Characterization of a new antibiotic of iturin group: bacillomycin D

The elucidation of the multimodal action of the investigational anti-Candida lipopeptide (AF4) lead from Bacillus subtilis

Background: Candida species are the main etiological agents for candidiasis, and Candida albicans are the most common infectious species. Candida species' growing resistance to conventional therapies necessitates more research into novel antifungal agents. Antifungal peptides isolated from microorganisms have potential applications as novel therapeutics. AF4 a Bacillus-derived lipopeptide demonstrating broad-spectrum antifungal activity has been investigated for its ability to cause cell death in Candida species via membrane damage and oxidative stress. Methods: Using biophysical techniques, the secondary structure of the AF4 lipopeptide was identified. Scanning electron microscopy and confocal microscopy with fluorescent dyes were performed to visualise the effect of the lipopeptide. The membrane disruption and permeabilization were assessed using the 1,6-diphenyl hexatriene (DPH) fluorescence assay and flow cytometric (FC) assessment of propidium iodide (PI) uptake, respectively. The reactive oxygen species levels were estimated using the FC assessment. The induction of apoptosis and DNA damage were studied using Annexin V-FITC/PI and DAPI. Results: Bacillus-derived antifungal variant AF4 was found to have structural features typical of lipopeptides. Microscopy imaging revealed that AF4 damages the surface of treated cells and results in membrane permeabilization, facilitating the uptake of the fluorescent dyes. A loss of membrane integrity was observed in cells treated with AF4 due to a decrease in DPH fluorescence and a dose-dependent increase in PI uptake. Cell damage was also determined from the log reduction of viable cells treated with AF4. AF4 treatment also caused elevated ROS levels, induced phosphatidylserine externalisation, late-stage apoptosis, and alterations to nuclear morphology revealed by DAPI fluorescence. Conclusion: Collectively, the mode of action studies revealed that AF4 acts primarily on the cell membrane of C. albicans and has the potential to act as an antifungal drug candidate.

Transcriptome Analysis Reveals That C17 Mycosubtilin Antagonizes Verticillium dahliae by Interfering with Multiple Functional Pathways of Fungi

Verticillium wilt is a kind of soil-borne plant fungal disease caused by Verticillium dahliae (Vd). Vd 991 is a strong pathogen causing cotton Verticillium wilt. Previously, we isolated a compound from the secondary metabolites of Bacillus subtilis J15 (BS J15), which showed a significant control effect on cotton Verticillium wilt and was identified as C17 mycosubtilin. However, the specific fungistatic mechanism by which C17 mycosubtilin antagonizes Vd 991 is not clear. Here, we first showed that C17 mycosubtilin inhibits the growth of Vd 991 and affects germination of spores at the minimum inhibitory concentration (MIC). Morphological observation showed that C17 mycosubtilin treatment caused shrinking, sinking, and even damage to spores; the hyphae became twisted and rough, the surface was sunken, and the contents were unevenly distributed, resulting in thinning and damage to the cell membrane and cell wall and swelling of mitochondria of fungi. Flow cytometry analysis with ANNEXINV-FITC/PI staining showed that C17 mycosubtilin induces necrosis of Vd 991 cells in a time-dependent manner. Differential transcription analysis showed that C17 mycosubtilin at a semi-inhibitory concentration (IC50) treated Vd 991 for 2 and 6 h and inhibited fungal growth mainly by destroying synthesis of the fungal cell membrane and cell wall, inhibiting its DNA replication and transcriptional translation process, blocking its cell cycle, destroying fungal energy and substance metabolism, and disrupting the redox process of fungi. These results directly showed the mechanism by which C17 mycosubtilin antagonizes Vd 991, providing clues for the mechanism of action of lipopeptides and useful information for development of more effective antimicrobials.

