presence of the pathogen Botrytis cinerea on apple: new possible targets for biocontrol improvement

Yeast Pichia anomala strain Kh6 Kurtzman (Saccharomycetales: Endomycetaceae) exhibits biological control properties that provide an alternative to the chemical fungicides currently used by fruit or vegetable producers against main post-harvest pathogens, such as Botrytis cinerea (Helotiales: Sclerotiniaceae). Using an in situ model that takes into account interactions between organisms and a proteomic approach, we aimed to identify P. anomala metabolic pathways influenced by the presence of B. cinerea. A total of 105 and 60 P. anomala proteins were differentially represented in the exponential and stationary growth phases, respectively. In the exponential phase and in the presence of B. cinerea, the pentose phosphate pathway seems to be enhanced and would provide P. anomala with the needed nucleic acids and energy for the wound colonisation. In the stationary phase, P. anomala would use alcoholic fermentation both in the absence and presence of the pathogen. These results would suggest that the competitive colonisation of apple wounds could be implicated in the mode of action of P. anomala against B. cinerea.

Comparative proteome analysis of Penicillium verrucosum grown under light of short wavelength shows an induction of stress-related proteins associated with modified mycotoxin biosynthesis

In this study the differentially expressed protein population of Penicillium verrucosum grown either in the dark or under light with a wavelength of 450nm has been analyzed. Light of short wavelength led to oxidative stress in the fungal cell; under this condition the mycotoxin biosynthesis revealed a mutual shift from ochratoxin A to citrinin. Using a proteomic approach combining an optimized protein extraction method with 2-dimensional SDS-PAGE followed by HPLC-ESI-TOF-MS/MS mass spectrometric analysis, initially 56 significantly differential proteins (light vs. dark) were detected comprising proteins of a broad range of isoelectric points and molecular masses. In total, 46 proteins could be identified further by database query, most of these proteins are assumed to be involved in response to stress (e.g. antioxidative proteins, heat shock proteins) and general metabolic processes (e.g. glycolysis, ATP supply). Proteome analyses are necessary to unravel the regulation of secondary metabolite biosynthesis at a translational level. This may enable identification of proteins which are involved in mycotoxin biosynthesis, adaption processes or even stress compensation mechanisms. This study depicts the first proteome analysis of P. verrucosum.

Making a protein extract from plant pathogenic fungi for gel- and LC-based proteomics

Proteomic technologies have become a successful tool to provide relevant information on fungal biology. In the case of plant pathogenic fungi, this approach would allow a deeper knowledge of the interaction and the biological cycle of the pathogen, as well as the identification of pathogenicity and virulence factors. These two elements open up new possibilities for crop disease diagnosis and environment-friendly crop protection. Phytopathogenic fungi, due to its particular cellular characteristics, can be considered as a recalcitrant biological material, which makes it difficult to obtain quality protein samples for proteomic analysis. This chapter focuses on protein extraction for gel- and LC-based proteomics with specific protocols of our current research with Botrytis cinerea.

Proteomic analysis of proteins differentially expressed in conidia and mycelium of the entomopathogenic fungus Aschersonia placenta

The infection of insects by the entomopathogenic fungus Aschersonia placenta depends on conidia. To identify proteins differentially expressed in A. placenta conidia vs mycelia, we performed a comparative proteomic analysis of A. placenta using 2-dimensional gel electrophoresis (2-DE) and matrix-assisted laser desorption ionization/time-of-flight mass spectrometry (MALDI-TOF-MS). We detected 1022 2-DE protein spots in conidia and 1049 in mycelia and analyzed 48 (13 from conidia and 35 from mycelia) using MALDI-TOF-MS. Finally, we identified 28 proteins (7 from conidia and 21 from mycelia). The identified proteins exclusive to conidia included major proteins participating in oxidation–reduction processes and vegetative insecticidal protein 1 (Vip1), a protein that is likely involved in pathogenicity. The identified proteins exclusive to mycelia were those involved in biosynthesis and metabolism, including uridine diphosphate galactopyranose mutase, which might play key roles in hyphal morphogenesis. This report provides the first proteomic analysis of different developmental stages of an Aschersonia species. Although only a small number of proteins were identified, the data represent a useful foundation for future studies concerning the molecular basis of entomopathogenicity in the species A. placenta and in the genus Aschersonia.

