Quantitative proteomics reveals new insights into calcium-mediated resistance mechanisms in Aspergillus flavus against the antifungal protein PgAFP in cheese

Screening Microbial Interactions During Inulin Utilization Reveals Strong Competition and Proteomic Changes in Lacticaseibacillus paracasei M38

Competition for resources is a common microbial interaction in the gut microbiome. Inulin is a well-studied prebiotic dietary fiber that profoundly shapes gut microbiome composition. Several community members and some probiotics, such as Lacticaseibacillus paracasei, deploy multiple molecular strategies to access fructans. In this work, we screened bacterial interactions during inulin utilization in representative gut microbes. Unidirectional and bidirectional assays were used to evaluate the effects of microbial interactions and global proteomic changes on inulin utilization. Unidirectional assays showed the total or partial consumption of inulin by many gut microbes. Partial consumption was associated with cross-feeding of fructose or short oligosaccharides. However, bidirectional assays showed strong competition from L. paracasei M38 against other gut microbes, reducing the growth and quantity of proteins found in the latter. L. paracasei dominated and outcompeted other inulin utilizers, such as Ligilactobacillus ruminis PT16, Bifidobacterium longum PT4, and Bacteroides fragilis HM714. The importance of strain-specific characteristics of L. paracasei, such as its high fitness for inulin consumption, allows it to be favored for bacterial competence. Proteomic studies indicated an increase in inulin-degrading enzymes in co-cultures, such as β-fructosidase, 6-phosphofructokinase, the PTS D-fructose system, and ABC transporters. These results reveal that intestinal metabolic interactions are strain-dependent and might result in cross-feeding or competition depending on total or partial consumption of inulin. Partial degradation of inulin by certain bacteria favors coexistence. However, when L. paracasei M38 totally degrades the fiber, this does not happen. The synergy of this prebiotic with L. paracasei M38 could determine the predominance in the host as a potential probiotic.

Proteomic analyses of Bacteroides ovatus and Bifidobacterium longum in xylan bidirectional culture shows sugar cross-feeding interactions

The intestinal microbiome is a community of anaerobic microorganisms whose activities significantly impact human health. Its composition can be modulated by consuming foods rich in dietary fiber, such as xylan, a complex polysaccharide that can be considered an emerging prebiotic. In this work, we evaluated how certain gut bacteria acted as primary degraders, fermenting dietary fibers, and releasing metabolites that other bacteria can further use. Different bacterial strains of Lactobacillus, Bifidobacterium, and Bacteroides were evaluated for their ability to consume xylan and interact with one another. Results from unidirectional assays gave indications of possible cross-feeding between bacteria using xylan as a carbon source. Bidirectional assays showed that Bifidobacterium longum PT4 increased its growth in the presence of Bacteroides ovatus HM222. Proteomic analyses indicated that B. ovatus HM222 synthesizes enzymes facilitating xylan degradation, such as β-xylanase, arabinosidase, L-arabinose isomerase, and xylosidase. Interestingly, the relative abundance of these proteins remains largely unaffected in the presence of Bifidobacterium longum PT4. In the presence of B. ovatus, B. longum PT4 increased the production of enzymes such as α-L-arabinosidase, L-arabinose isomerase, xylulose kinase, xylose isomerase, and sugar transporters. These results show an example of positive interaction between bacteria mediated by xylan consumption. Bacteroides degraded this substrate to release xylooligosaccharides, or monosaccharides (xylose, arabinose), which might support the growth of secondary degraders such as B. longum.

