Species-Specific Differences in the Susceptibility of Fungi to the Antifungal Protein AFP Depend on C-3 Saturation of Glycosylceramides

Role of cell membrane homeostasis in the pathogenicity of pathogenic filamentous fungi

The cell membrane forms a fundamental part of all living cells and participates in a variety of physiological processes, such as material exchange, stress response, cell recognition, signal transduction, cellular immunity, apoptosis, and pathogenicity. Here, we review the mechanisms and functions of the membrane structure (lipid components of the membrane and the biosynthesis of unsaturated fatty acids), membrane proteins (transmembrane proteins and proteins contributing to membrane curvature), transcriptional regulation, and cell wall components that influence the virulence and pathogenicity of filamentous fungi.

Novel findings about the mode of action of the antifungal protein PeAfpA against Saccharomyces cerevisiae

Antifungal proteins (AFPs) from filamentous fungi offer the potential to control fungal infections that threaten human health and food safety. AFPs exhibit broad antifungal spectra against harmful fungi, but limited knowledge of their killing mechanism hinders their potential applicability. PeAfpA from Penicillium expansum shows strong antifungal potency against plant and human fungal pathogens and stands above other AFPs for being active against the yeast Saccharomyces cerevisiae. We took advantage of this and used a model laboratory strain of S. cerevisiae to gain insight into the mode of action of PeAfpA by combining (i) transcriptional profiling, (ii) PeAfpA sensitivity analyses of deletion mutants available in the S. cerevisiae genomic deletion collection and (iii) cell biology studies using confocal microscopy. Results highlighted and confirmed the role of the yeast cell wall (CW) in the interaction with PeAfpA, which can be internalized through both energy-dependent and independent mechanisms. The combined results also suggest an active role of the CW integrity (CWI) pathway and the cAMP-PKA signalling in the PeAfpA killing mechanism. Besides, our studies revealed the involvement of phosphatidylinositol metabolism and the participation of ROX3, which codes for the subunit 19 of the RNA polymerase II mediator complex, in the yeast defence strategy. In conclusion, our study provides clues about both the killing mechanism of PeAfpA and the fungus defence strategies against the protein, suggesting also targets for the development of new antifungals. KEY POINTS: • PeAfpA is a cell-penetrating protein with inhibitory activity against S. cerevisiae. • The CW integrity (CWI) pathway is a key player in the PeAfpA killing mechanism. • Phosphatidylinositol metabolism and ROX3 are involved in the yeast defence strategy.

Rationally designed antifungal protein chimeras reveal new insights into structure-activity relationship

Antifungal proteins (AFPs) are promising antimicrobial compounds that represent a feasible alternative to fungicides. Penicillium expansum encodes three phylogenetically distinct AFPs (PeAfpA, PeAfpB and PeAfpC) which show different antifungal profiles and fruit protection effects. To gain knowledge about the structural determinants governing their activity, we solved the crystal structure of PeAfpB and rationally designed five PeAfpA::PeAfpB chimeras (chPeAFPV1-V5). Chimeras showed significant differences in their antifungal activity. chPeAFPV1 and chPeAFPV2 improved the parental PeAfpB potency, and it was very similar to that of PeAfpA. chPeAFPV4 and chPeAFPV5 showed an intermediate profile of activity compared to the parental proteins while chPeAFPV3 was inactive towards most of the fungi tested. Structural analysis of the chimeras evidenced an identical scaffold to PeAfpB, suggesting that the differences in activity are due to the contributions of specific residues and not to induced conformational changes or structural rearrangements. Results suggest that mannoproteins determine protein interaction with the cell wall and its antifungal activity while there is not a direct correlation between binding to membrane phospholipids and activity. This work provides new insights about the relevance of sequence motifs and the feasibility of modifying protein specificity, opening the door to the rational design of chimeras with biotechnological applicability.

