Fighting pathogenic yeasts with plant defensins and anti-fungal proteins from fungi

Recent Advances in the Development of Antifungal Agents: Beyond Azoles, Polyenes, and Echinocandins

The escalating incidence of antimicrobial resistance to antifungal agents, alongside the emergence of drug-resistant fungal strains, constitutes a significant threat to a potential global fungal pandemic. In response, researchers are intensifying efforts to identify novel antifungal compounds through diverse methodologies. Emerging strategies focus on innovative therapeutic targets that may reduce the risk of resistance development while offering broad-spectrum efficacy against fungal infections. Additionally, these approaches present potential cost-effectiveness and accelerated development timelines. This review systematically categorizes a range of novel antifungal compounds, including antifungal peptides, cationic amphiphiles, small molecules, polymers, and repurposed drugs, based on their efficacy in inhibiting fungal growth and associated virulence factors. These compounds exhibit notable antimicrobial activity across in silico, in vitro, and in vivo systems against various pathogenic fungal strains, with several showing substantial promise for clinical application. Furthermore, the review highlights the limitations of standard antifungals and elucidates the mechanisms by which fungal strains develop resistance. This work aims to engage researchers in the distinctive field of fungal biology and foster the exploration of new antifungal strategies.

Identification of the Plant Defensin (MsPDF) Gene Family in Medicago sativa and Analysis of Expression Patterns Under Abiotic Stress

Medicago sativa L. (alfalfa) is a major forage crop due to its high yield and stress resilience. However, its growth and productivity are often compromised by abiotic stresses, including cold, drought, and salinity. The plant defensin (PDF) gene family plays a crucial role in resistance to abiotic stress. In this study, a total of 11 MsPDF gene family members were identified in the alfalfa genome and classified into three groups. Phylogenetic and conserved motif analyses revealed that the MsPDF genes are highly conserved. Promoter analysis, gene regulatory network analysis (GRN), and gene ontology (GO)-enrichment analyses were used to infer the potential functions of MsPDF genes. The results showed that the gene actively responds to abiotic stress, participates in phytohormonal responses, and regulates plant growth and development through gene interactions. Transcriptome and qRT-PCR analyses showed that most of the MsPDF genes were significantly up-regulated under cold, drought, and salinity stresses. Among them, the MsPDF03 exhibited superior performance under cold stress. The MsPDF04, MsPDF08, and MsPDF09 genes were able to respond positively to drought and salt stresses. Finally, the monomeric, dimeric, and tetrameric structures of the proteins encoded by the MsPDF genes were predicted using AlphaFold 2 software. This study lays the foundation for the identification and evolutionary relationship analysis of the MsPDF gene family, and provides a new reference for subsequent research on abiotic stress resistance.

ML-AMPs designed through machine learning show antifungal activity against C. albicans and therapeutic potential on mice model with candidiasis

AIMS

C. albicans resistant strains have led to increasingly severe treatment challenges. Antimicrobial peptides with low resistance-inducing propensity for pathogens have been developed. A series of antimicrobial peptides de novo designed through machine learning by our research team were named ML-AMPs. In the present research, the antifungal activity of ML-AMPs against C. albicans and its therapeutic potential on Candidiasis mice model were studied.

MAIN METHODS

MTT methodology was performed to measure the minimum inhibitory concentrations. Absorbance photometry was utilized to evaluate the erythrocyte toxicity. Optical microscopy was operated to observe C. albicans hyphae. Crystal violet staining was employed to assess biofilm inhibition and reduction. Colony counting was performed to determine the time-kill kinetics. Scanning electron microscopy and fluorescent staining were used to investigate the underlying mechanism of antifungal action. Candidiasis mice model was established to evaluate the in vivo efficacy of ML-AMP2.

KEY FINDINGS

ML-AMPs exhibited strong anti-Candida activity, with minimum inhibitory concentrations against C. albicans ranging from 3.85 to 12.37 μg/mL. Notably, they exhibited robust fungicidal effects on fluconazole-resistant C. albicans. Moreover, they exhibited fast-killing kinetics, as well as low resistance potential. Additionally, ML-AMPs could effectively inhibit the formation of mycelium and biofilm, and more prominently, their ability to reduce biofilm was higher than that of fluconazole. ML-AMPS increased the permeability of C. albicans cell membrane and induced ROS accumulation. Among ML-AMPs, ML-AMP2 performed the best, which promoted the recovery of Candidiasis mice model.

SIGNIFICANCE

ML-AMP2 holds great promise as a candidate molecule for effectively treating drug-resistant C. albicans infections.

Effects of the Tobacco Defensin NaD1 Against Susceptible and Resistant Strains of Candida albicans

Today, Candida albicans is still the most common cause of both local and life-threatening systemic candidiasis. The spread of resistant fungal strains has resulted in an urgent need to search for new promising antimycotics. Here, we investigated the antifungal action of the tobacco defensin NaD1 against susceptible and resistant to azoles and echinocandins strains of C. albicans. We demonstrated that NaD1 was equally effective and fungicidal against all tested strains. The MIC and MFC values were 6.25 and 12.5 µM, respectively. We showed for the first time that NaD1 could act synergistically not only with caspofungin but also with human host defense antimicrobial peptides cathelicidin LL-37 and β-defensin-2 (HBD2) against susceptible and resistant fungal strains. Using flow cytometry, we demonstrated that NaD1 in combinations with LL-37 or HBD2 can reinforce each other by enhancing membrane disruption. Using the Caco-2 cell monolayer model, we demonstrated that NaD1 impaired the adhesion of C. albicans cells to the human epithelium. Moreover, NaD1 inhibited the formation of fungal biofilms in Sabouraud broth and less markedly in nutrient-rich RPMI-1640 medium, and enhanced the antibiofilm activity of caspofungin. Thus, we hypothesized that NaD1 might affect the development of candidiasis in vivo, including that caused by resistant fungal strains.

