Fungal defensins, an emerging source of anti-infective drugs

Plectasin: from evolution to truncation, expression, and better druggability

Non-computational classical evolution analysis of plectasin and its functional relatives can especially contribute tool value during access to meet requirements for their better druggability in clinical use. Staphylococcus aureus is a zoonotic pathogen that can infect the skin, blood, and other tissues of humans and animals. The impact of pathogens on humans is exacerbated by the crisis of drug resistance caused by the misuse of antibiotics. In this study, we analyzed the evolution of anti-Staphylococcus target functional sequences, designed a series of plectasin derivatives by truncation, and recombinantly expressed them in Pichia pastoris X-33, from which the best recombinant Ple-AB was selected for the druggability study. The amount of total protein reached 2.9 g/L following 120 h of high-density expression in a 5-L fermenter. Ple-AB was found to have good bactericidal activity against gram-positive bacteria, with minimum inhibitory concentration (MIC) values ranging between 2 and 16 μg/mL. It showed good stability and maintained its bactericidal activity during high temperatures, strong acid and alkali environments. Notably, Ple-AB exhibited better druggability, including excellent trypsin resistance, and still possessed approximately 50% of its initial activity following exposure to simulated intestinal fluids for 1 h. In vitro safety testing of Ple-AB revealed low hemolytic activity against mouse erythrocytes and cytotoxicity against murine-derived macrophages. This study successfully realized the high expression of a new antimicrobial peptide (AMP), Ple-AB, in P. pastoris and the establishment of its oral administration as an additive form with high trypsin resistance; the study also revealed its antibacterial properties, indicating that truncation design is a valuable tool for improving druggability and that the candidate Ple-AB may be a novel promising antimicrobial agent.

Fungus-insect interactions beyond bilateral regimes: the importance and strategy to outcompete host ectomicrobiomes by fungal parasites

Fungus-insect interactions have long been investigated at the bilateral level to unveil the factors involved in mediating fungal entomopathogenicity and insect antifungal immunity. Emerging evidence has shown that insect cuticles are inhabited by different bacteria that can delay and deter fungal parasite infections. Entomopathogenic fungi (EPF), however, have evolved strategies to combat the colonization resistance mediated by insect ectomicrobiomes by producing antimicrobial peptides or antibiotic compounds. Deprivation of micronutrients may also be employed by EPF to counteract the ectomicrobiome antagonism. Further investigations of insect ectomicrobiome assemblage and fungal factors involved in outcompeting cuticular microbiomes may benefit the development of cost-effective mycoinsecticides while protecting ecologically and economically important insect species.

The second N-terminal aromatic residue of the fungal defensin, blapersin, of Blastomyces percursus is essential for its antibacterial activity

Studies have shown that the second N-terminal residue of fungal defensins is closely involved in the binding of defensins to lipid II, a bacterial cell wall precursor, and plays an important role in antibacterial activity. We found that the N-terminal residue is always aromatic in nature. In this study, 29 fungal defensin-like peptides were found via the genomic search strategy. Based on the type of aromatic residue at the second N-terminal site, we mainly divided these peptides into Phe, Trp, and Tyr types. We selected and characterized a defensin, blapersin, derived from Blastomyces percursus as a molecular model to investigate the functional significance of the N-terminal site. The native blapersin killed a wide spectrum of gram-positive bacteria at low molecular concentrations. Its aromatic mutants, W2F and W2Y, displayed enhanced antimicrobial activity, especially against the vancomycin-resistant Enterococcus faecium. The aromatic side chains containing Phe² and Tyr² seem to be more favorable for the antibacterial activity of blapersin those containing Trp². However, the nonaromatic mutant W2A had almost no antibacterial activity. This indicates that the second N-terminal aromatic residue is essential for the antimicrobial action of blapersin. All these defensins have high stability and low toxicity. This is the first report on the enhancement of antibacterial activity by calibration of the N-terminal aromatic residue.

A Centipede Toxin Family Defines an Ancient Class of CSαβ Defensins

Disulfide-rich peptides (DRPs) play diverse physiological roles and have emerged as attractive sources of pharmacological tools and drug leads. Here we describe the 3D structure of a centipede venom peptide, U-SLPTX₁₅-Sm2a, whose family defines a unique class of one of the most widespread DRP folds known, the cystine-stabilized α/β fold (CSαβ). This class, which we have named the two-disulfide CSαβ fold (2ds-CSαβ), contains only two internal disulfide bonds as opposed to at least three in all other confirmed CSαβ peptides, and constitutes one of the major neurotoxic peptide families in centipede venoms. We show the 2ds-CSαβ is widely distributed outside centipedes and is likely an ancient fold predating the split between prokaryotes and eukaryotes. Our results provide insights into the ancient evolutionary history of a widespread DRP fold and highlight the usefulness of 3D structures as evolutionary tools.