The Epichloë festucae Antifungal Protein Efe-AfpA Protects Creeping Bentgrass (Agrostis stolonifera) from the Plant Pathogen Clarireedia jacksonii, the Causal Agent of Dollar Spot Disease

Dollar spot disease, caused by the fungal pathogen Clarireedia jacksonii, is a major problem in many turfgrass species, particularly creeping bentgrass (Agrostis stolonifera). It is well-established that strong creeping red fescue (Festuca rubra subsp. rubra) exhibits good dollar spot resistance when infected by the fungal endophyte Epichloë festucae. This endophyte-mediated disease resistance is unique to the fine fescues and has not been observed in other grass species infected with other Epichloë spp. The mechanism underlying the unique endophyte-mediated disease resistance in strong creeping red fescue has not yet been established. We pursued the possibility that it may be due to the presence of an abundant secreted antifungal protein produced by E. festucae. Here, we compare the activity of the antifungal protein expressed in Escherichia coli, Pichia pastoris, and Penicillium chrysogenum. Active protein was recovered from all systems, with the best activity being from Pe. chrysogenum. In greenhouse assays, topical application of the purified antifungal protein to creeping bentgrass and endophyte-free strong creeping red fescue protected the plants from developing severe symptoms caused by C. jacksonii. These results support the hypothesis that Efe-AfpA is a major contributor to the dollar spot resistance observed with E. festucae-infected strong creeping red fescue in the field, and that this protein could be developed as an alternative or complement to fungicides for the management of this disease on turfgrasses.

Single-Molecule Real-Time Sequencing to Explore the Mycobiome Diversity in Malt

This study determined the composition of fungal communities and characterized the enriched fungal species in raw and roasted malts via the third-generation PacBio-based full-length single-molecule real-time (SMRT) sequencing of the full-length amplicon of the internal transcribed spacer (ITS) region. In total, one kingdom, six phyla, 23 classes, 56 orders, 120 families, 188 genera, 333 species, and 780 operational taxonomic units (OTUs) were detected with satisfactory sequencing depth and sample size. Wickerhamomyces (56%), Cyberlindnera (15%), Dipodascus (12%), and Candida (6.1%) were characterized as the dominant genera in the raw malts, and Aspergillus (35%), Dipodascus (21%), Wickerhamomyces (11%), and Candida (3.5%) in the roasted malts. Aspergillus proliferans, Aspergillus penicillioides, and Wickerhamomyces anomalus represented the crucial biomarkers causing intergroup differences. Correlation analysis regarding environmental factors indicated that the water activity (a_w) of the samples affected the composition of the fungal communities in the malts. In practice, special attention should be paid to the mycotoxin-producing fungi, as well as other fungal genera that are inversely correlated with their growth, to ensure the safe use of malt and its end products.

IMPORTANCE Fungal contamination and secondary metabolite accumulation in agricultural products represent a global food safety challenge. Although high-throughput sequencing (HTS) is beneficial for explaining fungal communities, it presents disadvantages, such as short reads, species-level resolution, and uncertain identification. This work represents the first attempt to characterize the fungal community diversity, with a particular focus on mycotoxin-producing fungi, in malt via the third-generation PacBio-based full-length SMRT sequencing of the ITS region, aiming to explore and compare the differences between the fungal communities of raw and roasted malts. The research is beneficial for developing effective biological control and conservation measures, including improving the roasting conditions, monitoring the environmental humidity and a_w, and effectively eliminating and degrading fungi in the industry chain according to the diverse fungal communities determined, for the safe use of malts and their end products, such as beers. In addition, the third-generation SMRT sequencing technology allows highly efficient analysis of fungal community diversity in complex matrices, yielding fast, high-resolution long reads at the species level. It can be extended to different research fields, updating modern molecular methodology and bioinformatics databases.

Structure-Activity Predictions From Computational Mining of Protein Databases to Assist Modular Design of Antimicrobial Peptides

Antimicrobial peptides (AMPs) are naturally produced by pro- and eukaryotes and are promising alternatives to antibiotics to fight multidrug-resistant microorganisms. However, despite thousands of AMP entries in respective databases, predictions about their structure-activity relationships are still limited. Similarly, common or dissimilar properties of AMPs that have evolved in different taxonomic groups are nearly unknown. We leveraged data entries for 10,987 peptides currently listed in the three antimicrobial peptide databases APD, DRAMP and DBAASP to aid structure-activity predictions. However, this number reduced to 3,828 AMPs that we could use for computational analyses, due to our stringent quality control criteria. The analysis uncovered a strong bias towards AMPs isolated from amphibians (1,391), whereas only 35 AMPs originate from fungi (0.9%), hindering evolutionary analyses on the origin and phylogenetic relationship of AMPs. The majority (62%) of the 3,828 AMPs consists of less than 40 amino acids but with a molecular weight higher than 2.5 kDa, has a net positive charge and shares a hydrophobic character. They are enriched in glycine, lysine and cysteine but are depleted in glutamate, aspartate and methionine when compared with a peptide set of the same size randomly selected from the UniProt database. The AMPs that deviate from this pattern (38%) can be found in different taxonomic groups, in particular in Gram-negative bacteria. Remarkably, the γ-core motif claimed so far as a unifying structural signature in cysteine-stabilised AMPs is absent in nearly 90% of the peptides, questioning its relevance as a prerequisite for antimicrobial activity. The disclosure of AMPs pattern and their variation in producing organism groups extends our knowledge of the structural diversity of AMPs and will assist future peptide screens in unexplored microorganisms. Structural design of peptide antibiotic drugs will benefit using natural AMPs as lead compounds. However, a reliable and statistically balanced database is missing which leads to a large knowledge gap in the AMP field. Thus, thorough evaluation of the available data, mitigation of biases and standardised experimental setups need to be implemented to leverage the full potential of AMPs for drug development programmes in the clinics and agriculture.

