Knockout of rapC Improves the Bacillomycin D Yield Based on De Novo Genome Sequencing of Bacillus amyloliquefaciens fmbJ

Production, characterization, and potential applications of lipopeptides in food systems: A comprehensive review

Lipopeptides are a class of lipid-peptide-conjugated compounds with differing structural features. This structural diversity is responsible for their diverse range of biological properties, including antimicrobial, antioxidant, and anti-inflammatory activities. Lipopeptides have been attracting the attention of food scientists due to their potential as food additives and preservatives. This review provides a comprehensive overview of lipopeptides, their production, structural characteristics, and functional properties. First, the classes, chemical features, structure-activity relationships, and sources of lipopeptides are summarized. Then, the gene expression and biosynthesis of lipopeptides in microbial cell factories and strategies to optimize lipopeptide production are discussed. In addition, the main methods of purification and characterization of lipopeptides have been described. Finally, some biological activities of the lipopeptides, especially those relevant to food systems along with their mechanism of action, are critically examined.

Enhanced Iturin A Production of Engineered Bacillus amyloliquefaciens by Knockout of Endogenous Plasmid and Rap Phosphatase Genes

Iturin A biosynthesis has garnered considerable interest, yet bottlenecks persist in its low productivity in wild strains and the ability to engineer Bacillus amyloliquefaciens producers. This study reveals that deleting the endogenous plasmid, plas1, from the wild-type B. amyloliquefaciens HM618 notably enhances iturin A synthesis, likely related to the effect of the Rap phosphatase gene within plas1. Furthermore, inactivating Rap phosphatase-related genes (rapC, rapF, and rapH) in the genome of the strain also improved the iturin A level and specific productivity while reducing cell growth. Strategic rap genes and plasmid elimination achieved a synergistic balance between cell growth and iturin A production. Engineered strain HM-DR13 exhibited an increase in iturin A level to 849.9 mg/L within 48 h, significantly shortening the production period. These insights underscore the critical roles of endogenous plasmids and Rap phosphatases in iturin A biosynthesis, presenting a novel engineering strategy to optimize iturin A production in B. amyloliquefaciens.

Improvement of lipopeptide production in Bacillus subtilis HNDF2-3 by overexpression of the sfp and comA genes

Bacillus subtilis HNDF2-3 can produce a variety of lipopeptide antibiotics with lower production. To improve its lipopeptide production, three genetically engineered strains were constructed. The results of real-time PCR showed that the highest transcriptional levels of the sfp gene in F2-3sfp, F2-3comA and F2-3sfp-comA were 29.01, 6.65 and 17.50 times of the original strain, respectively, while the highest transcriptional levels of the comA gene in F2-3comA and F2-3sfp-comA were 10.44 and 4.13 times of the original strain, respectively. The results of ELISA showed that the malonyl-CoA transacylase activity of F2-3comA was the highest, reaching 18.53 IU/L at 24 h, the data was 32.74% higher than that of the original strain. The highest total lipopeptide production of F2-3sfp, F2-3comA and F2-3sfp-comA induced by IPTG at optimal concentration were 33.51, 46.05 and 38.96% higher than that of the original strain, respectively. The results of HPLC showed that iturin A production of F2-3sfp-comA was the highest, which was 63.16% higher than that of the original strain. This study laid the foundation for further construction of genetically engineered strains with high lipopeptide production.

Available strategies for improving the biosynthesis of surfactin: a review

Surfactin is an excellent biosurfactant with a wide range of application prospects in many industrial fields. However, its low productivity and high cost have largely limited its commercial applications. In this review, the pathways for surfactin synthesis in Bacillus strains are summarized and discussed. Further, the latest strategies for improving surfactin production, including: medium optimization, genome engineering methods (rational genetic engineering, genome reduction, and genome shuffling), heterologous synthesis, and the use of synthetic biology combined with metabolic engineering approaches to construct high-quality artificial cells for surfactin production using xylose, are described. Finally, the prospects for improving surfactin synthesis are discussed in detail.

