Proteomics of filamentous fungi

Advances in the Degradation of Polycyclic Aromatic Hydrocarbons by Yeasts: A Review

Polycyclic aromatic hydrocarbons (PAHs) are toxic organic compounds produced during the incomplete combustion of organic materials and are commonly found in the environment due to anthropogenic activities such as industrial and vehicular emissions as well as natural sources, mainly volcanic eruptions and forest fires. PAHs are well known for their bioaccumulative capacity and environmental persistence, raising concerns due to their adverse effects on human health, including their carcinogenic potential. In recent years, bioremediation has emerged as a promising, effective, and sustainable solution for the degradation of PAHs in contaminated environments. In this context, yeasts have proven to be key microorganisms in the degradation of these compounds, owing to their ability to metabolize them through a series of enzymatic pathways. This review explores the advancements in yeast-mediated degradation of PAHs, with a particular focus on the role of enzymes such as cytochrome P450 (CYPs), epoxide hydrolases (EHs), and glutathione S-transferases (GSTs), which facilitate the breakdown of these compounds. The review also discusses the applications of genetic engineering to enhance the efficiency of yeasts in PAH degradation and the use of omics technologies to predict the catabolic potential of these organisms. Additionally, it examines studies addressing the degradation of benzo[a]pyrene (BaP) by yeasts such as Debaryomyces hansenii, and the potential future implications of omics sciences for developing new bioremediation.

Increasing the production of the bioactive compounds in medicinal mushrooms: an omics perspective

Macroscopic fungi, mainly higher basidiomycetes and some ascomycetes, are considered medicinal mushrooms and have long been used in different areas due to their pharmaceutically/nutritionally valuable bioactive compounds. However, the low production of these bioactive metabolites considerably limits the utilization of medicinal mushrooms both in commerce and clinical trials. As a result, many attempts, ranging from conventional methods to novel approaches, have been made to improve their production. The novel strategies include conducting omics investigations, constructing genome-scale metabolic models, and metabolic engineering. So far, genomics and the combined use of different omics studies are the most utilized omics analyses in medicinal mushroom research (both with 31% contribution), while metabolomics (with 4% contribution) is the least. This article is the first attempt for reviewing omics investigations in medicinal mushrooms with the ultimate aim of bioactive compound overproduction. In this regard, the role of these studies and systems biology in elucidating biosynthetic pathways of bioactive compounds and their contribution to metabolic engineering will be highlighted. Also, limitations of omics investigations and strategies for overcoming them will be provided in order to facilitate the overproduction of valuable bioactive metabolites in these valuable organisms.

Comparative proteomic analysis reveals differential protein expression of Hypsizygus marmoreus in response to different light qualities

Light is important environmental stress that influences the growth, development, and metabolism of Hypsizygus marmoreus (white var.). However, the molecular basis of the light effect on H. marmoreus remains unclear. In this study, a label-free comparative proteomic analysis was applied to investigate the global protein expression profile of H. marmoreus mycelia growing under white, red, green, and blue light qualities and darkness (control). Among 3149 identified proteins in H. marmoreus, 2288 were found to be expressed in all tested conditions. Data of Each light quality was compared with darkness for further analysis, numerous differentially expressed proteins (DEPs) were identified and the white light group showed the most. All the up-regulated and down-regulated DEPs were annotated and analyzed with the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database. The KEGG enrichment analysis revealed that light stress was associated with primary metabolism, glycolysis/gluconeogenesis, MAPK, proteasome, and carbohydrate-active enzyme pathways. This study advances valuable insights into the molecular mechanisms underlying the role of different light qualities in mushroom growth and development.

Comparative sub-cellular proteome analyses reveals metabolic differentiation and production of effector-like molecules in the dieback phytopathogen Phytophthora cinnamomi

Phytopathogenic oomycetes pose a significant threat to global biodiversity and food security. The proteomes of these oomycetes likely contain important factors that contribute to their pathogenic success, making their discovery crucial for elucidating pathogenicity. Phytophthora cinnamomi is a root pathogen that causes dieback in a wide variety of crops and native vegetation world-wide. Virulence proteins produced by P. cinnamomi are not well defined and a large-scale approach to understand the biochemistry of this pathogen has not been documented. Soluble mycelial, zoospore and secreted proteomes were obtained and label-free quantitative proteomics was used to compare the composition of the three sub-proteomes. A total of 4635 proteins were identified, validating 17.7% of the predicted gene set. The mycelia were abundant in transporters for nutrient acquisition, metabolism and cellular proliferation. The zoospores had less metabolic related ontologies but were abundant in energy generating, motility and signalling associated proteins. Virulence-associated proteins were identified in the secretome such as candidate effector and effector-like proteins, which interfere with the host immune system. These include hydrolases, cell wall degrading enzymes, putative necrosis-inducing proteins and elicitins. The secretome elicited a hypersensitive response on the roots of a model host and thus suggests evidence of effector activity. SIGNIFICANCE: Phytophthora cinnamomi is a phytopathogenic oomycete that causes dieback disease in native vegetation and several horticultural crops such as avocado, pineapple and macadamia. Whilst this pathogen has significance world-wide, its pathogenicity and virulence have not been described in depth. We carried out comparative label-free proteomics of the mycelia, zoospores and secretome of P. cinnamomi. This study highlights the differential metabolism and cellular processes between the sub-proteomes. Proteins associated with metabolism, nutrient transport and cellular proliferation were over represented in the mycelia. The zoospores have a specialised proteome showing increased energy generation geared towards motility. Candidate effectors and effector-like secreted proteins were also identified, which can be exploited for genetic resistance. This demonstrates a better understanding of the biology and pathogenicity of P. cinnamomi infection that can subsequently be used to develop effective methods of disease management.

