Detection of secreted antimicrobial peptides isolated from cell-free culture supernatant of Paenibacillus alvei AN5

The Characterization, Biological Activities, and Potential Applications of the Antimicrobial Peptides Derived from Bacillus spp.: A Comprehensive Review

This paper provides a comprehensive review of antimicrobial peptides (AMPs) derived from Bacillus spp. The classification and structure of Bacillus-derived AMPs encompass a diverse range. There are 89 documented Bacillus-derived AMPs, which exhibit varied sources, amino acid sequences, and molecular structures. These AMPs can be categorized into classes I, Ia, IIa, IIb, IIc, and IId. The synthesis pathway of the AMPs primarily involves either ribosomally synthesized or non-ribosomally synthesized approaches. Additionally, the antimicrobial activity of these AMPs is versatile, targeting bacteria, fungi, and viruses, through disrupting intracellular DNA and the cell wall and membrane, as well as modulating immune responses. Moreover, the Bacillus-derived AMPs demonstrate promising application in the pharmaceutical industry, environmental protection, food preservation, and bio-control in agriculture. The commonly employed strategies for enhancing the production of Bacillus-derived AMPs involve optimizing cultivation conditions, implementing systems metabolic engineering, employing genome shuffling techniques, optimizing promoters, and improving expression host optimization. This review can provide a valuable reference for comprehending the current research status on advancements and sustainable production of Bacillus-derived AMPs.

Molecular farming for sustainable production of clinical-grade antimicrobial peptides

Antimicrobial peptides (AMPs) are emerging as next-generation therapeutics due to their broad-spectrum activity against drug-resistant bacterial strains and their ability to eradicate biofilms, modulate immune responses, exert anti-inflammatory effects and improve disease management. They are produced through solid-phase peptide synthesis or in bacterial or yeast cells. Molecular farming, i.e. the production of biologics in plants, offers a low-cost, non-toxic, scalable and simple alternative platform to produce AMPs at a sustainable cost. In this review, we discuss the advantages of molecular farming for producing clinical-grade AMPs, advances in expression and purification systems and the cost advantage for industrial-scale production. We further review how 'green' production is filling the sustainability gap, streamlining patent and regulatory approvals and enabling successful clinical translations that demonstrate the future potential of AMPs produced by molecular farming. Finally, we discuss the regulatory challenges that need to be addressed to fully realize the potential of molecular farming-based AMP production for therapeutics.

A Novel Antimicrobial Metabolite Produced by Paenibacillus apiarius Isolated from Brackish Water of Lake Balkhash in Kazakhstan

Four aerobic bacteria with bacteriolytic capabilities were isolated from the brackish water site Strait Uzynaral of Lake Balkhash in Kazakhstan. The morphology and physiology of the bacterial isolates have subsequently been analyzed. Using matrix assisted laser desorption ionization-time of flight mass spectrum and partial 16S rRNA gene sequence analyses, three of the isolates have been identified as Pseudomonas veronii and one as Paenibacillus apiarius. We determined the capability of both species to lyse pre-grown cells of the Gram-negative strains Pseudomonas putida SBUG 24 and Escherichia coli SBUG 13 as well as the Gram-positive strains Micrococcus luteus SBUG 16 and Arthrobacter citreus SBUG 321 on solid media. The bacteriolysis process was analyzed by creating growth curves and electron micrographs of co-cultures with the bacteriolytic isolates and the lysis sensitive strain Arthrobacter citreus SBUG 321 in nutrient-poor liquid media. One metabolite of Paenibacillus apiarius was isolated and structurally characterized by various chemical structure determination methods. It is a novel antibiotic substance.

In vivo and in silico screening for antimicrobial compounds from cyanobacteria

Due to the emerging rise of multi‐drug resistant bacteria, the discovery of novel antibiotics is of high scientific interest. Through their high chemodiversity of bioactive secondary metabolites, cyanobacteria have proven to be promising microorganisms for the discovery of antibacterial compounds. These aspects make appropriate antibacterial screening approaches for cyanobacteria crucial. Up to date, screenings are mostly carried out using a phenotypic methodology, consisting of cyanobacterial cultivation, extraction, and inhibitory assays. However, the parameters of these methods highly vary within the literature. Therefore, the common choices of parameters and inhibitory assays are summarized in this review. Nevertheless, less frequently used method variants are highlighted, which lead to hits from antimicrobial compounds. In addition to the considerations of phenotypic methods, this study provides an overview of developments in the genome‐based screening area, be it in vivo using PCR technique or in silico using the recent genome‐mining method. Though, up to date, these techniques are not applied as much as phenotypic screening.