Valorization of Soybean Residue (Okara) by Supercritical Carbon Dioxide Extraction: Compositional, Physicochemical, and Functional Properties of Oil and Defatted Powder

In the context of food waste valorization, the purpose of this study is to demonstrate the complete valorization of soybean residue (okara) through supercritical carbon dioxide extraction (SCE). Okara oil (OKO) was separated from full-fat powder (FFP) using SCE with and without ethanol (EtOH) as a cosolvent. The kinetics of extraction, chemical composition, and physicochemical, functional, and health-promoting properties of OKO and defatted powder (DFP) were determined. The process yielded 18.5% oil after 450 min. The soluble dietary fiber and protein of the DFP increased significantly; its water and oil absorption capacities increased despite the decrease in swelling capacity corresponding to particle size reduction. The OKO was rich in linoleic and oleic acids, with a ratio of ω6-to-ω3 fatty acids = 9.53, and EtOH increased its phenolic content (0.45 mg GAE/g), aglycone content (239.6 μg/g), and antioxidant capacity (0.195 mg TE/g). The DFP paste showed gel-like consistency and shear-thinning flow behavior, whereas the OKO showed characteristic transition of the product and affected lubrication at contact zones. Both fractions showed potential as food ingredients based on their nutritional and functional properties, as well as the capability of modifying the microstructure of a model food system.

Deciphering the underlying mechanisms of the oxidative perturbations and impaired meat quality in Wooden breast myopathy by label-free quantitative MS-based proteomics

The study aimed to investigate biochemical mechanisms occurred in Wooden breast (WB) chicken meat, with attention to the impact on meat quality. Commercial chicken breasts were classified as Normal (N, n = 12), WB-M (moderate degree; focal hardness on cranial region, n = 12) and WB-S (severe degree; extreme and diffused hardness over the entire surface, n = 12). Samples were analyzed for physico-chemical properties, oxidative damage to lipids and proteins, and discriminating sarcoplasmic proteins by using a Q-Exactive mass spectrometer. WB meat presented impaired composition and functionality and higher levels of lipid and protein oxidation markers than N meat. The proteomic profile of WB-S presents a dynamic regulation of the relevant proteins involved in redox homeostasis, carbohydrate, protein and lipid metabolisms. Proteomics results demonstrate that the physiological and metabolic processes of muscles affected by WB myopathy are involved in combating the inflammatory process and in repairing the damaged tissue by oxidative stress.

Synergistic Effect of Combination of Various Microbial Hurdles in the Biopreservation of Meat and Meat Products—Systematic Review

The control of spoilage microorganisms and foodborne pathogens in meat and meat products is a challenge for food producers, which potentially can be overcome through the combined use of biopreservatives, in the form of a mix of various microbial hurdles. The objective of this work is to systematically review the available knowledge to reveal whether various microbial hurdles applied in combination can pose an effective decontamination strategy for meat and meat products. PubMed, Web of Science, and Scopus were utilized to identify and evaluate studies through February 2023. Search results yielded 45 articles that met the inclusion criteria. The most common meat biopreservatives were combinations of various starter cultures (24 studies), and the use of mixtures of non-starter protective cultures (13 studies). In addition, studies evaluating antimicrobial combinations of bacteriocins with other bacteriocins, BLIS (bacteriocin-like inhibitory substance), non-starter protective cultures, reuterin, and S-layer protein were included in the review (7 studies). In one study, a biopreservative mixture comprised antifungal protein PgAFP and protective cultures. The literature search revealed a positive effect, in most of the included studies, of the combination of various bacterial antimicrobials in inhibiting the growth of pathogenic and spoilage bacteria in meat products. The main advantages of the synergistic effect achieved were: (1) the induction of a stronger antimicrobial effect, (2) the extension of the spectrum of antibacterial action, and (3) the prevention of the regrowth of undesirable microorganisms. Although further research is required in this area, the combination of various microbial hurdles can pose a green and valuable biopreservation approach for maintaining the safety and quality of meat products.

