Function of peptide antibiotics in producer organisms

Metagenomic nanopore sequencing for exploring the nature of antimicrobial metabolites of Bacillus haynesii

Multidrug-resistant (MDR) pathogens are a rising global health worry that imposes an urgent need for the discovery of novel antibiotics particularly those of natural origin. In this context, we aimed to use the metagenomic nanopore sequence analysis of soil microbiota coupled with the conventional phenotypic screening and genomic analysis for identifying the antimicrobial metabolites produced by promising soil isolate(s). In this study, whole metagenome analysis of the soil sample(s) was performed using MinION™ (Oxford Nanopore Technologies). Aligning and analysis of sequences for probable secondary metabolite gene clusters were extracted and analyzed using the antiSMASH version 2 and DeepBGC. Results of the metagenomic analysis showed the most abundant taxa were Bifidobacterium, Burkholderia, and Nocardiaceae (99.21%, followed by Sphingomonadaceae (82.03%) and B. haynesii (34%). Phenotypic screening of the respective soil samples has resulted in a promising Bacillus isolate that exhibited broad-spectrum antibacterial activities against various MDR pathogens. It was identified using microscopical, cultural, and molecular methods as Bacillus (B.) haynesii isolate MZ922052. The secondary metabolite gene analysis revealed the conservation of seven biosynthetic gene clusters of antibacterial metabolites namely, siderophore lichenicidin VK21-A1/A2 (95% identity), lichenysin (100%), fengycin (53%), terpenes (100%), bacteriocin (100%), Lasso peptide (95%) and bacillibactin (53%). In conclusion, metagenomic nanopore sequence analysis of soil samples coupled with conventional screening helped identify B. haynesii isolate MZ922052 harboring seven biosynthetic gene clusters of promising antimicrobial metabolites. This is the first report for identifying the bacteriocin, lichenysin, and fengycin biosynthetic gene clusters in B. haynesii MZ922052.

Microbial synthesis of bacitracin: Recent progress, challenges, and prospects

Microorganisms are important sources of various natural products that have been commercialized for human medicine and animal healthcare. Bacitracin is an important antibacterial natural product predominantly produced by Bacillus licheniformis and Bacillus subtilis, and it is characterized by a broad antimicrobial spectrum, strong activity and low resistance, thus bacitracin is extensively applied in animal feed and veterinary medicine industries. In recent years, various strategies have been proposed to improve bacitracin production. Herein, we systematically describe the regulation of bacitracin biosynthesis in genus Bacillus and its associated mechanism, to provide a theoretical basis for bacitracin overproduction. The metabolic engineering strategies applied for bacitracin production are explored, including improving substrate utilization, using an enlarged precursor amino acid pool, increasing ATP supply and NADPH generation, and engineering transcription regulators. We also present several approaches of fermentation process optimization to facilitate the industrial large-scale production of bacitracin. Finally, the challenges and prospects associated with microbial bacitracin synthesis are discussed to facilitate the establishment of high-yield and low-cost biological factories.

Increased flux through the TCA cycle enhances bacitracin production by Bacillus licheniformis DW2

The dodecapeptide antibiotic bacitracin, produced by several strains of Bacillus licheniformis and Bacillus subtilis, is widely used as an antibacterial animal feed additive. Several genetic strategies were explored to enhance its production. The availability of building block amino acids for bacitracin production was found to play an important role in its synthesis. In this study, the TCA cycle in the industrial strain B. licheniformis DW2 was strengthened by overexpression of the key enzymes citrate synthase and isocitrate dehydrogenase (ICDH). As the central metabolic pathway, the TCA cycle is a major source for energy supply and intermediates for anabolism. By enhancing flux through the TCA cycle, more energy and precursors were generated for amino acid biosynthesis and uptake, resulting in enlarged intracellular pool of bacitracin-containing amino acids for bacitracin production. This study unveiled the metabolic responses of the increased TCA cycle flux in B. licheniformis and provided a novel strategy for enhancing bacitracin production.

Optimization of Inexpensive Agricultural By-Products as Raw Materials for Bacitracin Production in Bacillus licheniformis DW2

Bacitracin is a broad-spectrum antibiotic used extensively as a feed additive. In this study, inexpensive agricultural by-products were used as nitrogen sources for bacitracin production. Based on both the orthogonal tests, a combination of 7% soybean meal (SBM) +2% low protein rapeseed cake (LPRC) was optimal for bacitracin production. Compared to the original formula, the titer of bacitracin increased by 20.5% reaching 910.4 U/ml in flasks. The titer of bacitracin and the ratio of bacitracin A increased by 12.4 and 6.8% in a 50-l fermentor. Furthermore, this study also explored the effects of exogenously adding different amino acids on the yield of bacitracin. The addition of Cys and Glu enhanced bacitracin production by 5.7 and 5.0%, respectively. This study provided the inexpensive nutrient inputs into efficient bacitracin production and also the insight to further research enabling better utilization of oil cakes for economic viability of the bioprocess industry.