Effect of Fomes fomentarius Cultivation Conditions on Its Adsorption Performance for Anionic and Cationic Dyes

Lab-cultivated mycelia of Fomes fomentarius (FF), grown on a solid lignocellulose medium (FF-SM) and a liquid glucose medium (FF-LM), and naturally grown fruiting bodies (FF-FB) were studied as biosorbents for the removal of organic dyes methylene blue and Congo red (CR). Both the chemical and microstructural differences were revealed using X-ray photoelectron spectroscopy, Fourier-transform infrared spectroscopy, zeta potential analysis, and scanning electron microscopy, illuminating the superiority of FF-LM and FF-SM over FF-FB in dye adsorption. The adsorption process of CR on FF-LM and FF-SM is best described by the Redlich-Peterson model with β constants close to 1, that is, approaching the monolayer Langmuir model, which reach maximum adsorption capacities of 48.8 and 13.4 mg g^-1, respectively, in neutral solutions. Adsorption kinetics follow the pseudo-second-order model where chemisorption is the rate-controlling step. While the desorption efficiencies were low, adsorption performances were preserved and even enhanced under simulated dye effluent conditions. The results suggest that F. fomentarius can be considered an attractive biosorbent in industrial wastewater treatment and that its cultivation conditions can be specifically tailored to tune its cell wall composition and adsorption performance.

Inhibition of Serine Protease, α-Amylase and Growth of Phytopathogenic Fungi by Antimicrobial Peptides from Capsicum chinense Fruits

Plant fungal diseases cause major problems for the global economy. Antimicrobial peptides have aroused great interest in the control of phytopathogens, as they are natural molecules and have a broad spectrum of inhibitory activity. Herein, we have tried to identify and characterize antimicrobial peptides present in fruits of Capsicum chinense and to evaluate their enzymatic and antifungal activities. The retained fraction obtained in the anion exchange chromatography with strong antifungal activity was subjected to molecular exclusion chromatography and obtained four fractions named G1, G2, G3, and G4. The 6.0-kDa protein band of G2 showed similarity with protease inhibitors type II, and it was able to inhibit 100% of trypsin and α-amylase activities. The protein band with approximately 6.5 kDa of G3 showed similarity with sequences of protease inhibitors from genus Capsicum and showed growth inhibition of 48% for Colletotrichum lindemuthianum, 49% for Fusarium lateritium, and 51% for F. solani and F. oxysporum. Additionally, G3 causes morphological changes, membrane permeabilization, and ROS increase in F. oxysporum cells. The 9-kDa protein band of G4 fraction was similar to a nsLTP type 1, and a protein band of 6.5 kDa was similar to a nsLTP type 2. The G4 fraction was able to inhibit 100% of the activities of glycosidases tested and showed growth inhibition of 35 and 50% of F. oxysporum and C. lindemuthianum, respectively. C. chinense fruits have peptides with antifungal activity and enzyme inhibition with biotechnological potential.

Membrane-Interacting Antifungal Peptides

The incidence of invasive fungal infections is increasing worldwide, resulting in more than 1.6 million deaths every year. Due to growing antifungal drug resistance and the limited number of currently used antimycotics, there is a clear need for novel antifungal strategies. In this context, great potential is attributed to antimicrobial peptides (AMPs) that are part of the innate immune system of organisms. These peptides are known for their broad-spectrum activity that can be directed toward bacteria, fungi, viruses, and/or even cancer cells. Some AMPs act via rapid physical disruption of microbial cell membranes at high concentrations causing cell leakage and cell death. However, more complex mechanisms are also observed, such as interaction with specific lipids, production of reactive oxygen species, programmed cell death, and autophagy. This review summarizes the structure and mode of action of antifungal AMPs, thereby focusing on their interaction with fungal membranes.