Antimicrobial Bacillus: Metabolites and Their Mode of Action

The agricultural industry utilizes antibiotic growth promoters to promote livestock growth and health. However, the World Health Organization has raised concerns over the ongoing spread of antibiotic resistance transmission in the populace, leading to its subsequent ban in several countries, especially in the European Union. These restrictions have translated into an increase in pathogenic outbreaks in the agricultural industry, highlighting the need for an economically viable, non-toxic, and renewable alternative to antibiotics in livestock. Probiotics inhibit pathogen growth, promote a beneficial microbiota, regulate the immune response of its host, enhance feed conversion to nutrients, and form biofilms that block further infection. Commonly used lactic acid bacteria probiotics are vulnerable to the harsh conditions of the upper gastrointestinal system, leading to novel research using spore-forming bacteria from the genus Bacillus. However, the exact mechanisms behind Bacillus probiotics remain unexplored. This review tackles this issue, by reporting antimicrobial compounds produced from Bacillus strains, their proposed mechanisms of action, and any gaps in the mechanism studies of these compounds. Lastly, this paper explores omics approaches to clarify the mechanisms behind Bacillus probiotics.

Iturinic Lipopeptide Diversity in the Bacillus subtilis Species Group - Important Antifungals for Plant Disease Biocontrol Applications

Iturins and closely related lipopeptides constitute a family of antifungal compounds known as iturinic lipopeptides that are produced by species in the Bacillus subtilis group. The compounds that comprise the family are: iturin, bacillomycin D, bacillomycin F, bacillomycin L, mycosubtilin, and mojavensin. These lipopeptides are prominent in many Bacillus strains that have been commercialized as biological control agents against fungal plant pathogens and as plant growth promoters. The compounds are cyclic heptapeptides with a variable length alkyl sidechain, which confers surface activity properties resulting in an affinity for fungal membranes. Above a certain concentration, enough molecules enter the fungal cell membrane to create a pore in the cell wall, which leads to loss of cell contents and cell death. This study identified 330 iturinic lipopeptide clusters in publicly available genomes from the B. subtilis species group. The clusters were subsequently assigned into distinguishable types on the basis of their unique amino acid sequences and then verified by HPLC MS/MS analysis. The results show some lipopeptides are only produced by one species, whereas certain others can produce up to three. In addition, four species previously not known to produce iturinic lipopeptides were identified. The distribution of these compounds among the B. subtilis group species suggests that they play an important role in their speciation and evolution.

Bioactive Secondary Metabolites from Bacillus subtilis: A Comprehensive Review

Bacillus subtilis is widely underappreciated for its inherent biosynthetic potential. This report comprehensively summarizes the known bioactive secondary metabolites from B. subtilis and highlights potential applications as plant pathogen control agents, drugs, and biosurfactants. B. subtilis is well known for the production of cyclic lipopeptides exhibiting strong surfactant and antimicrobial activities, such as surfactins, iturins, and fengycins. Several polyketide-derived macrolides as well as nonribosomal peptides, dihydroisocoumarins, and linear lipopeptides with antimicrobial properties have been reported, demonstrating the biosynthetic arsenal of this bacterium. Promising efforts toward the application of B. subtilis strains and their natural products in areas of agriculture and medicine are underway. However, industrial-scale availability of these compounds is currently limited by low fermentation yields and challenging accessibility via synthesis, necessitating the development of genetically engineered strains and optimized cultivation processes. We hope that this review will attract renewed interest in this often-overlooked bacterium and its impressive biosynthetic skill set.

Compost: its role, mechanism and impact on reducing soil-borne plant diseases

Soil-borne plant pathogens are responsible for causing many crop plant diseases, resulting in significant economic losses. Compost application to agricultural fields is an excellent natural approach, which can be taken to fight against plant pathogens. The application of organic waste products is also an environmentally friendly alternative to chemical use, which unfortunately is the most common approach in agriculture today. This review analyses pioneering and recent compost research, and also the mechanisms and mode of action of compost microbial communities for reducing the activity of plant pathogens in agricultural crops. In addition, an approach for improving the quality of composts through the microbial communities already present in the compost is presented. Future agricultural practices will almost definitely require integrated research strategies to help combat plant diseases.

A novel antifungal protein of Bacillus subtilis B25

Bacillus subtilis B25 was isolated from banana rhizosphere soil. It has been confirmed for B25 to have stronger antagonism against Fusarium oxysporum f.sp.cubense, Additionally B25 has good inhibitory to plant pathogens, including Corynespora cassiicola, Alternaria solani, Botrytis cinerea and Colletotrichum gloeosporioides on potato dextrose agar (PDA) plates. The antagonistic substance can be extracted from cell-free culture broth supernatants by 70% (w/v) (NH4)2 SO4 saturation. Clear blank band was observed between the protein and a pathogen. The examination of antagonistic mechanism under light microscope showed that the antifungal protein of B25 appeared to inhibit pathogens by leading to mycelium and spores tumescence, distortion, abnormality. The isolation procedure comprised ion exchange chromatography on DEAE-Sephadex Fast Flow and gel filtration chromatography on SephadexG-100. The purified antifungal fraction showed a single band in sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The active fraction was identified by NanoLC-ESI-MS/MS The amino acid sequences of 17 peptides segments were obtained. The analysis of the protein suggested that it was a hypothetical protein (gi154685475), with a relative molecular mass of 38708.67 Da and isoelectric point (pI) of 5.63.