Antimicrobial peptides: mechanism of action, activity and clinical potential

The management of bacterial infections is becoming a major clinical challenge due to the rapid evolution of antibiotic resistant bacteria. As an excellent candidate to overcome antibiotic resistance, antimicrobial peptides (AMPs) that are produced from the synthetic and natural sources demonstrate a broad-spectrum antimicrobial activity with the high specificity and low toxicity. These peptides possess distinctive structures and functions by employing sophisticated mechanisms of action. This comprehensive review provides a broad overview of AMPs from the origin, structural characteristics, mechanisms of action, biological activities to clinical applications. We finally discuss the strategies to optimize and develop AMP-based treatment as the potential antimicrobial and anticancer therapeutics.

Analysis of Antimicrobial Peptide Metabolome of Bacterial Endophyte Isolated From Traditionally Used Medicinal Plant Millettia pachycarpa Benth

Increasing prevalence of antimicrobial resistance (AMR) has posed a major health concern worldwide, and the addition of new antimicrobial agents is diminishing due to overexploitation of plants and microbial resources. Inevitably, alternative sources and new strategies are needed to find novel biomolecules to counter AMR and pandemic circumstances. The association of plants with microorganisms is one basic natural interaction that involves the exchange of biomolecules. Such a symbiotic relationship might affect the respective bio-chemical properties and production of secondary metabolites in the host and microbes. Furthermore, the discovery of taxol and taxane from an endophytic fungus, Taxomyces andreanae from Taxus wallachiana, has stimulated much research on endophytes from medicinal plants. A gram-positive endophytic bacterium, Paenibacillus peoriae IBSD35, was isolated from the stem of Millettia pachycarpa Benth. It is a rod-shaped, motile, gram-positive, and endospore-forming bacteria. It is neutralophilic as per Joint Genome Institute’s (JGI) IMG system analysis. The plant was selected based on its ethnobotany history of traditional uses and highly insecticidal properties. Bioactive molecules were purified from P. peoriae IBSD35 culture broth using 70% ammonium sulfate and column chromatography techniques. The biomolecule was enriched to 151.72-fold and the yield percentage was 0.05. Peoriaerin II, a highly potent and broad-spectrum antimicrobial peptide against Staphylococcus aureus ATCC 25923, Escherichia coli ATCC 25922, and Candida albicans ATCC 10231 was isolated. LC-MS sequencing revealed that its N-terminal is methionine. It has four negatively charged residues (Asp + Glu) and a total number of two positively charged residues (Arg + Lys). Its molecular weight is 4,685.13 Da. It is linked to an LC-MS/MS inferred biosynthetic gene cluster with accession number A0A2S6P0H9, and blastp has shown it is 82.4% similar to fusaricidin synthetase of Paenibacillus polymyxa SC2. The 3D structure conformation of the BGC and AMP were predicted using SWISS MODEL homology modeling. Therefore, combining both genomic and proteomic results obtained from P. peoriae IBSD35, associated with M. pachycarpa Benth., will substantially increase the understanding of antimicrobial peptides and assist to uncover novel biological agents.

Screening and characterization of a novel Antibiofilm polypeptide derived from filamentous Fungi

In the present study, 120 fungal isolates were locally isolated from soil and selected according to their ability to antimicrobial activity. Then, selected isolates were tested for their ability to prevent biofilm formation and only one isolate (A01) showed an antibiofilm effect. The isolate A01 identified as Aspergillus tubingensis by sequencing of the 18S ITS region and a segment of β-tubulin gene. Then, 5 fractions were prepared from the culture filtrate of A. tubingensis A01 using the ultrafiltration technique to find active polypeptide fraction. The experiments revealed that one of them had an antibiofilm activity. The MALDI-TOF/MS analyses demonstrated that this polypeptide composed of 92 amino acids and had a molecular mass of 10,087 Da. The sequence alignment showed homology with hypothetical protein (OJI81679.1). The gene coding for this polypeptide consisting of 279 nucleotides, herein we called astucin, was cloned and sequenced from A. tubingensis A01 to confirm results. The MIC of the purified polypeptide was 32 m/L and 128 μg/mL and the MBIC was 2 and 8 μg/mL against Staphylococcus aureus and MRSA, respectively. The results demonstrated that the antimicrobial and antibiofilm activity of astucin, together with its lack of cytotoxicity, makes it an alternative for application in medicine. SIGNIFICANCE: Antibiotic resistance is a global problem and the emergence of antibiotic resistant bacteria reduce the effect the current treatment approaches. In this context, antimicrobial peptides stand out as potentional agents to combat bacterial infection especially, biofilm related infections. Importantly, this study have greatly considered our understanding for fungal derived antibiofilm polypeptides. In this study, traditional selection method combined with crystal violet assay is used to investigate antibiofilm polypeptides. We identified antibiofilm polypeptides purified from A. tubingensis A01. This protein shows antimicrobial and antibiofilm activity against S. aureus.