Dynamics of interaction and internalisation of the antifungal protein PeAfpA into Penicillium digitatum morphotypes

Antifungal proteins (AFPs) as the highly active PeAfpA from Penicillium expansum or PdAfpB from Penicillium digitatum exert promising antifungal activity, but their mode of action is not fully understood. We characterised the interaction of PeAfpA against P. digitatum, comparing it to the less active PdAfpB. Despite similar effect on conidia germination, PeAfpA did not induce a burst of reactive oxygen species as PdAfpB. Live-cell fluorescence microscopy revealed complex dynamics of interaction and internalisation of both proteins with distinct P. digitatum morphotypes (quiescent conidia, swollen conidia, germlings and hyphae). Labelled PeAfpA co-localised at the cell wall of quiescent conidia, where its localisation was punctate and not uniformly distributed. This pattern changed during germination to a uniform distribution with increased intensity. Conidia from mutants of genes involved in melanin biosynthesis (pksP/alb1 or arp2) showed an altered distribution of PeAfpA but later mimicked the wild type trend of changes during germination. In swollen conidia and germlings, PeAfpA remained attached to the cell wall. In hyphae, PeAfpA was internalised through the growing hyphal tip after binding to the cell wall, in a non-endocytic but energy-dependent process that caused vacuolisation, which preceded cell death. These results may help the development of biofungicides based on AFPs.

Navigating the fungal battlefield: cysteine-rich antifungal proteins and peptides from Eurotiales

Fungi are ubiquitous in the environment and play a key role in the decomposition and recycling of nutrients. On the one hand, their special properties are a great asset for the agricultural and industrial sector, as they are used as source of nutrients, producers of enzymes, pigments, flavorings, and biocontrol agents, and in food processing, bio-remediation and plant growth promotion. On the other hand, they pose a serious challenge to our lives and the environment, as they are responsible for fungal infections in plants, animals and humans. Although host immunity opposes invading pathogens, certain factors favor the manifestation of fungal diseases. The prevalence of fungal infections is on the rise, and there is an alarming increase in the resistance of fungal pathogens to approved drugs. The limited number of antimycotics, the obstacles encountered in the development of new drugs due to the poor tolerability of antifungal agents in patients, the limited number of unique antifungal targets, and the low species specificity contribute to the gradual depletion of the antifungal pipeline and newly discovered antifungal drugs are rare. Promising candidates as next-generation therapeutics are antimicrobial proteins and peptides (AMPs) produced by numerous prokaryotic and eukaryotic organisms belonging to all kingdom classes. Importantly, filamentous fungi from the order Eurotiales have been shown to be a rich source of AMPs with specific antifungal activity. A growing number of published studies reflects the efforts made in the search for new antifungal proteins and peptides (AFPs), their efficacy, species specificity and applicability. In this review, we discuss important aspects related to fungi, their impact on our life and issues involved in treating fungal infections in plants, animals and humans. We specifically highlight the potential of AFPs from Eurotiales as promising alternative antifungal therapeutics. This article provides insight into the structural features, mode of action, and progress made toward their potential application in a clinical and agricultural setting. It also identifies the challenges that must be overcome in order to develop AFPs into therapeutics.

Increasing the efficiency of CRISPR/Cas9-mediated genome editing in the citrus postharvest pathogen Penicillium digitatum

BACKGROUND

Penicillium digitatum is a fungal plant pathogen that causes the green mold disease in harvested citrus fruits. Due to its economical relevance, many efforts have focused on the development of genetic engineering tools for this fungus. Adaptation of the CRISPR/Cas9 technology was previously accomplished with self-replicative AMA1-based plasmids for marker-free gene editing, but the resulting efficiency (10%) limited its practical implementation. In this study, we aimed to enhance the efficiency of the CRISPR/Cas9-mediated gene editing in P. digitatum to facilitate its practical use.

RESULTS

Increasing the culture time by performing additional culture streaks under selection conditions in a medium that promotes slower growth rates significantly improved the gene editing efficiency in P. digitatum up to 54-83%. To prove this, we disrupted five candidate genes that were chosen based on our previous high-throughput gene expression studies aimed at elucidating the transcriptomic response of P. digitatum to the antifungal protein PdAfpB. Two of these genes lead to visual phenotypic changes (PDIG_53730/pksP, and PDIG_54100/arp2) and allowed to start the protocol optimization. The other three candidates (PDIG_56860, PDIG_33760/rodA and PDIG_68680/dfg5) had no visually associated phenotype and were targeted to confirm the high efficiency of the protocol.

CONCLUSION

Genome editing efficiency of P. digitatum was significantly increased from 10% to up to 83% through the modification of the selection methodology, which demonstrates the feasibility of the CRISPR/Cas9 system for gene disruption in this phytopathogenic fungus. Moreover, the approach described in this study might help increase CRISPR/Cas9 gene editing efficiencies in other economically relevant fungal species for which editing efficiency via CRISPR/Cas9 is still low.