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.

Comparative Proteomic Analysis of Wild Type and Mutant Lacking an SCF E3 Ligase F-Box Protein in Magnaporthe oryzae

Magnaporthe oryzae (M. oryzae) is a pathogenic, filamentous fungus that is a primary cause of rice blast disease. The M. oryzae protein MGG_13065, SCF E3 ubiquitin ligase complex F-box protein, has been identified as playing a crucial role in the infection process, specifically, as part of the ubiquitin mediated proteolysis pathway. Proteins targeted by MGG_13065 E3 ligase are first phosphorylated and then ubiquitinated by E3 ligase. In this study, we used a label-free quantitative global proteomics technique to probe the role of ubiquitination and phosphorylation in the mechanism of how E3 ligase regulates change in virulence of M. oryzae. To do this, we compared the WT M. oryzae 70-15 strain with a gene knock out (E3 ligase KO) strain. After applying a ≥ 5 normalized spectral count cutoff, a total of 4432 unique proteins were identified comprised of 4360 and 4372 in the WT and E3 ligase KO samples, respectively. Eighty proteins drastically increased in abundance, while 65 proteins decreased in abundance in the E3 ligase KO strain. Proteins (59) were identified only in the WT strain; 13 of these proteins had both phosphorylation and ubiquitination post-translational modifications. Proteins (71) were revealed to be only in the E3 ligase KO strain; 23 of the proteins have both phosphorylation and ubiquitination post-translational modifications. Several of these proteins were associated with key biological processes. These data greatly assist in the selection of future genes for functional studies and enable mechanistic insight related to virulence.

Proteome of the fungus Phoma macdonaldii, the causal agent of black stem of sunflower

Phoma macdonaldii causes black stem of sunflower, which severely affects sunflower yield and quality. There is currently little molecular information available for this pathogenic fungus. In this study, a global proteomic analysis of P. macdonaldii was performed to determine the biological characteristics and pathogenicity of this pathogen. A total of 1498 proteins were identified by LC-MS/MS in all biological replicates. Among the identified proteins, 1420 proteins were classified into the three main GO categories (biological process, cellular component, and molecular function) while 806 proteins were annotated into the five major KEGG database (metabolism, genetic information processing, environmental information processing, cellular processes, and organismal systems). The regulated expression levels of eight genes encoding selected identified proteins were investigated to assess their potential effects on fungal development and pathogenesis. To the best of our knowledge, this is the first study to characterize the proteome of the necrotrophic fungus P. macdonaldii. The presented results provide novel insights into the development and pathogenesis of P. macdonaldii and possibly other Phoma species. SIGNIFICANCE: Black stem of sunflower is a devastating disease caused by the necrotrophic fungus Phoma macdonaldii. Relatively little is known regarding the molecular characteristics of this pathogen, and no proteomic investigation has been reported. Thus, we conducted a global proteomic analysis of P. macdonaldii. Many proteins were found to be differentially regulated during fungal development and pathogenesis, suggesting they may be important for these two processes. This is the first proteomic study of P. macdonaldii, and the data presented herein will be useful for elucidating the molecular characteristics of this fungus as well as other Phoma species.

Increasing Coverage of Proteome Identification of the Fruiting Body of Agaricus bisporus by Shotgun Proteomics

To increase coverage of protein identification of an Agaricus bisporus fruiting body, we analyzed the crude protein fraction of the fruiting body by using a shotgun proteomics approach where 7 MudPIT (Multi-Protein identification Technology) runs were conducted and the MS/MS spectra from the 7 MudPIT runs were merged. Overall, 3093 non-redundant proteins were identified to support the expression of those genes annotated in the genome database of Agaricus bisporus. The physicochemical properties of the identified proteins, i.e., wide pI value range and molecular mass range, were indicative of unbiased protein identification. The relative quantification of the identified proteins revealed that K5XI50 (Aldedh domain-containing protein) and K5XEW1 (Ubiquitin-like domain-containing protein) were highly abundant in the fruiting body. Based on the information in the Uniprot (Universal Protein Resource) database for A. bisporus, only approximately 53% of the 3093 identified proteins have been functionally described and approximately 47% of the proteins remain uncharacterized. Gene Ontology analysis revealed that the majority of proteins were annotated with a biological process, and proteins associated with coiled-coil (12.8%) and nucleotide binding (8.21%) categories were dominant. The Kyoto Encyclopedia of Genes and Genome analysis revealed that proteins involved in biosynthesis of secondary metabolites and tyrosine metabolism were enriched in a fruiting body of Agaricus bisporus, suggesting that the proteins are associated with antioxidant metabolites.