Paenibacillus alvei MP1 as a Producer of the Proteinaceous Compound with Activity against Important Human Pathogens, Including Staphylococcus aureus and Listeria monocytogenes

An emerging need for new classes of antibiotics is, on the one hand, evident as antimicrobial resistance continues to rise. On the other hand, the awareness of the pros and cons of chemically synthesized compounds’ extensive use leads to a search for new metabolites in already known reservoirs. Previous research showed that Paenibacillus strain (P. alvei MP1) recovered from a buckwheat honey sample presented a wide spectrum of antimicrobial activity against both Gram-positive and Gram-negative pathogens. Recent investigation has confirmed that P. alvei MP1 (deposited at DDBJ/ENA/GenBank under the accession WSQB00000000) produces a proteinaceous, heat-stable compound(s) with the maximum antimicrobial production obtained after 18 h of P. alvei MP1 growth in LB medium at 37 °C with continuous shaking at 200 RPM. The highest activity was found in the 40% ammonium sulfate precipitate, with high activity also remaining in the 50% and 60% ammonium sulfate precipitates. Moderate to high antimicrobial activity that is insensitive to proteases or heat treatment, was confirmed against pathogenic bacteria that included L. monocytogenes FSL – X1-0001 (strain 10403S), S. aureus L1 – 0030 and E. coli O157: H7. Further studies, including de novo sequencing of peptides by mass spectrometry, are in progress.

In Silico Structural Evaluation of Short Cationic Antimicrobial Peptides

Cationic peptides with antimicrobial properties are ubiquitous in nature and have been studied for many years in an attempt to design novel antibiotics. However, very few molecules are used in the clinic so far, sometimes due to their complexity but, mostly, as a consequence of the unfavorable pharmacokinetic profile associated with peptides. The aim of this work is to investigate cationic peptides in order to identify common structural features which could be useful for the design of small peptides or peptido-mimetics with improved drug-like properties and activity against Gram negative bacteria. Two sets of cationic peptides (AMPs) with known antimicrobial activity have been investigated. The first reference set comprised molecules with experimentally-known conformations available in the protein databank (PDB), and the second one was composed of short peptides active against Gram negative bacteria but with no significant structural information available. The predicted structures of the peptides from the first set were in excellent agreement with those experimentally-observed, which allowed analysis of the structural features of the second group using computationally-derived conformations. The peptide conformations, either experimentally available or predicted, were clustered in an “all vs. all” fashion and the most populated clusters were then analyzed. It was confirmed that these peptides tend to assume an amphipathic conformation regardless of the environment. It was also observed that positively-charged amino acid residues can often be found next to aromatic residues. Finally, a protocol was evaluated for the investigation of the behavior of short cationic peptides in the presence of a membrane-like environment such as dodecylphosphocholine (DPC) micelles. The results presented herein introduce a promising approach to inform the design of novel short peptides with a potential antimicrobial activity.

Ecotoxicological assessment of oil-based paint using three-dimensional multi-species bio-testing model: pre- and post-bioremediation analysis

The present study validates the oil-based paint bioremediation potential of Bacillus subtilis NAP1 for ecotoxicological assessment using a three-dimensional multi-species bio-testing model. The model included bioassays to determine phytotoxic effect, cytotoxic effect, and antimicrobial effect of oil-based paint. Additionally, the antioxidant activity of pre- and post-bioremediation samples was also detected to confirm its detoxification. Although, the pre-bioremediation samples of oil-based paint displayed significant toxicity against all the life forms. However, post-bioremediation, the cytotoxic effect against Artemia salina revealed substantial detoxification of oil-based paint with LD₅₀ of 121 μl ml^-1 (without glucose) and > 400 μl ml^-1 (with glucose). Similarly, the reduction in toxicity against Raphanus raphanistrum seeds germination (%FG = 98 to 100%) was also evident of successful detoxification under experimental conditions. Moreover, the toxicity against test bacterial strains and fungal strains was completely removed after bioremediation. In addition, the post-bioremediation samples showed reduced antioxidant activities (% scavenging = 23.5 ± 0.35 and 28.9 ± 2.7) without and with glucose, respectively. Convincingly, the present multi-species bio-testing model in addition to antioxidant studies could be suggested as a validation tool for bioremediation experiments, especially for middle and low-income countries. Graphical abstract ᅟ.