Detection and evaluation of volatile and non-volatile antifungal compounds produced by Bacillus spp. strains

The identification of antifungal compounds produced by microorganisms is crucial in the context of sustainable agriculture. Bacteria of the genus Bacillus have a broad spectrum of action that can influence plant growth and control pests, vectors of public health relevance and phytopathogens. Lipopeptides are the main compounds related to the biological control of several pathogen species. Strains with biotechnological potential are identified by means of in vitro bioassays and molecular tests. In this study, strains from the Bacillus Bank of Brazilian Agricultural Research Corporation (EMBRAPA/DF/Brazil) were selected to control the fungal pathogens Sclerotinia sclerotiorum and Fusarium oxysporum by pairing assays. The detection of genes for biosynthesis of antifungal compounds from strains with high pathogen-inhibition capacity was correlated with peptide synthesis, such as bacillomycin D, fengycin d, bacilysin and surfactin. Their gene expression in contact with the pathogen was analyzed by Real-Time PCR. The volatile organic compounds produced by selected Bacillus strains were identified and quantified. In co-culture assays, the inhibition zone between Bacillus strains and Sclerotinia sclerotiorum was evaluated by scanning electron microscopy. Thirteen potentially anti-pathogenic strains were selected. Genes related to the synthesis of antifungal peptides were detected in 11 of them. In five strains, all tested genes were detected. Bacillomycin was the most frequently found lipopeptide gene. The fungus-bacteria interaction potentiated the production of volatiles. Several ketones and other volatile compounds with antifungal activity were identified. Relevant morphological changes in the fungus were observed when paired with bacteria. The study demonstrated the efficacy of the selected strains with regard to the biological control of phytopathogens and their biotechnological potential.

A review on surfactin: molecular regulation of biosynthesis

Surfactin has many biological activities, such as inhibiting plant diseases, resisting bacteria, fungi, viruses, tumors, mycoplasma, anti-adhesion, etc. It has great application potential in agricultural biological control, clinical medical treatment, environmental treatment and other fields. However, the low yield has been the bottleneck of its popularization and application. It is very important to understand the synthesis route and control strategy of surfactin to improve its yield and purity. In this paper, based on the biosynthetic pathway and regulatory factors of surfactin, its biosynthesis regulation strategy was comprehensively summarized, involving enhancement of endogenous and exogenous precursor supply, modification of the synthesis pathway of lipid chain and peptide chain, improvement of secretion and efflux, and manipulation some global regulatory factors, such as Spo0A, AbrB, ComQXP, phrCSF, etc. to directly or indirectly stimulate surfactin synthesis. And the current production and separation and purification process of surfactin are briefly described. This review also provides a scientific reference for promoting surfactin production and its applications in various fields.

Deletion of Rap-phosphatases for quorum sensing control in Bacillus and its effect on surfactin production

The complex regulatory network in Bacillus, known as quorum sensing, offers many opportunities to modify bacterial gene expression and hence to control bioprocesses. One target regulated by this mechanism is the activity of the P_srfA promoter, which is engaged in the formation of lipopeptide surfactin. It was hypothesised that deletion of rapC, rapF and rapH, encoding for prominent Rap-phosphatases known to affect P_srfA activity, would enhance surfactin production. Therefore, these genes were deleted in a sfp⁺ derivative of B. subtilis 168 with subsequent evaluation of quantitative data. Up to the maximum product formation of the reference strain B. subtilis KM1016 after 16 h of cultivation, the titers of the rap deletion mutants did not exceed the reference. However, an increase in both product yield per biomass Y_P/X and specific surfactin productivity q_surfactin was observed, without any considerable effect on the ComX activity. By extending the cultivation time, a 2.7-fold increase in surfactin titer was observed after 24 h for strain CT10 (ΔrapC) and a 2.5-fold increase for CT11 (ΔrapF) compared to the reference strain KM1016. In addition, Y_P/X was again increased for strains CT10 and CT11, with values of 1.33 g/g and 1.13 g/g, respectively. Interestingly, the effect on surfactin titer in strain CT12 (ΔrapH) was not as distinct, although it achieved the highest promoter activity (P_srfA-lacZ). The data presented support the possibility of involving the quorum sensing system of Bacillus in bioprocess control as shown here on the example of lipopeptide production.

Biocontrol potential of bacteria belonging to the Bacillus subtilis group against pests and diseases of agricultural interest through genome exploration

