A structural perspective of plant antimicrobial peptides

Gene expression and characterization of an antimicrobial peptide from Medicago sativa "Sazova" cultivar

In recent years, the discovery of new antimicrobial agents has become necessary because of the increase in antibiotic resistance, the development of herbicides and fungicides resistance. Among the antimicrobial agents, antimicrobial peptides (AMPs) stand out due to their stable structure. In this study, the aim was to identify a thermostable AMP from the seeds of M. sativa "Sazova" cultivar and to analyze gene expression during germination. Antimicrobial tests were performed for the seed peptides after heat treatment (85 °C for 10 min), revealing antimicrobial effects against S. aureus, E. coli, and C. albicans. Subsequently, the peptide band corresponding to the inhibition zone was identified as M. sativa Defensin 2.1 (MsDef2.1, MW: 5.2048 kDa). The gene expression analysis of MsDef2.1 in Sazova cultivar showed that the gene was expressed different plant organs, and the expression was decreased over time. As a result of the gene analysis of two cultivars (Sazova and LegenDairy) it was found that there are 5 base differences in the coding sequence and 3 amino acid differences between the sequences of MsDef2.1 isoforms from the LegenDairy and Sazova cultivars. The physiochemical properties, secondary, and tertiary structure of the Sazova Defensin 2.1 were predicted by using bioinformatic tools. Due to the amino acid substitutions in γ-core structures, the antimicrobial activity of the isoforms is expected to differ from each other. These findings demonstrated that the defensin MsDef2.1 can differ in M. sativa cultivars in respect of the gene and amino acid sequences and has a potential for future applications.

Microbial production systems and optimization strategies of antimicrobial peptides: a review

Antibiotic resistance has become a public safety issue of the twenty-first century, posing a growing threat and drawing increased attention. Compared to traditional antibiotics, antimicrobial peptides (AMPs), as naturally produced small peptides, can target multiple pathways within pathogens and render them less prone to developing resistance. This makes them promising alternatives to antibiotics. However, traditional chemical synthesis methods face challenges, such as high costs, low yields, and poor stability, limiting the large-scale industrial production of AMPs. Despite extensive research to improve AMP production efficiency, issues such as low yields and complex extraction processes continue to pose significant barriers to commercial application. Therefore, there is an urgent need for new biosynthesis strategies and optimization methods to enhance AMP production efficiency and quality. This review summarizes the sources, classification, mechanisms of action and recent advances in the microbial synthesis of AMPs. It also explores innovative production methods, including recombinant microbial expression systems, fusion tags, codon optimization, tandem multimer expression, and hybrid peptide expression. Furthermore, we review the applications of gene editing technologies and artificial intelligence in AMP production, providing new perspectives and strategies for efficient, large-scale AMP production.

Plant Antimicrobial Peptides and Their Main Families and Roles: A Review of the Literature

Antimicrobial peptides (AMPs) are constituent molecules of the innate defense system and are naturally produced by all organisms. AMPs are characterized by a relatively low molecular weight (less than 10 kDa) and a variable number of cysteine residues that form disulfide bonds and contribute to the stabilization of the tertiary structure. In addition, there is a wide repertoire of antimicrobial agents against bacteria, viruses, fungi, and protozoa that can provide a large number of prototype peptides for study and biochemical manipulation. In this sense, plant AMPs stand out because they have a wide range of biological functions against microorganisms and potential applications in medicine and agriculture. Herein, we describe a mini-review of the principal AMP families, such as defensins, lipid transfer proteins (LTPs), thionins, heveins, and cyclotides. The objective of this work was to present the main discoveries regarding the biological activities of these plant AMP families, especially in the last 20 years. We also discuss the current knowledge of their biological activities, gene expression, and possible uses as antimicrobial molecules and in plant biotechnology.

Computational Prediction and Structural Analysis of α-Hairpinins, a Ubiquitous Family of Antimicrobial Peptides, Using the Cysmotif Searcher Pipeline

BACKGROUND

α-Hairpinins are a family of antimicrobial peptides, promising antimicrobial agents, which includes only 12 currently revealed members with proven activity, although their real number is supposed to be much higher. α-Hairpinins are short peptides containing four cysteine residues arranged in a specific Cys-motif. These antimicrobial peptides (AMPs) have a characteristic helix-loop-helix structure with two disulfide bonds. Isolation of α-hairpinins by biochemical methods is cost- and labor-consuming, thus requiring reliable preliminary in silico prediction.

METHODS

In this study, we developed a special algorithm for the prediction of putative α-hairpinins on the basis of characteristic motifs with four (4C) and six (6C) cysteines deduced from translated plant transcriptome sequences. We integrated this algorithm into the Cysmotif searcher pipeline and then analyzed all transcriptomes available from the One Thousand Plant Transcriptomes project.