Proteomics as a New-Generation Tool for Studying Moulds Related to Food Safety and Quality

Mould development in foodstuffs is linked to both spoilage and the production of mycotoxins, provoking food quality and food safety concerns, respectively. The high-throughput technology proteomics applied to foodborne moulds is of great interest to address such issues. This review presents proteomics approaches useful for boosting strategies to minimise the mould spoilage and the hazard related to mycotoxins in food. Metaproteomics seems to be the most effective method for mould identification despite the current problems related to the bioinformatics tool. More interestingly, different high resolution mass spectrometry tools are suitable for evaluating the proteome of foodborne moulds able to unveil the mould's response under certain environmental conditions and the presence of biocontrol agents or antifungals, being sometimes combined with a method with limited ability to separate proteins, the two-dimensional gel electrophoresis. However, the matrix complexity, the high ranges of protein concentrations needed and the performing of multiple steps are some of the proteomics limitations for the application to foodborne moulds. To overcome some of these limitations, model systems have been developed and proteomics applied to other scientific fields, such as library-free data independent acquisition analyses, the implementation of ion mobility, and the evaluation of post-translational modifications, are expected to be gradually implemented in this field for avoiding undesirable moulds in foodstuffs.

Effects of antifungal agents on the fungal proteome: informing on mechanisms of sensitivity and resistance

INTRODUCTION

Antifungal agents are essential in the fight against serious fungal disease, however emerging resistance is threatening an already limited collection of therapeutics. Proteomic analyses of effects of antifungal agents can expand our understanding of multifactorial mechanisms of action and have also proven valuable to elucidate proteomic changes associated with antifungal resistance.

AREAS COVERED

This review covers the application of proteomic techniques to examine sensitivity and resistance to antifungals including commonly used therapeutics, amphotericin B, echinocandins and the azoles, based predominantly on studies involving Aspergillus fumigatus, Candida albicans and Candida glabrata from the last 10 years. In addition, non-clinical antimicrobial agents are also discussed, which highlight the potential of proteomics to identify new antifungal targets.

EXPERT COMMENTARY

Fungal proteomics has evolved in the last decade with increased genome availability and developments in mass spectrometry. Collectively, these have led to the advancement of proteomic techniques, allowing increased coverage of the proteome. Gel-based proteomics laid the foundation for these types of studies, which has now shifted to the more powerful gel-free proteomics. This has resulted in the identification of key mediators and potential biomarkers of antifungal resistance, as well as elucidating the mechanisms of action of novel and established antifungal agents.

Biological Control and Mitigation of Aflatoxin Contamination in Commodities

Aflatoxins (AFs) are toxic secondary metabolites produced mostly by Aspergillus species. AF contamination entering the feed and food chain has been a crucial long-term issue for veterinarians, medicals, agroindustry experts, and researchers working in this field. Although different (physical, chemical, and biological) technologies have been developed, tested, and employed to mitigate the detrimental effects of mycotoxins, including AFs, universal methods are still not available to reduce AF levels in feed and food in the last decades. Possible biological control by bacteria, yeasts, and fungi, their excretes, the role of the ruminal degradation, pre-harvest biocontrol by competitive exclusion or biofungicides, and post-harvest technologies and practices based on biological agents currently used to alleviate the toxic effects of AFs are collected in this review. Pre-harvest biocontrol technologies can give us the greatest opportunity to reduce AF production on the spot. Together with post-harvest applications of bacteria or fungal cultures, these technologies can help us strictly reduce AF contamination without synthetic chemicals.

Transcriptome Sequencing Revealed an Inhibitory Mechanism of Aspergillus flavus Asexual Development and Aflatoxin Metabolism by Soy-Fermenting Non-Aflatoxigenic Aspergillus