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.

Sesquiterpenoids from Trichoderma atroviride, an endophytic fungus in Cephalotaxus fortunei

Two new sesquiterpenoids, identified as (rel 1S, 3R, 4R, 7R)-3-[5-hydroxy-4-methylpent-3-enyl]-1, 3, 7-trimethyl-2-oxabicyclo [2, 2, 1] heptane (1) and (rel 1S, 3R, 4R, 7R)-3-[3, 4-dihydroxy-4-methylpentyl]-1, 3, 7-trimethyl-2-oxabicyclo [2, 2, 1] heptane (2), were isolated from cultures of Trichoderma atroviride (strain no. S361), an endophytic fungal strain residing in the bark of Cephalotaxus fortunei. The structures of compounds 1 and 2 were elucidated by detailed spectroscopic analyses on the basis of NMR, IR, and MS data. Both compounds 1 and 2 were potent inhibitors on NO production in LPS-stimulated RAW264.7 cells, with IC₅₀ values of 15.3 and 9.1μM, respectively.

Identification of mycoparasitism-related genes in Trichoderma atroviride

A high-throughput sequencing approach was utilized to carry out a comparative transcriptome analysis of Trichoderma atroviride IMI206040 during mycoparasitic interactions with the plant-pathogenic fungus Rhizoctonia solani. In this study, transcript fragments of 7,797 Trichoderma genes were sequenced, 175 of which were host responsive. According to the functional annotation of these genes by KOG (eukaryotic orthologous groups), the most abundant group during direct contact was "metabolism." Quantitative reverse transcription (RT)-PCR confirmed the differential transcription of 13 genes (including swo1, encoding an expansin-like protein; axe1, coding for an acetyl xylan esterase; and homologs of genes encoding the aspartyl protease papA and a trypsin-like protease, pra1) in the presence of R. solani. An additional relative gene expression analysis of these genes, conducted at different stages of mycoparasitism against Botrytis cinerea and Phytophthora capsici, revealed a synergistic transcription of various genes involved in cell wall degradation. The similarities in expression patterns and the occurrence of regulatory binding sites in the corresponding promoter regions suggest a possible analog regulation of these genes during the mycoparasitism of T. atroviride. Furthermore, a chitin- and distance-dependent induction of pra1 was demonstrated.

A proteomics approach to study synergistic and antagonistic interactions of the fungal-bacterial consortium Fusarium oxysporum wild-type MSA 35

Fusarium oxysporum is an important plant pathogen that causes severe damage of many economically important crop species. Various microorganisms have been shown to inhibit this soil-borne plant pathogen, including non-pathogenic F. oxysporum strains. In this study, F. oxysporum wild-type (WT) MSA 35, a biocontrol multispecies consortium that consists of a fungus and numerous rhizobacteria mainly belonging to gamma-proteobacteria, was analyzed by two complementary metaproteomic approaches (2-DE combined with MALDI-Tof/Tof MS and 1-D PAGE combined with LC-ESI-MS/MS) to identify fungal or bacterial factors potentially involved in antagonistic or synergistic interactions between the consortium members. Moreover, the proteome profiles of F. oxysporum WT MSA 35 and its cured counter-part CU MSA 35 (WT treated with antibiotics) were compared with unravel the bacterial impact on consortium functioning. Our study presents the first proteome mapping of an antagonistic F. oxysporum strain and proposes candidate proteins that might play an important role for the biocontrol activity and the close interrelationship between the fungus and its bacterial partners.