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

Monilinia laxa is a necrotrophic plant pathogen able to infect and produce substantial losses on stone fruit. Three different isolates of M. laxa were characterized according to their aggressiveness on nectarines. M. laxa 8L isolate was the most aggressive on fruit, 33L isolate displayed intermediated virulence level, and 5L was classified as a weak aggressive isolate. Nectarine colonization process by the weak isolate 5L was strongly delayed. nLC-MS/MS proteomic studies using in vitro peach cultures provided data on exoproteomes of the three isolates at equivalent stages of brown rot colonization; 3 days for 8L and 33L, and 7 days for 5L. A total of 181 proteins were identified from 8L exoproteome and 289 proteins from 33L at 3 dpi, and 206 proteins were identified in 5L exoproteome at 7 dpi. Although an elevated number of proteins lacked a predicted function, the vast majority of proteins belong to OG group "metabolism", composed of categories such as "carbohydrate transport and metabolism" in 5L, and "energy production and conversion" most represented in 8L and 33L. Among identified proteins, 157 that carried a signal peptide were further examined and classified. Carbohydrate-active enzymes and peptidases were the main groups revealing different protein alternatives with the same function among isolates. Our data suggested a subset of secreted proteins as possible markers of differential virulence in more aggressive isolates, MlPG1 MlPME3, NEP-like, or endoglucanase proteins. A core-exoproteome among isolates independently of their virulence but time-dependent was also described. This core included several well-known virulence factors involved in host-tissue factors like cutinase, pectin lyases, and acid proteases. The secretion patterns supported the assumption that M. laxa deploys an extensive repertoire of proteins to facilitate the host infection and colonization and provided information for further characterization of M. laxa pathogenesis.

Recent trends in molecular diagnostics of yeast infections: from PCR to NGS

The incidence of opportunistic yeast infections in humans has been increasing over recent years. These infections are difficult to treat and diagnose, in part due to the large number and broad diversity of species that can underlie the infection. In addition, resistance to one or several antifungal drugs in infecting strains is increasingly being reported, severely limiting therapeutic options and showcasing the need for rapid detection of the infecting agent and its drug susceptibility profile. Current methods for species and resistance identification lack satisfactory sensitivity and specificity, and often require prior culturing of the infecting agent, which delays diagnosis. Recently developed high-throughput technologies such as next generation sequencing or proteomics are opening completely new avenues for more sensitive, accurate and fast diagnosis of yeast pathogens. These approaches are the focus of intensive research, but translation into the clinics requires overcoming important challenges. In this review, we provide an overview of existing and recently emerged approaches that can be used in the identification of yeast pathogens and their drug resistance profiles. Throughout the text we highlight the advantages and disadvantages of each methodology and discuss the most promising developments in their path from bench to bedside.

Identification of proteins responding to pathogen-infection in the red alga Pyropia yezoensis using iTRAQ quantitative proteomics

BACKGROUND

Pyropia yezoensis is an important marine crop which, due to its high protein content, is widely used as a seafood in China. Unfortunately, red rot disease, caused by Pythium porphyrae, seriously damages P. yezoensis farms every year in China, Japan, and Korea. Proteomic methods are often used to study the interactions between hosts and pathogens. Therefore, an iTRAQ-based proteomic analysis was used to identify pathogen-responsive proteins following the artificial infection of P. yezoensis with P. porphyrae spores.

RESULTS

A total of 762 differentially expressed proteins were identified, of which 378 were up-regulated and 384 were down-regulated following infection. A large amount of these proteins were involved in disease stress, carbohydrate metabolism, cell signaling, chaperone activity, photosynthesis, and energy metabolism, as annotated in the KEGG database. Overall, the data showed that P. yezoensis resists infection by inhibiting photosynthesis, and energy and carbohydrate metabolism pathways, as supported by changes in the expression levels of related proteins. The expression data are available via ProteomeXchange with the identifier PXD009363.

CONCLUSIONS

The current data provide an overall summary of the red algae responses to pathogen infection. This study improves our understanding of infection resistance in P. yezoensis, and may help in increasing the breeding of P. porphyrae-infection tolerant macroalgae.

Genetic Variability and Proteome Profiling of a Radiation Induced Cellulase Mutant Mushroom Pleurotus florida

We report the genetic similarity changes between a mutant mushroom (Pleurotus florida, designated as PfCM4) having increased cellulolytic activity developed through radiation mutagenesis and its wild type by amplified fragment length polymorphism (AFLP). On average, 23 AFLP fragments were amplified per primer combination, and a total of 286 polymorphic fragments (78.57% polymorphism) with maximal fragment length of 1365 base pairs (bp) were obtained. The genetic similarity between wild type and PfCM4 was found to be 22.30%. In addition, mycelial and secreted protein profiling by 2D-PAGE showed at least three and five different protein spots in the range of 25 kD to 100 kD, respectively, in PfCM4. It seems that the variation in genetic similarity and different expression of both mycelial and secreted proteins in PfCM4 in comparison to the wild type could likely be correlated with its increased cellulolytic activity effected by the irradiation.

A Comparative Proteome Approach Reveals Metabolic Changes Associated with Flammulina velutipes Mycelia in Response to Cold and Light Stress

In some industrial processes, cold and light stresses are recognized as two important environmental triggers for the transformation of mycelia into fruit-bodies via intermediate primordia in Flammulina velutipes cultivation. To gain insights into the mechanism of regulation of F. velutipes mycelia in response to cold and light stress, proteins expressed abundantly and characteristically at particular stress states were investigated by using the isobaric tags for the relative and absolute quantitation labeling technique. Among the 1046 nonredundant proteins identified with a high degree of confidence, 264 proteins, which were detected as differentially expressed proteins, were associated with 176 specific KEGG pathways. In-depth data analysis revealed that the regulatory network underlying the cold and light response mechanisms of F. velutipes mycelia was complex and multifaceted, as it included varied functions such as rapid energy supply, the biosynthesis of lysine, phenylalanine, tyrosine, and γ-aminobutyric acid, the calcium signal transduction process, dynein-dependent actin and microtubule cytoskeleton formation, autolysis, oxidative stress adaptation, pigment secretion, tissue and organ morphogenesis, and other interesting stress-related processes. Insights into the proteins might shed light on an intuitive understanding of the cold and light stress response mechanism underlying the fruiting processes of F. velutipes. Furthermore, the data might also provide further insights into the stress response mechanism of macro-fungi and valuable information for scientific improvement of some mushroom cultivation techniques in practice.