RESULTS

We predicted more than 2000 putative α-hairpinins belonging to various plant sources including algae, mosses, ferns, and true flowering plants. These data make α-hairpinins one of the ubiquitous antimicrobial peptides, being widespread among various plants. The largest numbers of α-hairpinins were revealed in the Papaveraceae family and in Papaver somniferum in particular.

CONCLUSIONS

By analyzing the primary structure of α-hairpinins, we concluded that more predicted peptides with the 6C motif are likely to have potent antimicrobial activity in comparison to the ones possessing 4C motifs. In addition, we found 30 α-hairpinin precursors containing from two to eight Cys-rich modules. A striking similarity between some α-hairpinin modules belonging to diverse plants was revealed. These data allowed us to assume that the evolution of α-hairpinin precursors possibly involved changing the number of Cys-rich modules, leading to some missing middle and C-terminal modules, in particular.

Structural and Biochemical Characterization of Three Antimicrobial Peptides from Capsicum annuum L. var. annuum Leaves for Anti-Candida Use

The emergence of resistant microorganisms has reduced the effectiveness of currently available antimicrobials, necessitating the development of new strategies. Plant antimicrobial peptides (AMPs) are promising candidates for novel drug development. In this study, we aimed to isolate, characterize, and evaluate the antimicrobial activities of AMPs isolated from Capsicum annuum. The antifungal potential was tested against Candida species. Three AMPs from C. annuum leaves were isolated and characterized: a protease inhibitor, a defensin-like protein, and a lipid transporter protein, respectively named CaCPin-II, CaCDef-like, and CaCLTP2. All three peptides had a molecular mass between 3.5 and 6.5 kDa and caused morphological and physiological changes in four different species of the genus Candida, such as pseudohyphae formation, cell swelling and agglutination, growth inhibition, reduced cell viability, oxidative stress, membrane permeabilization, and metacaspase activation. Except for CaCPin-II, the peptides showed low or no hemolytic activity at the concentrations used in the yeast assays. CaCPin-II inhibited α-amylase activity. Together, these results suggest that these peptides have the potential as antimicrobial agents against species of the genus Candida and can serve as scaffolds for the development of synthetic peptides for this purpose.

Understanding the mechanism of action of protease inhibitors in controlling the growth of the Candida Genus: potential candidates for development of new antifungal molecules

There is a growing imperative for research into alternative compounds for the treatment of the fungal infections. Thus, many studies have focused on the analysis of antifungal proteins and peptides from different plant sources. Among these molecules are protease inhibitors (PIs). Previously, PIs present in the peptide-rich fractions called PEF1, PEF2 and PEF3 were identified from Capsicum chinense seeds, which have strong activity against phytopathogenic fungi. The aim of this study was to evaluate the mechanism of action and antimicrobial activity of PIs from PEF2 and PEF3 on the growth of yeasts of the genus Candida. In this work, analyses of their antimicrobial activity and cell viability were carried out. Subsequently, the mechanism of action by which the PIs cause the death of the yeasts was evaluated. Cytotoxicity was assessed in vitro by erythrocytes lysis and in vivo in Galleria mellonella larvae. PEF2 and PEF3 caused 100% of the growth inhibition of C. tropicalis and C. buinensis. For C. albicans inhibition was approximately 60% for both fractions. The PEF2 and PEF3 caused a reduction in mitochondrial functionality of 54% and 46% for C. albicans, 26% and 30% for C. tropicalis, and 71% and 68% for C. buinensis, respectively. These fractions induced morphological alterations, led to membrane permeabilization, elevated ROS levels, and resulted in necrotic cell death in C. tropicalis, whilst demonstrating low toxicity toward host cells. From the results obtained here, we intend to contribute to the understanding of the action of PIs in the control of fungal diseases of medical importance.

Anti-Candida Potential of Peptides from Immature and Ripe Fruits of Capsicum chinense Jacq