Differential susceptibility of mycotoxin-producing fungi to distinct antifungal proteins (AFPs)

The global challenge to prevent fungal spoilage and mycotoxin contamination on foods and feeds require the development of new antifungal strategies. Filamentous fungi encode diverse antifungal proteins (AFPs), which offer a great potential for the control of contaminant fungi. In this study, four AFPs from Penicillium digitatum (PdAfpB) and Penicillium expansum (PeAfpA, PeAfpB and PeAfpC) belonging to classes A, B and C, were tested against a representative panel of mycotoxin-producing fungi. They included a total of 38 strains representing 32 different species belonging to the genera Alternaria, Aspergillus, Byssochlamys, Fusarium and Penicillium. PeAfpA exhibited a potent antifungal activity, since the growth of all tested fungi was completely inhibited by concentrations ranging from 0.5 to 16 μg/mL. PdAfpB and PeAfpB, although less effective than PeAfpA, showed significant activity against most of the mycotoxigenic fungi tested. Importantly, PeAfpC previously described as inactive, showed a powerful inhibition against B. spectabilis strains, which are important spoilage and mycotoxin fungi in pasteurized foods. Although less effective than in liquid media, AFPs affected fungal growth on solid media. This study also underlines the potential of these AFPs, in particular PeAfpA, as future antifungal agents for applications in foods, on growing crops or during postharvest storage.

The Antifungal Protein AfpB Induces Regulated Cell Death in Its Parental Fungus Penicillium digitatum

Disease-causing fungi pose a serious threat to human health and food safety and security. The limited number of licensed antifungals, together with the emergence of pathogenic fungi with multiple resistance to available antifungals, represents a serious challenge for medicine and agriculture. Therefore, there is an urgent need for new compounds with high fungal specificity and novel antifungal mechanisms. Antifungal proteins in general, and AfpB from Penicillium digitatum in particular, are promising molecules for the development of novel antifungals. This study on AfpB’s mode of action demonstrates its potent, specific fungicidal activity through the interaction with multiple targets, presumably reducing the risk of evolving fungal resistance, and through a regulated cell death process, uncovering this protein as an excellent candidate for a novel biofungicide. The in-depth knowledge on AfpB mechanistic function presented in this work is important to guide its possible future clinical and agricultural applications.

Filamentous fungi produce small cysteine-rich proteins with potent, specific antifungal activity, offering the potential to fight fungal infections that severely threaten human health and food safety and security. The genome of the citrus postharvest fungal pathogen Penicillium digitatum encodes one of these antifungal proteins, namely AfpB. Biotechnologically produced AfpB inhibited the growth of major pathogenic fungi at minimal concentrations, surprisingly including its parental fungus, and conferred protection to crop plants against fungal infections. This study reports an in-depth characterization of the AfpB mechanism of action, showing that it is a cell-penetrating protein that triggers a regulated cell death program in the target fungus. We prove the importance of AfpB interaction with the fungal cell wall to exert its killing activity, for which protein mannosylation is required. We also show that the potent activity of AfpB correlates with its rapid and efficient uptake by fungal cells through an energy-dependent process. Once internalized, AfpB induces a transcriptional reprogramming signaled by reactive oxygen species that ends in cell death. Our data show that AfpB activates a self-injury program, suggesting that this protein has a biological function in the parental fungus beyond defense against competitors, presumably more related to regulation of the fungal population. Our results demonstrate that this protein is a potent antifungal that acts through various targets to kill fungal cells through a regulated process, making AfpB a promising compound for the development of novel biofungicides with multiple fields of application in crop and postharvest protection, food preservation, and medical therapies.

IMPORTANCE Disease-causing fungi pose a serious threat to human health and food safety and security. The limited number of licensed antifungals, together with the emergence of pathogenic fungi with multiple resistance to available antifungals, represents a serious challenge for medicine and agriculture. Therefore, there is an urgent need for new compounds with high fungal specificity and novel antifungal mechanisms. Antifungal proteins in general, and AfpB from Penicillium digitatum in particular, are promising molecules for the development of novel antifungals. This study on AfpB’s mode of action demonstrates its potent, specific fungicidal activity through the interaction with multiple targets, presumably reducing the risk of evolving fungal resistance, and through a regulated cell death process, uncovering this protein as an excellent candidate for a novel biofungicide. The in-depth knowledge on AfpB mechanistic function presented in this work is important to guide its possible future clinical and agricultural applications.