iTRAQ-based quantitative proteomic analysis of conidia and mycelium in the filamentous fungus Metarhizium robertsii

Metarhizium robertsii is widely applied in biological control via conidia application. To clarify the proteomic differences between conidia and mycelia and explore the underlying mechanisms of conidia as a unit responsible for dispersal and environmental stress, we carried out an iTRAQ (isobaric tags for relative and absolute quantitation)-based quantitative proteomic analysis for two developmental stages from M. robertsii. A total of 2052 proteins were detected, and 90 showed differential protein abundance between the conidia and mycelia. These 90 proteins were primarily associated with stress resistance, amino acid and protein metabolism, and energy metabolism. Further bioinformatics analysis showed that these proteins could be mapped to 52 pathways, five of which were significantly enriched after mapping to KEGG pathways. Interestingly, many proteins involved in the significantly enriched pathway of peroxisome, biosynthesis of secondary metabolites and glyoxylate and dicarboxylate metabolism, including catalase, peroxisomal membrane anchor protein, formate dehydrogenase and isocitrate lyase, were identified with higher abundance in conidia. The results deepened our understanding of the conidia proteome in M. robertsii and provide a basis for further exploration for improving the efficiency of the fungi as biocontrol agents.

Enhancement of Environmental Hazard Degradation in the Presence of Lignin: a Proteomics Study

Proteomics studies of fungal systems have progressed dramatically based on the availability of more fungal genome sequences in recent years. Different proteomics strategies have been applied toward characterization of fungal proteome and revealed important gene functions and proteome dynamics. Presented here is the application of shot-gun proteomic technology to study the bio-remediation of environmental hazards by white-rot fungus. Lignin, a naturally abundant component of the plant biomass, is discovered to promote the degradation of Azo dye by white-rot fungus Irpex lacteus CD2 in the lignin/dye/fungus system. Shotgun proteomics technique was used to understand degradation mechanism at the protein level for the lignin/dye/fungus system. Our proteomics study can identify about two thousand proteins (one third of the predicted white-rot fungal proteome) in a single experiment, as one of the most powerful proteomics platforms to study the fungal system to date. The study shows a significant enrichment of oxidoreduction functional category under the dye/lignin combined treatment. An in vitro validation is performed and supports our hypothesis that the synergy of Fenton reaction and manganese peroxidase might play an important role in DR5B dye degradation. The results could guide the development of effective bioremediation strategies and efficient lignocellulosic biomass conversion.

Genetics, Molecular, and Proteomics Advances in Filamentous Fungi

Filamentous fungi play a dynamic role in health and the environment. In addition, their unique and complex hyphal structures are involved in their morphogenesis, integrity, synthesis, and degradation, according to environmental and physiological conditions and resource availability. However, in biotechnology, it has a great value in the production of enzymes, pharmaceuticals, and food ingredients. The beginning of nomenclature of overall fungi started in early 1990 after which the categorization, interior and exterior mechanism, function, molecular and genetics study took pace. This mini-review has emphasized some of the important aspects of filamentous fungi, their pattern of life cycle, history, and development of different strategic methods applied to exploit this unique organism. New trends and concepts that have been applied to overcome obstacle because of their basic structure related to genomics and systems biology has been presented. Furthermore, the future aspects and challenges that need to be deciphered to get a bigger and better picture of filamentous fungi have been discussed.

Comparative Proteome Reveals Metabolic Changes during the Fruiting Process in Flammulina velutipes

Understanding the molecular mechanisms regulating the fruiting process in macro-fungi, especially industrially cultivated mushrooms, has long been a goal in mycological research. To gain insights into the events accompanying the transformation of mycelia into fruit-bodies in Flammulina velutipes, proteins expressed characteristically and abundantly at primordium and fruit-body stages were investigated by using the iTRAQ labeling technique. Among the 171 differentially expressed proteins, a total of 68 displayed up-regulated expression levels that were associated with 84 specific KEGG pathways. Some up-regulated proteins, such as pyruvate carboxylase, aldehyde dehydrogenase, fatty acid synthase, aspartate aminotransferase, 2-cysteine peroxiredoxin, FDS protein, translation elongation factor 1-alpha, mitogen-activated protein kinases (MAPKs), and heat-shock protein 70 that are involved in carbohydrate metabolism, carotenoid formation, the TCA cycle, MAPK signaling pathway, and the biosynthesis of fatty acids and branched-chain amino acids, could serve as potential stage-specific biomarkers to study the fruiting process in F. velutipes. Knowledge of the proteins might provide valuable evidence to better understand the molecular mechanisms of fruit-body initiation and development in basidiomycete fungi. Furthermore, this study also offers valuable evidence for yield improvement and quality control of super golden-needle mushroom in practice.