The objective of this work was to purify and evaluate the antifungal potential of peptides present in immature and ripe fruits of Capsicum chinense Jacq. (accession UENF 1706) on the medical importance yeasts. Initially the proteins of these seedless fruits were extracted, precipitated with ammonium sulfate at 70% saturation, followed by heating at 80 °C. Subsequently, the peptide-rich extract was fractionated by DEAE-Sepharose anion exchange. The whole process was monitored by tricine-SDS-PAGE. The results revealed that the fraction retained in anion exchange column, called D2, of immature and ripe fruits significantly inhibit the growth of Candida albicans and C. tropicalis yeasts. Due to the higher yield, the D2 fraction of immature fruits was selected for further purification by reverse phase chromatography on HPLC, where sixteen different fractions (H1-H16) were obtained and these were subjected to antifungal assay at 50 µg mL-1. Although almost all fractions tested had significant growth inhibition, the HI9 fraction inhibit 99% of the two yeasts tested. The effect of treatment with HI3, HI8, HI9, and HI14 fractions on the viability of yeast cells was analyzed due to their strong growth inhibition. We observed that only 50 μg mL-1 of the HI9 fraction is the lethal dose for 100% of the cells of C. albicans and C. tropicalis in the original assay. Although the HI9 fraction had a fungicidal effect on both tested yeasts, we only observed membrane permeabilization for C. tropicalis cells treated with 50 µg mL-1 of this fraction. Through mass spectrometry, we identified that the 6 kDa peptide band of HI9 fraction showed similarity with antimicrobial peptides belonging to the plant defensin family.

Expression of radish defensin (RsAFP2) gene in chickpea (Cicer arietinum L.) confers resistance to Fusarium wilt disease

BACKGROUND

Chickpea (Cicer arietinum L.), a major nutritional source cultivated worldwide, is vulnerable to several abiotic and biotic stresses, including different types of soil-borne pathogens like Fusarium oxysporum f. sp. ciceri, which causes root rot disease and severely affects productivity.

METHODS AND RESULTS

In this study, putative transgenic plants were obtained with the Radish defensin (Rs-AFP2) gene through Agrobacterium tumefaciens mediated transformation using the embryo axis explants. Transgenes were confirmed in 18 putative transgenic plants with PCR-specific primers for nptII and Rs-AFP2 genes. Twelve transgenic plants were established successfully under greenhouse conditions. The T0 plants were allowed for self-pollination to obtain T1 seeds. The T1 plants, selected for Fusarium wilt assay using Fusarium oxysporum f. sp. Cicero, showed different resistance levels, from moderate to high levels in comparison to control plants (wild-type) which exhibited severe wilt symptoms.

CONCLUSION

Our results suggest the application of Radish defensins (RsAFP1/RsAFP2 genes) for improving pathogen resistance in chickpea.

Advances on chemically modified antimicrobial peptides for generating peptide antibiotics

Antimicrobial peptides (AMPs) are pinpointed as promising molecules against antibiotic-resistant bacterial infections. Nevertheless, there is a discrepancy between the AMP sequences generated and the tangible outcomes in clinical trials. AMPs' limitations include enzymatic degradation, chemical/physical instability and toxicity toward healthy human cells. These factors compromise AMPs' bioavailability, resulting in limited therapeutic potential. To overcome such obstacles, peptidomimetic approaches, including glycosylation, PEGylation, lipidation, cyclization, grafting, D-amino acid insertion, stapling and dendrimers are promising strategies to fine-tune AMPs. Here we focused on chemical modifications applied for AMP optimization and how they have helped these peptide-based antibiotic candidates' design and translational potential.

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.

Overexpression of Rice OsS1Fa1 Gene Confers Drought Tolerance in Arabidopsis

Small peptides and proteins play critical regulatory roles in plant development and environmental stress responses; however, only a few of these molecules have been identified and characterized to date because of their poor annotation and other experimental challenges. Here, we present that rice (Oryza sativa L.) OsS1Fa1, a small 76-amino acid protein, confers drought stress tolerance in Arabidopsis thaliana. OsS1Fa1 was highly expressed in leaf, culm, and root tissues of rice seedlings during vegetative growth and was significantly induced under drought stress. OsS1Fa1 overexpression in Arabidopsis induced the expression of selected drought-responsive genes and enhanced the survival rate of transgenic lines under drought. The proteasome inhibitor MG132 protected the OsS1Fa1 protein from degradation. Together, our data indicate that the small protein OsS1Fa1 is induced by drought and is post-translationally regulated, and the ectopic expression of OsS1Fa1 protects plants from drought stress.

De Novo Design of Antimicrobial Peptides With a Special Charge Pattern and Their Application in Combating Plant Pathogens

Plant diseases are important issues in agriculture, and the development of effective and environment-friendly means of disease control is crucial and highly desired. Antimicrobial peptides (AMPs) are known as potential alternatives to chemical pesticides because of their potent broad-spectrum antimicrobial activity and because they have no risk, or have only a low risk, of developing chemical-resistant pathogens. In this study, we designed a series of amphipathic helical peptides with different spatial distributions of positive charges and found that the peptides that had a special sequence pattern "BBHBBHHBBH" ("B" for basic residue and "H" for hydrophobic residue) displayed excellent bactericidal and fungicidal activities in a wide range of economically important plant pathogens. The peptides with higher helical propensity had lower antimicrobial activity. When we modified the peptides with a long acyl chain at their N-terminus, their plant protection effect improved. Our application of the fatty acyl-modified peptides on the leaves of tomato and Arabidopsis plants lessened the infection caused by Pectobacterium carotovorum subsp. carotovorum and Botrytis cinerea. Our study provides important insights on the development of more potent novel AMPs for plant protection.