Proteomics of plant pathogenic fungi

Plant pathogenic fungi cause important yield losses in crops. In order to develop efficient and environmental friendly crop protection strategies, molecular studies of the fungal biological cycle, virulence factors, and interaction with its host are necessary. For that reason, several approaches have been performed using both classical genetic, cell biology, and biochemistry and the modern, holistic, and high-throughput, omic techniques. This work briefly overviews the tools available for studying Plant Pathogenic Fungi and is amply focused on MS-based Proteomics analysis, based on original papers published up to December 2009. At a methodological level, different steps in a proteomic workflow experiment are discussed. Separate sections are devoted to fungal descriptive (intracellular, subcellular, extracellular) and differential expression proteomics and interactomics. From the work published we can conclude that Proteomics, in combination with other techniques, constitutes a powerful tool for providing important information about pathogenicity and virulence factors, thus opening up new possibilities for crop disease diagnosis and crop protection.

Biology and biotechnology of Trichoderma

Fungi of the genus Trichoderma are soilborne, green-spored ascomycetes that can be found all over the world. They have been studied with respect to various characteristics and applications and are known as successful colonizers of their habitats, efficiently fighting their competitors. Once established, they launch their potent degradative machinery for decomposition of the often heterogeneous substrate at hand. Therefore, distribution and phylogeny, defense mechanisms, beneficial as well as deleterious interaction with hosts, enzyme production and secretion, sexual development, and response to environmental conditions such as nutrients and light have been studied in great detail with many species of this genus, thus rendering Trichoderma one of the best studied fungi with the genome of three species currently available. Efficient biocontrol strains of the genus are being developed as promising biological fungicides, and their weaponry for this function also includes secondary metabolites with potential applications as novel antibiotics. The cellulases produced by Trichoderma reesei, the biotechnological workhorse of the genus, are important industrial products, especially with respect to production of second generation biofuels from cellulosic waste. Genetic engineering not only led to significant improvements in industrial processes but also to intriguing insights into the biology of these fungi and is now complemented by the availability of a sexual cycle in T. reesei/Hypocrea jecorina, which significantly facilitates both industrial and basic research. This review aims to give a broad overview on the qualities and versatility of the best studied Trichoderma species and to highlight intriguing findings as well as promising applications.

A proteomic approach to identifying proteins differentially expressed in conidia and mycelium of the entomopathogenic fungus Metarhizium acridum

Metarhizium spp. is an important worldwide group of entomopathogenic fungi used as an interesting alternative to chemical insecticides in programs of agricultural pest and disease vector control. Metarhizium conidia are important in fungal propagation and also are responsible for host infection. Despite their importance, several aspects of conidial biology, including their proteome, are still unknown. We have established conidial and mycelial proteome reference maps for Metarhizium acridum using two-dimensional gel electrophoresis (2-DE) and matrix-assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF MS). In all, 1130±102 and 1200±97 protein spots were detected in ungerminated conidia and fast-growing mycelia, respectively. Comparison of the two protein-expression profiles reveled that only 35% of the protein spots were common to both developmental stages. Out of 94 2-DE protein spots (65 from conidia, 25 from mycelia and two common to both) analyzed using mass spectrometry, seven proteins from conidia, 15 from mycelia and one common to both stages were identified. The identified protein spots exclusive to conidia contained sequences similar to known fungal stress-protector proteins (such as heat shock proteins (HSP) and 6-phosphogluconate dehydrogenase) plus the fungal allergen Alt a 7, actin and the enzyme cobalamin-independent methionine synthase. The identified protein spots exclusive to mycelia included proteins involved in several cell housekeeping biological processes. Three proteins (HSP 90, 6-phosphogluconate dehydrogenase and allergen Alt a 7) were present in spots in conidial and mycelial gels, but they differed in their locations on the two gels.

New insights in Trichoderma harzianum antagonism of fungal plant pathogens by secreted protein analysis

Trichoderma harzianum ALL42 were capable of overgrowing and degrading Rhizoctonia solani and Macrophomina phaseolina mycelia, coiling around the hyphae with formation of apressoria and hook-like structures. Hyphae of T. harzianum ALL42 did not show any coiling around Fusarium sp. hyphae suggesting that mycoparasitism may be different among the plant pathogens. In this study, a secretome analysis was used to identify some extracellular proteins secreted by T. harzianum ALL42 after growth on cell wall of M. phaseolina, Fusarium sp., and R. solani. The secreted proteins were analyzed by two-dimensional electrophoresis and MALDI-TOF mass spectrometry. A total of 60 T. harzianum ALL42 secreted proteins excised from the gel were analyzed from the three growth conditions. While seven cell wall-induced proteins were identified, more than 53 proteins spots remain unidentified, indicating that these proteins are either novel proteins or proteins that have not yet been sequenced. Endochitinase, β-glucosidase, α-mannosidase, acid phosphatase, α-1,3-glucanase, and proteases were identified in the gel and also detected in the supernatant of culture.