The two-component regulatory system BacRS is associated with bacitracin 'self-resistance' of Bacillus licheniformis ATCC 10716

Bacitracin is a peptide antibiotic produced by several Bacillus licheniformis strains that is most active against other Gram-positive microorganisms, but not against the producer strain itself. Recently, heterologous expression of the bacitracin resistance mediating BcrABC transporter in Bacillus subtilis and Escherichia coli was described. In this study we could determine that the transporter encoding bcrABC genes are localized about 3 kb downstream of the 44-kb bacitracin biosynthetic operon bacABC. Between the bac operon and the bcrABC genes two orfs, designated bacR and bacS, were identified. They code for proteins with high homology to regulator and sensor proteins of two-component systems. A disruption mutant of the bacRS genes was constructed. While the mutant displayed no effects on the bacitracin production it exhibited highly increased bacitracin sensitivity compared to the wild-type strain. Western blot analysis of the expression of BcrA, the ATP-binding cassette of the transporter, showed in the wild-type a moderate BcrA induction in late stationary cells that accumulate bacitracin, whereas in the bacRS mutant cells the BcrA expression was constitutive. A comparison of bacitracin stressed and nonstressed wild-type cells in Western blot analysis revealed increasing amounts of BcrA and a decrease in BacR in the stressed cells. From these findings we infer that BacR acts as a negative regulator for controlling the expression of the bcrABC transporter genes.

The bacitracin biosynthesis operon of Bacillus licheniformis ATCC 10716: molecular characterization of three multi-modular peptide synthetases

BACKGROUND

The branched cyclic dodecylpeptide antibiotic bacitracin, produced by special strains of Bacillus, is synthesized nonribosomally by a large multienzyme complex composed of the three bacitracin synthetases BA1, BA2 and BA3. These enzymes activate and incorporate the constituent amino acids of bacitracin by a thiotemplate mechanism in a pathway driven by a protein template. The biochemical features of these enzymes have been studied intensively but little is known about the molecular organization of their genes.

RESULTS

The entire bacitracin synthetase operon containing the genes bacA-bacC was cloned and sequenced, identifying a modular structure typical of peptide synthetases. The bacA gene product (BA1, 598kDa) contains five modules, with an internal epimerization domain attached to the fourth; bacB encodes BA2 (297kDa), and has two modules and a carboxy-terminal epimerization domain; bacC encodes BA3, five modules (723kDa) with additional internal epimerization domains attached to the second and fourth. A carboxy-terminal putative thioesterase domain was also detected in BA3. A putative cyclization domain was found in BA1 that may be involved in thiazoline ring formation. The adenylation/thioester-binding domains of the first two BA1 modules were overproduced and the detected amino-acid specificity coincides with the first two amino acids in bacitracin. Disruption of chromosomal bacB resulted in a bacitracin-deficient mutant.

CONCLUSIONS

The genes encoding the bacitracin synthetases BA1, BA2 and BA3 are organized in an operon, the structure of which reflects the modular architecture expected of peptide synthetases. In addition, a putative thiazoline ring formation domain was identified in the BA1 gene.

Bacitracin production by a new strain of Bacillus subtilis. Extraction, purification, and characterization

A new strain of Bacillus subtilis C 126 was isolated from sugar cane fermentation and produced an antibiotic that inhibited the growth of Micrococcus flavus. The production of the antibiotic in culture medium followed to extraction with n-butanol, thin layer chromatography, and microbiological tests indicated that a polypeptide antibiotic was produced. The fraction obtained by Sephadex G-25 column and analyzed by HPLC indicated that bacitracin complex was produced.

Nonribosomal biosynthesis of peptide antibiotics

Peptide antibiotics are known to contain non-protein amino acids, D-amino acids, hydroxy acids, and other unusual constituents. In addition they may be modified by N-methylation and cyclization reactions. Their biosynthetic origin has been connected in many cases to an enzymatic system referred to as the 'thiotemplate multienzymic mechanism'. This mechanism includes the activation of the constituent residues as adenylates on the enzymic template, the acylation of specific template thiol groups, epimerization or N-methylation at this thioester stage, and polymerization in the sequence directed by the multienzymic structure with the aid of 4'-phosphopantetheine as a cofactor, including possible cyclization or terminal modification reactions. The reaction sequences leading to gramicidin S, tyrocidine, cyclosporine, bacitracin, polymyxin, actinomycin, enniatin, beauvericin, delta-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine and linear gramicidin are discussed. The structures of the multienzymes, their genetic organization, the biological functions of these peptides and results on related systems are discussed.