Aflatoxins (AFs) have always been regarded as the most effective carcinogens, posing a great threat to agriculture, food safety, and human health. Aspergillus flavus is the major producer of aflatoxin contamination in crops. The prevention and control of A. flavus and aflatoxin continues to be a global problem. In this study, we demonstrated that the cell-free culture filtrate of Aspergillus oryzae and a non-aflatoxigenic A. flavus can effectively inhibit the production of AFB1 and the growth and reproduction of A. flavus, indicating that both of the non-aflatoxigenic Aspergillus strains secrete inhibitory compounds. Further transcriptome sequencing was performed to analyze the inhibitory mechanism of A. flavus treated with fermenting cultures, and the results revealed that genes involved in the AF biosynthesis pathway and other biosynthetic gene clusters were significantly downregulated, which might be caused by the reduced expression of specific regulators, such as AflS, FarB, and MtfA. The WGCNA results further revealed that genes involved in the TCA cycle and glycolysis were potentially involved in aflatoxin biosynthesis. Our comparative transcriptomics also revealed that two conidia transcriptional factors, brlA and abaA, were found to be significantly downregulated, which might lead to the downregulation of conidiation-specific genes, such as the conidial hydrophobins genes rodA and rodB. In summary, our research provides new insights for the molecular mechanism of controlling AF synthesis to control the proliferation of A. flavus and AF pollution.

Biofungicidal Potential of Neosartorya (Aspergillus) Fischeri Antifungal Protein NFAP and Novel Synthetic γ-Core Peptides

Because of enormous crop losses worldwide due to pesticide-resistant plant pathogenic fungi, there is an increasing demand for the development of novel antifungal strategies in agriculture. Antifungal proteins (APs) and peptides are considered potential biofungicides; however, several factors limit their direct agricultural application, such as the high cost of production, narrow antifungal spectrum, and detrimental effects to plant development and human/animal health. This study evaluated the safety of the application of APs and peptides from the ascomycete Neosartorya fischeri as crop preservatives. The full-length N. fischeri AP (NFAP) and novel rationally designed γ-core peptide derivatives (PDs) γNFAP-opt and γNFAP-optGZ exhibited efficacy by inhibiting the growth of the agriculturally relevant filamentous ascomycetes in vitro. A high positive net charge, however, neither the hydrophilicity nor the primary structure supported the antifungal efficacy of these PDs. Further testing demonstrated that the antifungal activity did not require a conformational change of the β-pleated NFAP or the canonically ordered conformation of the synthetic PDs. Neither hemolysis nor cytotoxicity was observed when the NFAP and γNFAP-opt were applied at antifungally effective concentrations in human cell lines. Similarly, the Medicago truncatula plants that served as toxicity model and were grown from seedlings that were treated with NFAP, γNFAP-opt, or γNFAP-optGZ failed to exhibit morphological aberrations, reduction in primary root length, or the number of lateral roots. Crop protection experiments demonstrated that NFAP and associated antifungal active γ-core PDs were able to protect tomato fruits against the postharvest fungal pathogen Cladosporium herbarum.

Evaluation of the activity of the antifungal PgAFP protein and its producer mould against Penicillium spp postharvest pathogens of citrus and pome fruits

Postharvest fungal diseases are among the main causes of fresh fruit losses. Chemical control is against claims for "natural" or "chemical-free" products. Biocontrol agents, such as antifungal proteins or their producing moulds, may serve to combat unwanted pathogens. Since the effectiveness of these bioprotective agents depends on the food substrate, their effect must be tested on fruits. The objective of this work was to study the effect of the antifungal protein PgAFP and its producer, Penicillium chrysogenum, against Penicillium expansum and Penicillium digitatum growth on apple and oranges respectively, and the PgAFP effect on eleven P. expansum, Penicillium italicum, and P. digitatum strains in vitro, and on patulin production on apple substrate. The sensitivity upon PgAFP was P. digitatum > P. expansum > P. italicum. In oranges, broadly, no inhibitory effect was obtained. PgAFP and P. chrysogenum did not inhibit the P. expansum CMP-1 growth on Golden Delicious apples, however, a successful effect was achieved on Royal Gala apples. On apple substrate, patulin production by P. expansum CMP-1 rose in parallel to PgAFP concentrations, linked with high reactive oxygen species levels. PgAFP cannot be proposed as a bioprotective agent on apple. However, P. chrysogenum is a promising agent to be used on Royal Gala apples.