Translational research on Trichoderma: from 'omics to the field

Structural and functional genomics investigations are making an important impact on the current understanding and application of microbial agents used for plant disease control. Here, we review the case of Trichoderma spp., the most widely applied biocontrol fungi, which have been extensively studied using a variety of research approaches, including genomics, transcriptomics, proteomics, metabolomics, etc. Known for almost a century for their beneficial effects on plants and the soil, these fungi are the subject of investigations that represent a successful case of translational research, in which 'omics-generated novel understanding is directly translated in to new or improved crop treatments and management methods. We present an overview of the latest discoveries on the Trichoderma expressome and metabolome, of the complex and diverse biotic interactions established in nature by these microbes, and of their proven or potential importance to agriculture and industry.

Proteomic study of biocontrol mechanisms of Trichoderma harzianum ETS 323 in response to Rhizoctonia solani

To elucidate the entire range of proteins that are secreted by Trichoderma harzianum ETS 323 in its antagonism with Rhizoctonia solani, an in vivo interaction between them was mimicked and not only the secreted cell wall-degrading enzymes (CWDEs) but also all of the proteome were investigated. Seven CWDEs, chitinase, cellulase, xylanase, beta-1,3-glucanase, beta-1,6-glucanase, mannanase, and protease,were revealed by activity assay, in-gel activity stain, 2-DE, and LC-MS/MS analysis. Extracellular protein extracts from media that contained R. solani exhibited much higher CWDE activities than media that did not contain R. solani. Cellulase and mannanase activity, however, were insignificant. Activity stain also revealed that beta-1,3-glucanase, beta-1,6-glucanase, and xylanase activity occurred exclusively in media that contained R. solani. Furthermore, 35 of the 43 excised spots on the 2-DE gel were successfully analyzed by LC-MS/MS, and eight proteins were identified. They were two glycoside hydrolases, two proteases, two beta-glucosidases, one endochitinase and, interestingly, one amino acid oxidase. Additionally, a possible mechanism was proposed to elucidate how the cell walls of R. solani are systematically enveloped and disintegrated.

Experimental setups and considerations to study microbial interactions

Within ecosystems microorganisms coexist and interact. Knowledge of these interactions is of great importance in the fields of ecology, food production, and medicine. Such interactions often involve the synthesis of antibiotic secondary metabolites. Different kinds of s molecules or direct contacts are other forms of microbial interactions. Recently, modern molecular methods such as microarrays and proteomics have been employed to investigate such interactions. In this chapter, the use of proteomics for studies of microbial interactions is discussed. The choice of experimental setup is dependent on the aims of the specific study. One aspect of competition between microbes can be simulated by treatment of one microbe with antibiotics produced by a competing microbe. A more complicated approach involves cocultivation of the competitors, but in order to reveal species-specific protein patterns it is advisable to keep the organisms separated. Alternative techniques are to monitor alterations in the proteomes between the wild-type and mutant strains. The mutant can be either natural or created using random or targeted mutagenesis. Generally, a proteomic study will reveal proteins with both expected and surprising changes in abundance upon competition, but also previously unknown proteins are likely to be identified. A proteomic approach is usually insufficient to obtain a complete data set describing microbial interactions. Therefore, it is essential to follow up identification of proteins with changed abundance by, e.g., the creation of knockout strains for phenotypic analyses. Despite the limitations, proteomics is a useful method, and an important complement to other approaches for studies of microbial interactions.