Molecular biology of antibiotic production in Bacillus

Several species of the genus Bacillus produce peptide antibiotics which are synthesized either through a ribosomal or non-ribosomal mechanism. The antibiotics gramicidin, tyrocidine, and bacitracin are synthesized nonribosomally by the multienzyme thiotemplate mechanism. Surfactin and mycobacillin are also synthesized nonribosomally but by a mechanism that, apparently, is distinct from that of the multienzyme thiotemplate. Other antibiotics such as subtilin are gene encoded and are ribosomally synthesized. Molecular genetic and DNA sequence analysis have shown that biosynthesis genes for some antibiotics are clustered into polycistronic transcription units and are under the control of global regulatory systems that govern the expression of genes that are induced when Bacillus cells enter stationary phase of growth. Future experiments involving the molecular dissection of peptide antibiotic biosynthesis genes in Bacillus will be attempted in hopes of further examining the mechanism and regulation of antibiotic production.

[Secondary metabolites as endogenous effectors of microbial cytodifferentiation]

The present survey covers the regulatory role of microbial secondary metabolites and related compounds as endogenous signals of cell differentiation of the producing organisms. Several antibiotics have been shown to exert autoregulatory effects on differentiation-associated functions. The mechanisms of self-protection of the producing cells against the autotoxicity of secondary metabolites are discussed in terms of an integral part of the modulation of signal strength. As a further topic, the review deals with the hormone-like interference of particular metabolites with differentiating cells. Conclusive discussion concerns the potential use of microbial signal molecules either as tools for directed manipulations of product syntheses or as pharmaceutics.

The use of antibiotics for studies of morphogenesis and differentiation in microorganisms

Numerous antibodies with a known mechanism of action are utilized as possible means for studying morphogenesis and differentiation. Inhibitors of biosynthesis of nucleic acids and proteins, compounds intervening with the synthesis and/or function of cell walls and membranes or compounds influencing the energy metabolism are particularly useful. The use of antibiotics for studies of the life cycle of viruses, bacteria, fungi, myxomycetes, protozoa and algae is analyzed in the present communication. Certain aspects of morphogenesis and functions of mitochondria and plastids were clarified with the aid of antibiotics. Relationships between production of antibiotics and differentiation of their producers are discussed in the final part of the paper.

Bacitracin production by the high-yielding mutant Bacillus licheniformis strain AL: stimulatory effect of L-leucine

The high-yielding mutant Bacillus licheniformis AL produced only small amounts of bacitracin in the chemically defined M2 medium. L-leucine markedly stimulated bacitracin production and restored the mutant strain to its place as a superior producer as compared to Bacillus licheniformis ATCC 10716. Leucine also stimulated the growth rate of the mutant. The stimulatory effect of leucine on bacitracin production is discussed in relation to control mechanisms and overproduction of antibiotics.

Development of a chemically defined medium for the synthesis of actinomycin D by Streptomyces parvulus

A chemically defined medium, consisting of d-fructose, l-glutamic acid, l-histidine, K(2)HPO(4), MgSO(4).7H(2)O, ZnSO(4).7H(2)O, CaCl(2).2H(2)O, FeSO(4).7H(2)O, CoCl(2).6H(2)O, and deionized water, was developed for synthesis of high yields (500 to 600 mug/ml) of actinomycin D by Streptomyces parvulus. Under these nutritional conditions, growth and actinomycin formation did not follow a typical trophophase-idiophase pattern. The amino acids appeared to have a sparing action on the utilization of d-fructose which was slowly and incompletely metabolized during mycelium development and antibiotic production. A significant repression of actinomycin synthesis by S. parvulus was observed when d-glucose (0.01 to 0.25%) was added to the culture medium. The repression was not due to a decline in the pH of the medium during glucose catabolism.

Possible functions of peptide antibiotics during growth of producer organisms: bacitracin and metal (II) ion transport

The inhibitory effect of bacitracin upon growth of the producer strain Bacillus licheniformis ATCC 10716 was dependent upon the presence of several different metal (II) ions, particularly Mn (II), Co (II), or Zn (II) ions. This supports our previous suggestion that the normal function of bacitracin during growth of the producer organism may be to promote the uptake of several divalent metal ions. Due to the striking similarity between the antimicrobial effect of bacitracin towards susceptible organisms and the effect of bacitracin towards the producer organisms B. licheniformis ATCC 10716, the possibility that the antimicrobial effect of bacitracin may be an induction of uptake of toxic amounts of metal ions is discussed. The possibility that peptide antibiotics may normally participate in ion transport during growth of producer organisms is also discussed.