Structural characterisation of natural products by means of quantum chemical calculations of NMR parameters: new insights

In this review, we focus in all aspects of NMR simulation of natural products, from the fundamentals to the new computational toolboxes available, combining advanced quantum chemical calculations with upstream data processing and machine learning.

Defensins of Grasses: A Systematic Review

The grass family (Poaceae) is one of the largest families of flowering plants, growing in all climatic zones of all continents, which includes species of exceptional economic importance. The high adaptability of grasses to adverse environmental factors implies the existence of efficient resistance mechanisms that involve the production of antimicrobial peptides (AMPs). Of plant AMPs, defensins represent one of the largest and best-studied families. Although wheat and barley seed γ-thionins were the first defensins isolated from plants, the functional characterization of grass defensins is still in its infancy. In this review, we summarize the current knowledge of the characterized defensins from cultivated and selected wild-growing grasses. For each species, isolation of defensins or production by heterologous expression, peptide structure, biological activity, and structure-function relationship are described, along with the gene expression data. We also provide our results on in silico mining of defensin-like sequences in the genomes of all described grass species and discuss their potential functions. The data presented will form the basis for elucidation of the mode of action of grass defensins and high adaptability of grasses to environmental stress and will provide novel potent molecules for practical use in medicine and agriculture.

Crystal structure of rice defensin OsAFP1 and molecular insight into lipid-binding

Defensins are antibacterial peptides that function in the innate immune system. OsAFP1, a defensin identified from Oryza sativa (rice), exhibits antimicrobial activity against rice pathogens. Intriguingly, OsAFP1 was also shown to demonstrate potent antifungal activity against the human pathogenic fungus Candida albicans by inducing apoptosis in target cells, suggesting that OsAFP1 represents a potential new antibiotic candidate; however, further analyses, particularly at the structural level, are required to elucidate the mechanistic underpinnings of OsAFP1 antifungal activity. Here, we determined the three-dimensional structure of OsAFP1 using X-ray crystallography. OsAFP1 features the cysteine-stabilized αβ structure highly conserved in plant defensins and presents a dimeric structure that appears necessary for antifungal activity. Superimposition of the OsAFP1 structure with that of Nicotiana alata NaD1 complexed with phosphatidic acid indicated that the target molecule is likely trapped between the S2-S3 loops of each OsAFP1 dimer. In lipid-binding analyses performed using nitrocellulose membranes immobilized with various membrane lipid components, OsAFP1 was found to bind to phosphatidylinositols (PIPs) harboring phosphate groups, particularly PI(3)P. These results indicate that OsAFP1 exerts antifungal activity by binding to PI(3)P contained in the C. albicans cell membrane, thereby applying cellular stress and inducing apoptosis. Furthermore, the OsAFP1 structure and site-specific-mutation analyses revealed that Arg1, His2, Leu4, Arg9, and Phe10 play critical roles in OsAFP1 dimer formation. Thus, our study provides novel insights into the antifungal mechanism of OsAFP1.

Antifungal Activity of Anionic Defense Peptides: Insight into the Action of Galleria mellonella Anionic Peptide 2

Anionic antimicrobial peptides constitute an integral component of animal innate immunity, however the mechanisms of their antifungal activity are still poorly understood. The action of a unique Galleria mellonella anionic peptide 2 (AP2) against fungal pathogen Candida albicans was examined using different microscopic techniques and Fourier transform infrared (FTIR) spectroscopy. Although the exposure to AP2 decreased the survival rate of C. albicans cells, the viability of protoplasts was not affected, suggesting an important role of the fungal cell wall in the peptide action. Atomic force microscopy showed that the AP2-treated cells became decorated with numerous small clods and exhibited increased adhesion forces. Intensified lomasome formation, vacuolization, and partial distortion of the cell wall was also observed. FTIR spectroscopy suggested AP2 interactions with the cell surface proteins, leading to destabilization of protein secondary structures. Regardless of the anionic character of the whole AP2 molecule, bioinformatics analyses revealed the presence of amphipathic α-helices with exposed positively charged lysine residues. High content of the α-helical structure was confirmed after deconvolution of the IR absorption spectrum and during circular dichroism measurements. Our results indicated that the antimicrobial properties of G. mellonella AP2 rely on the same general characteristics found in cationic defense peptides.