Isolation of mycoparasitic-related transcripts by SSH during interaction of the mycoparasite Stachybotrys elegans with its host Rhizoctonia solani

Mycoparasitism by antagonistic fungi involves changes in the biochemistry and physiology of both partners. Analysis of genes that are expressed during mycoparasite-host interaction represents a powerful strategy to obtain insight into the molecular events underlying these changes. The aim of this study is to identify genes whose expression is upregulated when the mycoparasite Stachybotrys elegans is in direct confrontation with its host Rhizoctonia solani. Suppression subtractive hybridization (SSH) was used to create a subtracted cDNA library, and differential screening was applied to identify the over-expressed transcripts. We report the analysis of 2,166 clones, among which 47% were upregulated during mycoparasitism. Two hundred and sixty-one clones were sequenced that corresponded to 94 unique genes. Forty-four of these were identified as novel genes, while the remainder showed similarity to a broad diversity of genes with putative functions related to toxin production, pathogenicity, and metabolism. As a result of mycoparasitism, 15 genes belonged to R. solani among which 9 genes were assigned putative functions. Quantitative RT-PCR was used to examine the upregulation of 12 genes during the course of mycoparasitism. Seven genes showed significant upregulation at least at one-time point during interaction of the mycoparasite with its host. This study describes a first step toward knowledge of S. elegans genome. The results present the useful application of EST analysis on S. elegans and provide preliminary indication of gene expression putatively involved in mycoparasitism.

Proteomics of filamentous fungi

Proteomic analysis, defined here as the global assessment of cellular proteins expressed in a particular biological state, is a powerful tool that can provide a systematic understanding of events at the molecular level. Proteomic studies of filamentous fungi have only recently begun to appear in the literature, despite the prevalence of these organisms in the biotechnology industry, and their importance as both human and plant pathogens. Here, we review recent publications that have used a proteomic approach to develop a better understanding of filamentous fungi, highlighting sample preparation methods and whole-cell cytoplasmic proteomics, as well as subproteomics of cell envelope, mitochondrial and secreted proteins.

Novel insights in the use of hydrolytic enzymes secreted by fungi with biotechnological potential

Entomopathogenic and mycoparasitic fungi synthesize hydrolytic enzymes such as chitinases, proteinases and beta-glucanases. These enzymes can act synergistically, helping fungi to control insect pests and pathogens that attack productive crops, and offer potential economic benefit to agribusiness. A number of hydrolytic enzymes have also been utilized in industrial applications. This review focuses on biochemical and structural analyses of fungal enzymes, together with current research information on secretion mechanisms.

Advances in fungal proteomics

Proteomics, the global analysis of proteins, will contribute greatly to our understanding of gene function in the post-genomic era. This review summarizes recent developments in fungal proteomics and also generalizes protocols for sample preparation from plant pathogenic fungi. Challenges and future perspectives of proteomics are discussed as well.

Screening and secretomic analysis of enthomopatogenic Beauveria bassiana isolates in response to cowpea weevil (Callosobruchus maculatus) exoskeleton

The production of cowpea (Vigna unguiculata), an important self-sustained crop in Latin America and Africa, is severely affected by damage by the cowpea weevil Callosobruchus maculatus. The presence of a single larva in stored seeds can lead to losses of almost 40%. Control of C. maculatus currently relies on the inefficient use of chemical insecticides and post-harvest treatments. The use of entomopathogenic fungus became a reliable alternative for coleopteran pest control and has been extensively investigated. Among them, Beauveria bassiana and Metarhizium anisopliae were widely evaluated in order to measure their virulence toward many insects. In this report, we evaluated the insecticidal activity of ten strains of B. bassiana and the most lethal fungi strains were analyzed for proteinaceous secretions by two dimensional electrophoresis and for enzyme activities, including chitinolytic, proteolytic and alpha-amylolytic activities. This study could, in the near future, help to establish novel biotechnological tools to use for cowpea weevil control.