Inactive form of edeine in the edeine-producing Bacillus brevis Vm 4 cells

1. Exogenous edeine inhibits the synthesis of DNA and protein, but not that of RNA, in extracts of edeine-producing Bacillus brevis Vm 4 cells. This is analogous to the effect of edeine on extracts obtained from edeine-sensitive cells. 2. Producer cells, in contrast to sensitive ones, are not permeable to exogenous edeine. DNA synthesis in producer cells rendered permeable by toluene treatment becomes sensitive to edeine. 3. No free edeine could be detected in post-log producer cells during maximal synthesis of edeine. Nascent edeine exists in the cell in a biologically inactive form, bound to a fast-sedimenting fraction. Edeine B, identical to the antibiotic present in the medium, is released from this fraction by mild treatment with alkali.

Bacitracin production by the neotype; bacillus licheniformis ATCC 14580

A small but significant bacitracin production has been observed in the neotype Bacillus licheniformis ATCC 14580. This strain produces bacitracin only during the phase of rapid growth. The bacitracin production ceases before growth is completed, and the relationship between growth and antibiotic production was not influenced by different environmental conditions. The maximum titre produced by the neotype strain was about 1 i.u. bacitracin/ml. This maximum titre was not influenced by the environmental conditions which resulted in a great variability of the maximum titre of the known bacitracin producer Bacillus licheniformis ATCC 10716. In contrast to B. licheniformis ATCC 10716, the bacitracin production of the neotype B. licheniformis ATCC 14580 was not stimulated by Mn(II)ions. It is suggested that bacitracin may be incidentally overproduced by certain strains grown in certain environments. The controlled bacitracin production by the neotype is not consistent with the definition of secondary metabolites and the hypothesis concerning the function of secondary metabolites after growth of the producer organisms.

Enzyme-bound intermediates in the biosynthesis of bacitracin

1. Bacitracin synthetase, a three-component enzyme complex which catalyzes synthesis of the dodecapeptide bacitracin A, has been prepared from Bacillus licheniformis strains ATCC 10716, AL and SB 319. During synthesis of bacitracin, the amino acids (smaller amounts) and peptides are covalently bound to the enzyme complex. The nature of the bindings suggest that the amino acids and peptides are thioester linked. 2. The peptides, identified by thin-layer chromatography after performic acid liberation were Ile-Cys, Ile-Cys-Leu, Ile-Cys-Leu-Glu, Ile-Cys-Leu-Glu, Ile-Cys-Leu-Glu-Ile, Ile-Cys-Leu-Glu-Ile-Lys-Orn, Ile-Cys-Leu-Glu-Ile-Ile-Orn-Ile, Ile-Cys-L-EU-Glu-Ile-Lys-Orn-Ile-Phe, Ile-Cys-Leu-Glu-Ile-L-YS-Orn-Ile-Phe-His-Phe-His and Ile-Cys-Leu-Glu-Ile-Lys-Orn-Ile-Phe-His-Asp. 3. The labelled peptides covalently bound to bacitracin synthetase were intermediates in bacitracin synthesis. 4. Chain growth is initiated on one enzyme component (A) by the addition of isoleucine and cysteine. The sequential addition of the other amino acids proceeds in the C-terminal direction until the pentapeptide is formed. Further addition of amino acids and production of bacitracin are obtained by adding the other enzyme components (B and C) to the incubation mixture.

On the function of the polypeptide antibiotic bacitracin in the producer strain Bacillus licheniformis

The growth of the bacitracin producing strain Bacillus licheniformis AL and the bacitracin-negative mutant SB 319 have been compared at different cultural conditions. Concentrations of the metal chelator EDTA which strongly inhibited the growth of the non-producer only slightly inhibited the growth of the bacitracin producer. The inhibitory effect of EDTA upon SB 319 was reversed by the addition of excess manganese(II)ions, cobalt(II)ions, or zinc(II)ions to the culture. The addition of several other ions had no such effect. The addition of bacitracin to the EDTA inhibited mutant also promoted growth. When the non-producer was mutated back to bacitracin production, the inhibitory effect of EDTA was lost. It is suggested that bacitracin may normally promote the uptake of several trace metals during growth of the producer organism.

The effect of bacitracin and Mn(II)ions upon the producer strain Bacillus licheniformis

The peptide antibiotic bacitracin is inhibitory to growth of the producer strain Bacillus licheniformis only in the presence of excess manganese(II)ions. Both the early and the late growth are inhibited in a similar manner upon addition of bacitracin and manganese(II)ions. Thus, B. licheniformis does not develop resistance to its own antibiotic during growth. Added bacitracin is stimulatory to growth of B. licheniformis in media with a very low content of manganese(II)ions. These results support the hypothesis that bacitracin participates in the manganese transport of the producer strain B. licheniformis.