Identification and characterization of a novel antimicrobial peptide compound produced by Bacillus megaterium strain isolated from oral microflora

In recent years, the decreased efficacy of existing antibiotics toward management of emergent drug-resistant strains has necessitated the search for novel antibiotics from natural products. In this regard, Bacillus sp is well known for producing variety of secondary metabolites of potential use. Therefore, we performed an investigation to isolate and identify Bacillus sp from oral cavity for production of novel antimicrobial compounds. We extracted, purified, and identified a novel bioactive compound by B. megaterium (KC246043.1). The optimal production of compound was observed on de Man Rogosa and Sharpe broth by incubating at 37 °C, and pH 7.0 for 4 days. The bioactive compound was extracted by using n-butanol (2:1 v/v), purified on TLC plates with detection at R_f 7.8 cm; further characterized and identified as a cyclic ploypeptide sharing structural similarity with bacitracin. Minimum inhibitory concentration of bioactive compound was found to be 0.25, 0.5, 1.0, 3.125 and 6.25 μg/ml against Micrococcus luteus ATCC10240, Salmonella typhi ATCC19430, Escherichia coli ATCC35218. Pseudomonas aeruginosa ATCC27853 and Staphylococcus aureus ATCC25923 respectively, with no activity against Candida albicans ATCC10231. Our findings have revealed a novel cyclic peptide compound from B. megaterium with broad spectrum antimicrobial activity against both Gram positive and Gram negative bacteria.

The antibacterial activity and modes of LI-F type antimicrobial peptides against Bacillus cereus in vitro

AIMS

LI-Fs are a family of highly potent cyclic lipodepsipeptide antibiotics with a broad antimicrobial spectrum (Gram-positive bacteria and fungi). In this study, LI-F-type antimicrobial peptides (AMP-jsa9) composing of LI-F03a, LI-F03b, LI-F04a, LI-F04b and LI-F05b were isolated from Paenibacillus polymyxa JSA-9. To better understand the antimicrobial mechanism of AMP-jsa9, the potency and action(s) of AMP-jsa9 against Bacillus cereus were examined.

METHODS AND RESULTS

Flow cytometry, confocal laser microscopy, scanning electron microscopy, transmission electron microscopy (TEM) and atomic force microscopy observation, as well as determination of peptidoglycan and cell wall-associated protein and other methods were used. The results indicate that AMP-jsa9 exhibits strong, broad-spectrum antimicrobial activity. Moreover, AMP-jsa9 targets the cell wall and membrane of B. cereus to impair membrane integrity, increase membrane permeability and enhance cytoplasm leakage (e.g. K⁺ , protein, nucleic acid). This leads to bacterial cells with irregular, withered and coarse surfaces. In addition, AMP-jsa9 is also able to bind to DNA and break down B. cereus biofilms.

CONCLUSIONS

In this study, the action mechanism of LI-Fs against B. cereus was clarified in details.

SIGNIFICANCE AND IMPACT OF THE STUDY

The results of this study provide a theoretical basis for utilizing AMP-jsa9 or similar analogues as natural and effective preservatives in the food and feed industries. These efforts could also stimulate research activities interested in understanding the specific effects of other antimicrobial agents.

Evaluation of morphological changes of Staphylococcus aureus and Escherichia coli induced with the antimicrobial peptide AN5-1

The mechanisms of action of AN5-1 against Gram-negative and Gram-positive bacteria were investigated by evaluations of the intracellular content leakage and by microscopic observations of the treated cells. Escherichia coli and Staphylococcus aureus were used for this investigation. Measurements of DNA, RNA, proteins, and β-galactosidase were taken, and the results showed a significant increase in the cultivation media after treatment with AN5-1 compared with the untreated cells. The morphological changes of treated cells were shown using transmission electron microscopy (TEM) and atomic force microscopy (AFM). The observations showed that AN5-1 acts against E. coli and against S. aureus in similar ways, by targeting the cell wall, causing disruptions; at a high concentration (80 AU/ml), these disruptions led to cell lysis. The 3D AFM imaging system showed that at a low concentration of 20 AU/ml, the effect of AN5-1 is restricted to pore formation only. Moreover, a separation between the cell wall and the cytoplasm was observed when Gram-negative bacteria were treated with a low concentration (20 AU/ml) of AN5-1.