Sensing and transduction of nutritional and chemical signals in filamentous fungi: Impact on cell development and secondary metabolites biosynthesis

Filamentous fungi respond to hundreds of nutritional, chemical and environmental signals that affect expression of primary metabolism and biosynthesis of secondary metabolites. These signals are sensed at the membrane level by G protein coupled receptors (GPCRs). GPCRs contain usually seven transmembrane domains, an external amino terminal fragment that interacts with the ligand, and an internal carboxy terminal end interacting with the intracellular G protein. There is a great variety of GPCRs in filamentous fungi involved in sensing of sugars, amino acids, cellulose, cell-wall components, sex pheromones, oxylipins, calcium ions and other ligands. Mechanisms of signal transduction at the membrane level by GPCRs are discussed, including the internalization and compartmentalisation of these sensor proteins. We have identified and analysed the GPCRs in the genome of Penicillium chrysogenum and compared them with GPCRs of several other filamentous fungi. We have found 66 GPCRs classified into 14 classes, depending on the ligand recognized by these proteins, including most previously proposed classes of GPCRs. We have found 66 putative GPCRs, representatives of twelve of the fourteen previously proposed classes of GPCRs, depending on the ligand recognized by these proteins. A staggering fortytwo putative members of the new GPCR class XIV, the so-called Pth11 sensors of cellulosic material as reported for Neurospora crassa and some other fungi, were identified. Several GPCRs sensing sex pheromones, known in yeast and in several fungi, were also identified in P. chrysogenum, confirming the recent unravelling of the hidden sexual capacity of this species. Other sensing mechanisms do not involve GPCRs, including the two-component systems (HKRR), the HOG signalling system and the PalH mediated pH transduction sensor. GPCR sensor proteins transmit their signals by interacting with intracellular heterotrimeric G proteins, that are well known in several fungi, including P. chrysogenum. These G proteins are inactive in the GDP containing heterotrimeric state, and become active by nucleotide exchange, allowing the separation of the heterotrimeric protein in active Gα and Gβγ dimer subunits. The conversion of GTP in GDP is mediated by the endogenous GTPase activity of the G proteins. Downstream of the ligand interaction, the activated Gα protein and also the Gβ/Gγ dimer, transduce the signals through at least three different cascades: adenylate cyclase/cAMP, MAPK kinase, and phospholipase C mediated pathways.

Programmed cell death in human pathogenic fungi - a possible therapeutic target

INTRODUCTION

Diseases caused by pathogenic fungi are increasing because of antibiotic overuse, the rise of immunosuppressive therapies, and climate change. The limited variety of antimycotics and the rapid adaptation of pathogenic fungi to antifungal agents serve to exacerbate this issue. Unfortunately, about 1.6 million people are killed by fungal infections annually. Areas covered: The discovery of the small antimicrobial proteins produced by microorganisms, animals, humans, and plants will hopefully overcome challenges in the treatment of fungal infections. These small proteins are highly stable and any resistance to them rarely evolves; therefore, they are potentially good candidates for the treatment and prevention of infections caused by pathogenic fungi. Some of these proteins target the programmed cell death machinery of pathogenic fungi; this is potentially a novel approach in antimycotic therapies. In this review, we highlight the elements of apoptosis in human pathogenic fungi and related model organisms and discuss the possible therapeutic potential of the apoptosis-inducing, small, antifungal proteins. Expert opinion: Small antimicrobial proteins may establish a new class of antimycotics in the future. The rarity of resistance and their synergistic effects with other frequently used antifungal agents may help pave the way for their use in the clinic.