SWATH label-free proteomics analyses revealed the roles of oxidative stress and antioxidant defensing system in sclerotia formation of Polyporus umbellatus

Understanding the initiation and maturing mechanisms is important for rational manipulating sclerotia differentiation and growth from hypha of Polyporus umbellatus. Proteomes in P. umbellatus sclerotia and hyphae at initial, developmental and mature phases were studied. 1391 proteins were identified by nano-liquid chromatograph-mass spectrometry (LC-MS) in Data Dependant Acquisition mode, and 1234 proteins were quantified successfully by Sequential Window Acquisition of all THeoretical fragment ion spectra-MS (SWATH-MS) technology. There were 347 differentially expressed proteins (DEPs) in sclerotia at initial phase compared with those in hypha, and the DEP profiles were dynamically changing with sclerotia growth. Oxidative stress (OS) in sclerotia at initial phase was indicated by the repressed proteins of respiratory chain, tricarboxylic acid cycle and the activation of glycolysis/gluconeogenesis pathways were determined based on DEPs. The impact of glycolysis/gluconeogenesis on sclerotium induction was further verified by glycerol addition assays, in which 5% glycerol significantly increased sclerotial differentiation rate and biomass. It can be speculated that OS played essential roles in triggering sclerotia differentiation from hypha of P. umbellatus, whereas antioxidant activity associated with glycolysis is critical for sclerotia growth. These findings reveal a mechanism for sclerotial differentiation in P. umbellatus, which may also be applicable for other fungi.

iTRAQ-based quantitative proteome revealed metabolic changes of Flammulina velutipes mycelia in response to cold stress

Temperature is one of the pivotal factors influencing mycelium growth and fruit-body formation of Flammulina velutipes. To gain insights into hyphae growth and fruit-body formation events and facilitate the identification of potential stage-specific biomarker candidates, we investigated the proteome response of F. velutipes mycelia to cold stresses using iTRAQ-coupled two-dimensional liquid chromatography tandem mass spectrometry (2D LC-MS/MS) technique. Among 1198 proteins identified with high confidence, a total of 63 displayed altered expression level after cold stress treatments. In-depth data analysis reveals that differentially expressed proteins were involved in a variety of cellular processes, particularly metabolic processes. Among the 31 up-regulated proteins, 24 (77.42%) were associated with 22 specific KEGG pathways. These up-regulated proteins could possibly serve as potential biomarkers to study the molecular mechanisms of F. velutipes mycelia response to cold stresses. These data of the proteins might provide valuable evidences to better understand the molecular mechanisms of mycelium resistance to cold stress and fruit-body formation in fungi.

BIOLOGICAL SIGNIFICANCE

Low-temperature is one of the pivotal factors in some Flammulina velutipes industrial processes influencing mycelium growth, inducing primordia and controlling fruit-body development. Preliminary study has indicated that effectively regulating cultivation could augment the yield by controlling optimal cold stress level on mycelia. However, we are still far from understanding the molecular and physiological mechanisms of adaptation of these fungi at cold stress. In the present study, the experiments reported above were undertaken to investigate chronological changes of protein expression during F. velutipes mycelia in response to cold stress by using iTRAQ-coupled 2D LC-MS/MS technique. This result would provide new insights to the underlying mycelium growth and fruit-body formation mechanisms of basidiomycetes under cold stress.

The Verticillium dahliae SnodProt1-Like Protein VdCP1 Contributes to Virulence and Triggers the Plant Immune System

During pathogenic infection, hundreds of proteins that play vital roles in the Verticillium dahliae-host interaction are secreted. In this study, an integrated proteomic analysis of secreted V. dahliae proteins was performed, and a conserved secretory protein, designated VdCP1, was identified as a member of the SnodProt1 phytotoxin family. An expression analysis of the vdcp1 gene revealed that the transcript is present in every condition studied and displays elevated expression throughout the infection process. To investigate the natural role of VdCP1 in V. dahliae, two vdcp1 knockout mutants and their complementation strains were generated. Bioassays of these mutants revealed no obvious phenotypic differences from the wild-type (WT) in terms of mycelial growth, conidial production or mycelial/spore morphology. However, compared with the WT, the vdcp1 knockout mutants displayed attenuated pathogenicity in cotton plants. Furthermore, treating plants with purified recombinant VdCP1 protein expressed in Pichia pastoris induced the accumulation of reactive oxygen species (ROS), expression of several defense-related genes, leakage of ion electrolytes, enhancement of defense-related enzyme activity and production of salicylic acid. Moreover, VdCP1 conferred resistance to Botrytis cinerea and Pseudomonas syringae pv. tabaci in tobacco and to V. dahliae in cotton. Further research revealed that VdCP1 possesses chitin-binding properties and that the growth of vdcp1 knockout mutants was more affected by treatments with chitinase, indicating that VdCP1 could protect V. dahliae cell wall from enzymatic degradation, which suggests an effector role of VdCP1 in infecting hosts.

Systematic analysis of the lysine acetylome in Fusarium graminearum

BACKGROUND

Lysine acetylation in proteins is a ubiquitous and conserved post-translational modification, playing a critical regulatory role in almost every aspect of living cells. Although known for many years, its function remains elusive in Fusarium graminearum, one of the most important necrotrophic plant pathogens with huge economic impact.

RESULTS

By the combination of affinity enrichment and high-resolution LC-MS/MS analysis, large-scale lysine acetylome analysis was performed. In total, 577 lysine acetylation sites matched to 364 different proteins were identified. Bioinformatics analysis of the acetylome showed that the acetylated proteins are involved in a wide range of cellular functions and exhibit diverse subcellular localizations. Remarkably, 10 proteins involved in the virulence or DON (deoxynivalenol) biosynthesis were found to be acetylated, including 4 transcription factors, 4 protein kinases and 2 phosphatases. Protein-protein interaction network analysis revealed that acetylated protein complexes are involved in diversified interactions.