Optimization of Culture Conditions for Biosynthesis of Lipopeptide by Bacillus Subtilis with Starch

Optimization of culture conditions for lipopeptide production of lipopeptide by Bacillus subtilis NEL-01 was carried out in shaker flask batch fermentations using composite central design of response surface methodology (RSM). A five-level three-factor central composite design was employed to determine the maximum lipopeptide production at optimum levels for culture temperature, initial pH and culture cycle. Culture temperature and culture cycle showed the significant linear main effects, while pH had no significant linear effect. The production was also significantly affected by quadratic effect of culture temperature and initial pH. Optimum fermentation parameters were predicted at temperature, initial pH, and culture cycle of 34.81 °C, 7.33g/l, 49.26 h, respectively. The prediction lipopeptide yield was 1879.56 mg/l. The subsequent experiments confirmed the prediction.

Conformational analyses of bacillomycin D, a natural antimicrobial lipopeptide, alone or in interaction with lipid monolayers at the air-water interface

Bacillomycin D is a natural antimicrobial lipopeptide belonging to the iturin family. It is produced by Bacillus subtilis strains. Bacillomycin D is characterized by its strong antifungal and hemolytic properties, due to its interaction with the plasma membrane of sensitive cells. Until now, only few limited analyses were conducted to understand the biological activities of bacillomycin D at the molecular level. Our purpose was to analyze the conformation of bacillomycin D using IR spectroscopy and to model its interactions with cytoplasmic membranes using Langmuir interfacial monolayers. Our findings indicate that bacillomycin D contains turns and allow to model its three-dimensional structure. Bacillomycin D formed a monolayer film at the air-water interface and kept its turn conformation, as shown by polarization modulation infrared reflection absorption spectroscopy (PM-IRRAS). To identify the membrane lipid target of bacillomycin D, its interactions with pure lipid monolayers were analyzed and an original behavior of the lipopeptide toward cholesterol-containing monolayers was shown. This original behavior was lost when bacillomycin D was interacting with pure cholesteryl acetate monolayers, suggesting the involvement of the alcohol group of cholesterol in the lipopeptide-cholesterol interaction.

Purification and characterization of a novel antifungal protein from Bacillus subtilis strain B29

An antifungal protein was isolated from a culture of Bacillus subtilis strain B29. The isolation procedure comprised ion exchange chromatography on diethylaminoethyl (DEAE)-52 cellulose and gel filtration chromatography on Bio-Gel P-100. The protein was absorbed on DEAE-cellulose and Bio-Gel P-100. The purified antifungal fraction was designated as B29I, with a molecular mass of 42.3 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), pI value 5.69 by isoelectric focusing (IEF)-PAGE, and 97.81% purity by high performance liquid chromatography (HPLC). B29I exhibited inhibitory activity on mycelial growth in Fusarium oxysporum, Rhizoctonia solani, Fusarium moniliforme, and Sclerotinia sclerotiorum. The 50% inhibitory concentrations (IC(50)) of its antifungal activity toward Fusarium oxysporum and Rhizoctonia solani were 45 and 112 micromol/L, respectively. B29I also demonstrated an inhibitory effect on conidial spore germination of Fusarium oxysporum and suppression of germ-tube elongation, and induced distortion, tumescence, and rupture of a portion of the germinated spores.

Marine natural products

This review covers the literature published in 2005 for marine natural products, with 704 citations (493 for the period January to December 2005) referring to compounds isolated from marine microorganisms and phytoplankton, green algae, brown algae, red algae, sponges, coelenterates, bryozoans, molluscs, tunicates and echinoderms. The emphasis is on new compounds (812 for 2005), together with their relevant biological activities, source organisms and country of origin. Biosynthetic studies, first syntheses, and syntheses that lead to the revision of structures or stereochemistries, have been included.