Use of molecular techniques to elucidate the mechanisms of action of fungal biocontrol agents: a review

Biological control of fungal plant pathogens appears as an attractive and realistic approach, and numerous microorganisms have been identified as biocontrol agents. There have been many efforts to understand the mechanisms of action of fungal biocontrol agents. Microbiological, microscopic, and biochemical techniques applied over many years have shed light on these mechanisms without fully demonstrating them. More recently, the development of molecular techniques has yielded innovative alternative tools for understanding and demonstrating the mechanisms underlying biocontrol properties. To date, more than 70 publications describe the use of molecular techniques for this purpose. They describe work exploiting targeted or non-targeted gene isolation, gene expression profiling, gene inactivation and/or overexpression, the study of regulatory factors. This work has shed considerable light on mechanisms underlying biocontrol properties. It has also fully demonstrated a number of targeted action mechanisms of some biocontrol agents. This review describes the techniques used in such studies, with their potential and limitations. It should provide a guide for researchers wanting to study the molecular basis of the biocontrol in diverse biocontrol agents.

Study of the three-way interaction between Trichoderma atroviride, plant and fungal pathogens by using a proteomic approach

The main molecular factors involved in the complex interactions occurring between plants (bean), two different fungal pathogens (Botrytis cinerea, Rhizoctonia solani) and an antagonistic strain of the genus Trichoderma were investigated. Two-dimensional (2-D) electrophoresis was used to analyze separately collected proteomes from each single, two- or three-partner interaction (i.e., plant, pathogenic and antagonistic fungus alone and in all possible combinations). Differential proteins were subjected to mass spectrometry and in silico analysis to search for homologies with known proteins. In the plant proteome, specific pathogenesis-related proteins and other disease-related factors (i.e., potential resistance genes) seem to be associated with the interaction with either one of the two pathogens and/or T. atroviride. This finding is in agreement with the demonstrated ability of Trichoderma spp. to induce systemic resistance against various microbial pathogens. On the other side, many differential proteins obtained from the T. atroviride interaction proteome showed interesting homologies with a fungal hydrophobin, ABC transporters, etc. Virulence factors, like cyclophilins, were up-regulated in the pathogen proteome during the interaction with the plant alone or with the antagonist too. We isolated and confidently identified a large number of protein factors associated to the multi-player interactions examined.

The Molecular Biology of the Interactions Between Trichoderma spp., Phytopathogenic Fungi, and Plants

ABSTRACT Trichoderma-based biofungicides are a reality in agriculture, with more than 50 formulations today available as registered products worldwide. Several strategies have been applied to identify the main genes and compounds involved in this complex, three-way cross-talk between the fungal antagonist, the plant, and microbial pathogens. Proteome and genome analysis have greatly enhanced our ability to conduct holistic and genome-based functional studies. We have identified and determined the role of a variety of novel genes and gene-products, including ABC transporters, enzymes and other proteins that produce or act as novel elicitors of induced resistance, proteins responsible for a gene-for-gene avirulent interaction between Trichoderma spp. and plants, mycoparasitism-related inducers, plant proteins specifically induced by Trichoderma, etc. We have transgenically demonstrated the ability of Trichoderma spp. to transfer heterologous proteins into plant during root colonization, and have used green fluorescent protein and other markers to study the interaction in vivo and in situ between Trichoderma spp. and the fungal pathogen or the plant.

Proteomic analysis of secreted proteins from Trichoderma harzianum

Trichoderma mycoparasitic activity depends on the secretion of complex mixtures of hydrolytic enzymes able to degrade the host cell wall. We have analysed the extracellular proteome secreted by T. harzianum CECT 2413 in the presence of different fungal cell walls. Significant differences were detected in 2DE maps, depending on the use of specific cell walls or chitin. A combination of MALDI-TOF and liquid chromatography mass spectrometry allowed the identification of a novel aspartic protease (P6281: MW 33 and pI 4.3) highly induced by fungal cell walls. A broad EST library from T. harzianum CECT 2413 was used to obtain the full-length sequence. The protein showed 44% identity with the polyporopepsin (EC 3.4.23.29) from the basidiomycete Irpex lacteus. Lower identity percentages were found with other pepsin-like proteases from filamentous fungi (<31%) and animals (<29%). Northern blot and promoter sequence analyses support the implication of the protease P6281 in mycoparasitism.