CONCLUSIONS

This work provides the first comprehensive survey of a possible lysine acetylome in F. graminearum and reveals previously unappreciated roles of lysine acetylation in the regulation of diverse biological processes. This work provides a resource for functional analysis of acetylated proteins in filamentous fungi.

Comparative Proteomic Analysis of Light-Induced Mycelial Brown Film Formation in Lentinula edodes

Light-induced brown film (BF) formation by the vegetative mycelium of Lentinula edodes is important for ensuring the quantity and quality of this edible mushroom. Nevertheless, the molecular mechanism underlying this phenotype is still unclear. In this study, a comparative proteomic analysis of mycelial BF formation in L. edodes was performed. Seventy-three protein spots with at least a twofold difference in abundance on two-dimensional electrophoresis (2DE) maps were observed, and 52 of them were successfully identified by matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry (MALDI-TOF/TOF/MS). These proteins were classified into the following functional categories: small molecule metabolic processes (39%), response to oxidative stress (5%), and organic substance catabolic processes (5%), followed by oxidation-reduction processes (3%), single-organism catabolic processes (3%), positive regulation of protein complex assembly (3%), and protein metabolic processes (3%). Interestingly, four of the proteins that were upregulated in response to light exposure were nucleoside diphosphate kinases. To our knowledge, this is the first proteomic analysis of the mechanism of BF formation in L. edodes. Our data will provide a foundation for future detailed investigations of the proteins linked to BF formation.

Acetylome analysis reveals the involvement of lysine acetylation in diverse biological processes in Phytophthora sojae

Lysine acetylation is a dynamic and highly conserved post-translational modification that plays an important regulatory role in almost every aspects of cell metabolism in both eukaryotes and prokaryotes. Phytophthora sojae is one of the most important plant pathogens due to its huge economic impact. However, to date, little is known about the functions of lysine acetylation in this Phytopthora. Here, we conducted a lysine acetylome in P. sojae. Overall, 2197 lysine acetylation sites in 1150 proteins were identified. The modified proteins are involved in diverse biological processes and are localized to multiple cellular compartments. Importantly, 7 proteins involved in the pathogenicity or the secretion pathway of P. sojae were found to be acetylated. These data provide the first comprehensive view of the acetylome of P. sojae and serve as an important resource for functional analysis of lysine acetylation in plant pathogens.

Label-Free Quantitative Proteomic Analysis of Puccinia psidii Uredospores Reveals Differences of Fungal Populations Infecting Eucalyptus and Guava

Puccinia psidii sensu lato (s.l.) is the causal agent of eucalyptus and guava rust, but it also attacks a wide range of plant species from the myrtle family, resulting in a significant genetic and physiological variability among populations accessed from different hosts. The uredospores are crucial to P. psidii dissemination in the field. Although they are important for the fungal pathogenesis, their molecular characterization has been poorly studied. In this work, we report the first in-depth proteomic analysis of P. psidii s.l. uredospores from two contrasting populations: guava fruits (PpGuava) and eucalyptus leaves (PpEucalyptus). NanoUPLC-MSE was used to generate peptide spectra that were matched to the UniProt Puccinia genera sequences (UniProt database) resulting in the first proteomic analysis of the phytopathogenic fungus P. psidii. Three hundred and fourty proteins were detected and quantified using Label free proteomics. A significant number of unique proteins were found for each sample, others were significantly more or less abundant, according to the fungal populations. In PpGuava population, many proteins correlated with fungal virulence, such as malate dehydrogenase, proteossomes subunits, enolases and others were increased. On the other hand, PpEucalyptus proteins involved in biogenesis, protein folding and translocation were increased, supporting the physiological variability of the fungal populations according to their protein reservoirs and specific host interaction strategies.

Proteomic Analysis of Anti-Cancerous Scopularide Production by a Marine Microascus brevicaulis Strain and Its UV Mutant

The marine fungus Microascus brevicaulis strain LF580 is a non-model secondary metabolite producer with high yields of the two secondary metabolites scopularides A and B, which exhibit distinct activities against tumour cell lines. A mutant strain was obtained using UV mutagenesis, showing faster growth and differences in pellet formation besides higher production levels. Here, we show the first proteome study of a marine fungus. Comparative proteomics were applied to gain deeper understanding of the regulation of production and of the physiology of the wild type strain and its mutant. For this purpose, an optimised protein extraction protocol was established. In total, 4759 proteins were identified. The central metabolic pathway of strain LF580 was mapped using the KEGG pathway analysis and GO annotation. Employing iTRAQ labelling, 318 proteins were shown to be significantly regulated in the mutant strain: 189 were down- and 129 upregulated. Proteomics are a powerful tool for the understanding of regulatory aspects: The differences on proteome level could be attributed to limited nutrient availability in the wild type strain due to a strong pellet formation. This information can be applied for optimisation on strain and process level. The linkage between nutrient limitation and pellet formation in the non-model fungus M. brevicaulis is in consensus with the knowledge on model organisms like Aspergillus niger and Penicillium chrysogenum.