Screening for biologically active metabolites with endosymbiotic bacilli isolated from arthropods

Endosymbiotic bacteria from the genus Bacillus were isolated from different compartments of the gut of various members of insects (Hexapoda) and millipedes (Diplopoda). They were grown in submerged culture and investigated by biological assays and HPLC-diode array analysis regarding their production of bioactive metabolites, which were isolated and determined in structure. Known compounds and yet unknown derivatives from the primary metabolism were detected, as well as antibacterially and antifungally acting peptide antibiotics.

Bacterial control of plant diseases

This article focuses on the effective biocontrol of plant diseases by microorganisms, which is attracting attention as an alternative to chemical control methods. As most research has so far been concentrated on fluorescent Pseudomonas species, the use of Bacillus species which has been considered to be less effective compared to that of pseudomonads, has been mainly introduced to demonstrate the effectiveness of the bacteria.

Molecular and biochemical characterization of the protein template controlling biosynthesis of the lipopeptide lichenysin

Lichenysins are surface-active lipopeptides with antibiotic properties produced nonribosomally by several strains of Bacillus licheniformis. Here, we report the cloning and sequencing of an entire 26.6-kb lichenysin biosynthesis operon from B. licheniformis ATCC 10716. Three large open reading frames coding for peptide synthetases, designated licA, licB (three modules each), and licC (one module), could be detected, followed by a gene, licTE, coding for a thioesterase-like protein. The domain structure of the seven identified modules, which resembles that of the surfactin synthetases SrfA-A to -C, showed two epimerization domains attached to the third and sixth modules. The substrate specificity of the first, fifth, and seventh recombinant adenylation domains of LicA to -C (cloned and expressed in Escherichia coli) was determined to be Gln, Asp, and Ile (with minor Val and Leu substitutions), respectively. Therefore, we suppose that the identified biosynthesis operon is responsible for the production of a lichenysin variant with the primary amino acid sequence L-Gln-L-Leu-D-Leu-L-Val-L-Asp-D-Leu-L-Ile, with minor Leu and Val substitutions at the seventh position.

Iturins, a special class of pore-forming lipopeptides: biological and physicochemical properties

Iturins are a family of lipopeptides extracted from the culture media of various strains of Bacillus subtilis. These amphiphilic compounds are characterized by a peptide ring of seven amino acid residues including an invariable D-Tyr2, with the constant chiral sequence LDDLLDL closed by a C14-C17 aliphatic beta-amino acid. They exhibit strong antifungal activities against a wide variety of pathogenic yeasts and fungi but their antibacterial activities are restricted to some bacteria such as Micrococcus luteus. The biological activity of the iturin lipopeptides is modulated by the primary structure of the peptide cycle as illustrated by the methylation of the D-Tyr2 residue which dramatically decreases the activity or by the inversion of the two adjacent Ser6-Asn7 residues which makes mycosubtilin more active than iturin A. The antifungal activity is related to the interaction of the iturin lipopeptides with the cytoplasmic membrane of target cells, the K+ permeability of which is greatly increased. The ability of iturin compounds to increase the membrane cell permeability is due to the formation of ion-conducting pores, the characteristics of which depend both on the lipid composition of the membrane and on the structure of the peptide cycle. From monolayer experiments it has been suggested that these ionic pores are the consequence of the presence of aggregates (lipopeptide aggregates or lipopeptide/phospholipid complex aggregates) in the phospholipid membrane. It has also been shown that, when active, iturins interact strongly with sterols, forming lipopeptide/cholesterol complexes. Therefore, the biologically efficient structure might be a ternary structure: iturin/phospholipid/sterol.

Structure of bacillomycin D, a new antibiotic of the iturin group

Bacillomycin D is an antifungal agent extracted from the culture medium of a strain of Bacillus subtilis. It is a mixture of two homologous lipopeptides: the lipid moiety consists of 3-amino-12-methyltridecanoic acid or 3-amino-12-methyltetradecanoic acid; the peptide moiety contains one residue of each of the following seven amino acid: D-asparagine, L-aspartate, L-glutamate, L-proline, D-serine, L-threonine and D- tyrosine. The peptide sequence and the cyclic structure were determined by structural analysis of the peptides obtained by mild acid hydrolysis and by cleavage of the molecule with N-bromosuccinimide.