Invasive fungi-derived defensins kill drug-resistant bacterial pathogens

Fungi-derived defensins are a class of antimicrobial peptides with therapeutic potential due to their high antibacterial efficacy and low toxicity. Based on the genomic strategy, we have identified 68 fungal defensin-like peptides (fDLPs) in five new genera, including Trichosporon, Apophysomyces, Lichtheimia, Beauveria and Scedosporium and characterized a new synthetic defensin (scedosporisin) from an invasive fungus. It was active against Gram-positive bacteria but not active against negative bacteria. Importantly, it killed several clinical resistant isolates such as methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococci at low molecular concentrations. Scedosporisin showed low hemolysis and cytotoxicity and high serum stability. The killing kinetics of scedosporisin-2 against a clinical isolate of MRSA showed that it killed the bacteria more rapidly than that of vancomycin. Homology modeling analysis show that scedosporisin adopted a typical cysteine stabilized α-helical and β-sheet fold with a local hydrophobic patch. Scedosporisin significantly improved the survival rate of mice in the peritonitis model. This work has greatly expanded the library of fDLPs, and successfully selected leading molecules for antimicrobial drug reserves.

New fungal defensin-like peptides provide evidence for fold change of proteins in evolution

Defensins containing a consensus cystine framework, Cys_[1]…Cys_[2]X₃Cys_[3]…Cys_[4]… Cys_[5]X₁Cys_[6] (X, any amino acid except Cys; …, variable residue numbers), are extensively distributed in a variety of multicellular organisms (plants, fungi and invertebrates) and essentially involved in immunity as microbicidal agents. This framework is a prerequisite for forming the cysteine-stabilized α-helix and β-sheet (CSαβ) fold, in which the two invariant motifs, Cys_[2]X₃Cys_[3]/Cys_[5]X₁Cys_[6], are key determinants of fold formation. By using a computational genomics approach, we identified a large superfamily of fungal defensin-like peptides (fDLPs) in the phytopathogenic fungal genus – Zymoseptoria, which includes 132 structurally typical and 63 atypical members. These atypical fDLPs exhibit an altered cystine framework and accompanying fold change associated with their secondary structure elements and disulfide bridge patterns, as identified by protein structure modelling. Despite this, they definitely are homologous with the typical fDLPs in view of their precise gene structure conservation and identical precursor organization. Sequence and structural analyses combined with functional data suggest that most of Zymoseptoria fDLPs might have lost their antimicrobial activity. The present study provides a clear example of fold change in the evolution of proteins and is valuable in establishing remote homology among peptide superfamily members with different folds.

Assessment of de novo assemblers for draft genomes: a case study with fungal genomes

BACKGROUND

Recently, large bio-projects dealing with the release of different genomes have transpired. Most of these projects use next-generation sequencing platforms. As a consequence, many de novo assembly tools have evolved to assemble the reads generated by these platforms. Each tool has its own inherent advantages and disadvantages, which make the selection of an appropriate tool a challenging task.

RESULTS

We have evaluated the performance of frequently used de novo assemblers namely ABySS, IDBA-UD, Minia, SOAP, SPAdes, Sparse, and Velvet. These assemblers are assessed based on their output quality during the assembly process conducted over fungal data. We compared the performance of these assemblers by considering both computational as well as quality metrics. By analyzing these performance metrics, the assemblers are ranked and a procedure for choosing the candidate assembler is illustrated.

CONCLUSIONS

In this study, we propose an assessment method for the selection of de novo assemblers by considering their computational as well as quality metrics at the draft genome level. We divide the quality metrics into three groups: g1 measures the goodness of the assemblies, g2 measures the problems of the assemblies, and g3 measures the conservation elements in the assemblies. Our results demonstrate that the assemblers ABySS and IDBA-UD exhibit a good performance for the studied data from fungal genomes in terms of running time, memory, and quality. The results suggest that whole genome shotgun sequencing projects should make use of different assemblers by considering their merits.

The fungal defensin family enlarged

Fungi are an emerging source of peptide antibiotics. With the availability of a large number of model fungal genome sequences, we can expect that more and more fungal defensin-like peptides (fDLPs) will be discovered by sequence similarity search. Here, we report a total of 69 new fDLPs encoded by 63 genes, in which a group of fDLPs derived from dermatophytes are defined as a new family (fDEF8) according to sequence and phylogenetic analyses. In the oleaginous fungus Mortierella alpine, fDLPs have undergone extensive gene expansion. Our work further enlarges the fungal defensin family and will help characterize new peptide antibiotics with therapeutic potential.