Comparative Proteomics Analyses of Two Races of Fusarium oxysporum f. sp. conglutinans that Differ in Pathogenicity

Fusarium oxysporum is a soil-inhabiting fungus that induces vascular wilt and root rot in a variety of plants. F. oxysporum f. sp. conglutinans (Foc), which comprises two races, can cause wilt disease in cabbage. Compared with race 1 (52557(-TM), R1), race 2 (58385(-TM), R2) exhibits much stronger pathogenicity. Here, we provide the first proteome reference maps for Foc mycelium and conidia and identify 145 proteins with different abundances among the two races. Of these proteins, most of the high-abundance proteins in the R2 mycelium and conidia are involved in carbohydrate, amino acid and ion metabolism, which indicates that these proteins may play important roles in isolate R2's stronger pathogenicity. The expression levels of 20 typical genes demonstrate similarly altered patterns compared to the proteomic analysis. The protein glucanosyltransferase, which is involved in carbohydrate metabolism, was selected for research. We knocked out the corresponding gene (gas1) and found that Foc-∆gas1 significantly reduced growth rate and virulence compared with wild type isolates. These results deepened our understanding of the proteins related to F. oxysporum pathogenicity in cabbage Fusarium wilt and provided new opportunities to control this disease.

Alteration of Genetic Make-up in Karnal Bunt Pathogen (Tilletia indica) of Wheat in Presence of Host Determinants

Alteration of genetic make-up of the isolates and monosporidial strains of Tilletia indica causing Karnal bunt (KB) disease in wheat was analyzed using DNA markers and SDS-PAGE. The generation of new variation with different growth characteristics is not a generalized feature and is not only dependant on the original genetic make up of the base isolate/monosporidial strains but also on interaction with host. Host determinant(s) plays a significant role in the generation of variability and the effect is much pronounced in monosporidial strains with narrow genetic base as compared to broad genetic base. The most plausible explanation of genetic variation in presence of host determinant(s) are the recombination of genetic material from two different mycelial/sporidia through sexual mating as well as through para-sexual means. The morphological and development dependent variability further suggests that the variation in T. indica strains predominantly derived through the genetic rearrangements.

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.

Proteomic profile of Aspergillus flavus in response to water activity

Aspergillus flavus, a common contaminant of crops and stored grains, can produce aflatoxins that are harmful to humans and other animals. Water activity (aw) is one of the key factors influencing both fungal growth and mycotoxin production. In this study, we used the isobaric tagging for relative and absolute quantitation (iTRAQ) technique to investigate the effect of aw on the proteomic profile of A. flavus. A total of 3566 proteins were identified, of which 837 were differentially expressed in response to variations in aw. Among these 837 proteins, 403 were over-expressed at 0.99 aw, whereas 434 proteins were over-expressed at 0.93 aw. According to Gene Ontology (GO) analysis, the secretion of extracellular hydrolases increased as aw was raised, suggesting that extracellular hydrolases may play a critical role in induction of aflatoxin biosynthesis. On the basis of Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) categorizations, we identified an exportin protein, KapK, that may down-regulate aflatoxin biosynthesis by changing the location of NirA. Finally, we considered the role of two osmotic stress-related proteins (Sln1 and Glo1) in the Hog1 pathway and investigated the expression patterns of proteins related to aflatoxin biosynthesis. The data uncovered in this study are critical for understanding the effect of water stress on toxin production and for the development of strategies to control toxin contamination of agricultural products.

Comparative proteomic analysis of Aureobasidium pullulans in the presence of high and low levels of nitrogen source

Pullulan, produced by Aureobasidium pullulans strain, has been broadly used in the food and medical industries. However, relatively little is known concerning the molecular basis of pullulan biosynthesis of this strain. In this paper, the effect of different concentrations of (NH4)2SO4 on pullulan fermentation was studied. Proteomics containing two-dimensional gel electrophoresis (2-DE) and matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectrometry (MALDI-TOF/TOF MS) were used to analyze the protein with different expressions of A. pullulans cells between the nitrogen limitation and nitrogen repletion. Maximum pullulan production reached 37.72 g/L when 0.6 g/L of initial (NH4)2SO4 was added. Excess nitrogen source would impel carbon flux flow toward biomass production, but decreased the pullulan production. Nitrogen limitation in A. pullulans seemed to influence the flux change of carbon flux flow toward exopolysaccharide accumulation. The findings indicated that 12 identified protein spots were involved in energy-generating enzymes, antioxidant-related enzymes, amino acid biosynthesis, glycogen biosynthesis, glycolysis, protein transport, and transcriptional regulation. These results presented more evidence of pullulan biosynthesis under nitrogen-limited environment, which would provide a molecular understanding of the physiological response of A. pullulans for optimizing the performance of industrial pullulan fermentation.

(Post-)genomics approaches in fungal research

To date, hundreds of fungal genomes have been sequenced and many more are in progress. This wealth of genomic information has provided new directions to study fungal biodiversity. However, to further dissect and understand the complicated biological mechanisms involved in fungal life styles, functional studies beyond genomes are required. Thanks to the developments of current -omics techniques, it is possible to produce large amounts of fungal functional data in a high-throughput fashion (e.g. transcriptome, proteome, etc.). The increasing ease of creating -omics data has also created a major challenge for downstream data handling and analysis. Numerous databases, tools and software have been created to meet this challenge. Facing such a richness of techniques and information, hereby we provide a brief roadmap on current wet-lab and bioinformatics approaches to study functional genomics in fungi.