Inhibitory Effect of PgAFP and Protective Cultures on Aspergillus parasiticus Growth and Aflatoxins Production on Dry-Fermented Sausage and Cheese

Aflatoxigenic molds can grow and produce aflatoxins on dry-fermented meat and cheese. The small, basic, cysteine-rich antifungal protein PgAFP displays a time-limited inhibitory ability against unwanted molds by increasing reactive oxygen species (ROS), which can lead to increased aflatoxin production. However, calcium abolishes the inhibitory effect of PgAFP on certain Aspergillus spp. To maximize the antifungal effect, this protein may be combined with protective cultures. Yeasts and lactic acid bacteria may counteract the impact of calcium on PgAFP fungal inhibition. The objective of this work was to study the effect of PgAFP and different combined treatments with Debaryomyces hansenii and/or Pediococcus acidilactici against growth of and aflatoxin production by an aflatoxigenic strain of Aspergillus parasiticus in both culture media and dry-fermented foods with low or high calcium levels. Aflatoxins production was increased by PgAFP but dramatically reduced by P. acidilactici in low calcium culture medium, whereas in the Ca-enriched culture medium, all treatments tested led to low aflatoxins levels. To study whether PgAFP and the protective microorganisms interfere with ROS and aflatoxin production, the relative expression of genes foxA, which is involved in peroxisomal β-oxidation, and aflP, which is required for aflatoxin biosynthesis, were evaluated. The aflatoxin overproduction induced by PgAFP seems not to be linked to peroxisomal β-oxidation. The combination of PgAFP and D. hansenii provided a successful inhibitory effect on A. parasiticus growth as well as on aflatoxin production on sliced dry-fermented sausage and cheese ripened up to 15 days, whereas P. acidilactici did not further enhance the protective effect of the two former agents. Therefore, the combined treatment of PgAFP and D. hansenii seems to provide a promising protective mean against aflatoxin-producing A. parasiticus on dry-fermented foods.

New Antimicrobial Potential and Structural Properties of PAFB: A Cationic, Cysteine-Rich Protein from Penicillium chrysogenum Q176

Small, cysteine-rich and cationic proteins with antimicrobial activity are produced by diverse organisms of all kingdoms and represent promising molecules for drug development. The ancestor of all industrial penicillin producing strains, the ascomycete Penicillium chryosgenum Q176, secretes the extensively studied antifungal protein PAF. However, the genome of this strain harbours at least two more genes that code for other small, cysteine-rich and cationic proteins with potential antifungal activity. In this study, we characterized the pafB gene product that shows high similarity to PgAFP from P. chrysogenum R42C. Although abundant and timely regulated pafB gene transcripts were detected, we could not identify PAFB in the culture broth of P. chrysogenum Q176. Therefore, we applied a P. chrysogenum-based expression system to produce sufficient amounts of recombinant PAFB to address unanswered questions concerning the structure and antimicrobial function. Nuclear magnetic resonance (NMR)-based analyses revealed a compact β-folded structure, comprising five β-strands connected by four solvent exposed and flexible loops and an “abcabc” disulphide bond pattern. We identified PAFB as an inhibitor of growth of human pathogenic moulds and yeasts. Furthermore, we document for the first time an anti-viral activity for two members of the small, cysteine-rich and cationic protein group from ascomycetes.

Proteomics of Parma Dry-Cured Ham: Analysis of Salting Exudates

The production of Parma dry-cured ham involves the steps of salting, drying, and ripening. Although sea salt is the only preserving agent, there are strategies being developed with the goal of reducing salt content in order to decrease its negative impact on consumer health. A 24 h pressure treatment was applied before salting to reduce thickness and inequalities in shape. To evaluate the potential impact of the pressure step on the process outcome, differential proteomic analyses by complementary 2D-PAGE and LC-MS/MS were carried out on exudates collected at day 1, 5, and 18 of the salting phase for hams treated or untreated with pressure. Specific proteins were found differentially abundant in exudates from pressed vs unpressed hams and as a function of time. These changes include glycolytic enzymes and several myofibrillar proteins. These findings indicate that pressure causes a faster loosening of the myofibrillar structure with the release of specific groups of proteins.