Differential protein accumulations in isolates of the strawberry wilt pathogen Fusarium oxysporum f. sp. fragariae differing in virulence

This study was conducted to define differences in Fusarium oxysporum f. sp. fragariae (Fof) isolates with different virulence efficiency to strawberry at the proteome level, in combination with their differences in mycelial growth, conidial production and germination. Comparative proteome analyses revealed substantial differences in mycelial proteomes between Fof isolates, where the 54 differentially accumulated protein spots were consistently over-accumulated or exclusively in the highly virulent isolate. These protein spots were identified through MALDI-TOF/TOF mass spectrometry analyses, and the identified proteins were mainly related to primary and protein metabolism, antioxidation, electron transport, cell cycle and transcription based on their putative functions. Proteins of great potential as Fof virulence factors were those involved in ubiquitin/proteasome-mediated protein degradation and reactive oxygen species detoxification; the hydrolysis-related protein haloacid dehalogenase superfamily hydrolase; 3,4-dihydroxy-2-butanone 4-phosphate synthase associated with riboflavin biosynthesis; and those exclusive to the highly virulent isolate. In addition, post-translational modifications may also make an important contribution to Fof virulence.

BIOLOGICAL SIGNIFICANCE

F. oxysporum f. sp. fragariae (Fof), the causal agent of Fusarium wilt in strawberry, is a serious threat to commercial strawberry production worldwide. However, factors and mechanisms contributing to Fof virulence remained unknown. This study provides knowledge of the molecular basis for the differential expression of virulence in Fof, allowing new possibilities towards developing alternative and more effective strategies to manage Fusarium wilt.

Ectomycorrhizal identification in environmental samples of tree roots by Fourier-transform infrared (FTIR) spectroscopy

Roots of forest trees are associated with various ectomycorrhizal (ECM) fungal species that are involved in nutrient exchange between host plant and the soil compartment. The identification of ECM fungi in small environmental samples is difficult. The present study tested the feasibility of attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy followed by hierarchical cluster analysis (HCA) to discriminate in situ collected ECM fungal species. Root tips colonized by distinct ECM fungal species, i.e., Amanita rubescens, Cenococcum geophilum, Lactarius subdulcis, Russula ochroleuca, and Xerocomus pruinatus were collected in mono-specific beech (Fagus sylvatica) and mixed deciduous forests in different geographic areas to investigate the environmental variability of the ECM FTIR signatures. A clear HCA discrimination was obtained for ECM fungal species independent of individual provenance. Environmental variability neither limited the discrimination between fungal species nor provided sufficient resolution to discern species sub-clusters for different sites. However, the de-convoluted FTIR spectra contained site-related spectral information for fungi with wide nutrient ranges, but not for Lactarius subdulcis, a fungus residing only in the litter layer. Specific markers for distinct ECM were identified in spectral regions associated with carbohydrates (i.e., mannans), lipids, and secondary protein structures. The present results support that FTIR spectroscopy coupled with multivariate analysis is a reliable and fast method to identify ECM fungal species in minute environmental samples. Moreover, our data suggest that the FTIR spectral signatures contain information on physiological and functional traits of ECM fungi.

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.

De novo transcriptome sequencing and analysis for Venturia inaequalis, the devastating apple scab pathogen

Venturia inaequalis is the causal agent of apple scab, one of the most devastating diseases of apple. Due to several distinct features, it has emerged as a model fungal pathogen to study various aspects of hemibiotrophic plant pathogen interactions. The present study reports de novo assembling, annotation and characterization of the transcriptome of V. inaequalis. Venturia transcripts expressed during its growth on laboratory medium and that expressed during its biotrophic stage of infection on apple were sequenced using Illumina RNAseq technology. A total of 94,350,055 reads (50 bp read length) specific to Venturia were obtained after filtering. The reads were assembled into 62,061 contigs representing 24,571 unique genes. GO analysis suggested prevalence of genes associated with biological process categories like metabolism, transport and response to stimulus. Genes associated with molecular function like binding, catalytic activities and transferase activities were found in majority. EC and KEGG pathway analyses suggested prevalence of genes encoding kinases, proteases, glycoside hydrolases, cutinases, cytochrome P450 and transcription factors. The study has identified several putative pathogenicity determinants and candidate effectors in V. inaequalis. A large number of transcripts encoding membrane transporters were identified and comparative analysis revealed that the number of transporters encoded by Venturia is significantly more as compared to that encoded by several other important plant fungal pathogens. Phylogenomics analysis indicated that V. inaequalis is closely related to Pyrenophora tritici-repentis (the causal organism of tan spot of wheat). In conclusion, the findings from this study provide a better understanding of the biology of the apple scab pathogen and have identified candidate genes/functions required for its pathogenesis. This work lays the foundation for facilitating further research towards understanding this host-pathogen interaction.

Comparative vesicle proteomics reveals selective regulation of protein expression in chestnut blight fungus by a hypovirus

The chestnut blight fungus (Cryphonectria parasitica) and hypovirus constitute a model system to study fungal pathogenesis and mycovirus-host interaction. Knowledge in this field has been gained largely from investigations at gene transcription level so far. Here we report a systematic analysis of the vesicle proteins of the host fungus with/without hypovirus infection. Thirty-three differentially expressed protein spots were identified in the purified vesicle protein samples by two-dimensional electrophoresis and mass spectrometry. Down-regulated proteins were mostly cargo proteins involved in primary metabolism and energy generation and up-regulated proteins were mostly vesicle associated proteins and ABC transporter. A virus-encoded protein p48 was found to have four forms with different molecular mass in vesicles from the virus-infected strain. While a few of the randomly selected differentially expressed proteins were in accordance with their transcription profiles, majority were not in agreement with their mRNA accumulation patterns, suggesting that an extensive post-transcriptional regulation may have occurred in the host fungus upon a hypovirus infection.