The usage of microorganisms as biocontrol agents and biofertilizers has been recommended and recognized as an ecologically correct alternative to maintaining the productivity and safety of crops. Thus, the objectives of this work were to characterize twelve strains belonging to Invertebrate Bacteria Collection of Embrapa Genetic Resources and Biotechnology by molecular, morphological, and biochemical methods and to evaluate the pathogenicity of these strains against pests and diseases of agricultural interest. The morphological characteristic of the strains was performed according to the principles of Bergy's Manual of Systematic Bacteriology. The genomes of the 12 strains were sequenced in Macrogen, Inc. (Seoul, Korea) using the HiSeq2000 and GS-FLX Plus high-performance platforms. In the determination of antibiotic sensibility profiles, disc-diffusion methods (Cefar Diagnótica Ltda) were adopted©. Selective bioassays were carried out with insects of the Lepidoptera (Spodoptera frugiperda, Helicoverpa armigera, and Chrysodeixis includens), Coleoptera (Anthonomus grandis), Diptera (Aedes aegypti) and Hemiptera (Euschistus heros) orders, and with the nematode Caenorhabditis elegans. In addition, the antagonistic action of the phytopathogens Fusarium oxysporum f. sp. vasinfectum and Sclerotinia sclerotiorum against the strains under study, and in vitro assays of phosphate solubilization were also performed. Sequencing of the complete genome of the 12 strains determined that all of them belonged to the Bacillus subtilis sensu lato group. In the strains genome were detected genic clusters responsible for encoding secondary metabolites such as surfactin, iturin, fengycins/plipastatin, bacillomycin, bacillisin, and siderophores. Due to the production of these compounds, there was a survival reduction of the Lepidoptera order insects and a reduction in the phytopathogens mycelial growth. These results show that the species of group B. subtilis s.l. can become promising microbiological alternatives to pest and disease control.

Effect and regulation of fatty acids on bacillomycin D synthesis

Bacillomycin D is a cyclic antimicrobial lipopeptide that has excellent antifungal effects, but its application is limited due to its low yield. At present, it is not clear whether fatty acids regulate the synthesis of bacillomycin D. Therefore, the effects of nine fatty acids on the yield of bacillomycin D produced by Bacillus amyloliquefaciens fmbJ were studied. The results showed that sodium propionate, propionic acid, and butyric acid could increase the yield of bacillomycin D by 44, 40, and 10%, respectively. Reverse transcription polymerase chain reaction (RT-PCR) was used to detect the expression levels of bacillomycin D synthesis gene, signaling factors and genes related to fatty acid metabolism, so as to explore the mechanism of sodium propionate regulating bacillomycin D synthesis. In conclusion, sodium propionate could accelerate the tricarboxylic acid cycle and promoted spore formation, cell movement, the secretion of extracellular protease and the transcription of bacillomycin D synthesis gene by upregulating the expression of signal factors degU, degQ, sigH, sigM and spo0A and ultimately promoted the synthesis of bacillomycin D. In this study, the mechanism of sodium propionate increasing bacillomycin D production was explored from multiple perspectives, which provided theoretical support for the large-scale production of bacillomycin D and was expected to promote its wide application in food, agriculture and medicine fields.

Anti-toxicogenic fungi and toxin-reducing effects of bacillomycin D in combination with fungicides

Mycotoxins are toxic secondary metabolites produced by fungus including Aspergillus and Fusarium. They can contaminate food and cause major health issues. Bacillomycin D (BD) is a natural antimicrobial lipopeptide generated by Bacillus that has excellent antifungal capabilities, but its high price prevents it from being widely used. Chemically produced and essential oil-based fungicides are also currently the most frequent types. In the study, the effects of combining BD with two types of fungicides on the growth of toxicogenic fungi as well as the generation of deoxynivalenol (DON) and fumonisin B₁ (FB₁) were examined. It was discovered that BD was more effective in suppressing molds than the other two types of fungicides, and it could be combined with synthetic or essential oil-based fungicides to provide a synergistic or additive effect. BD 31.25 μg/mL + Thymol (Thy) 7.81 μg/mL and BD 11.45 μg/mL + Cinnamon oil (Cin) 3.90 μg/mL inhibited F. graminearum, respectively. The combination of BD+Thy and BD+Cin at this concentration considerably reduced 60%-80% spore germination, when DON dropped below 300 ng/L. Furthermore, both combinations suppressed F. moniliforme growth and FB₁ synthesis in a dose-dependent manner at lower concentrations. At an action dose of 2 MIC, FB₁ production might be reduced to less than 100 ng/L. Our findings indicated that BD might interact synergistically with various fungicides, suggesting that it could be useful in the field of antifungal and toxicity reduction in food.

TetR-Type Regulator Lp_2642 Positively Regulates Plantaricin EF Production Based on Genome-Wide Transcriptome Sequencing of Lactiplantibacillus plantarum 163

Whole-genome and transcriptome sequences of Lactiplantibacillus plantarum 163 are provided. There was one circular chromosome and four circular plasmids, with sizes of 3,131,367; 56,674; 49,140; 43,628; and 36,387 bp, respectively, in L. plantarum 163. The regulator Lp_2642 was selected from the genome data, the overexpression of which increased the transcriptional levels of related genes in plantaricin EF biosynthesis and enhanced plantaricin EF production. Its production was 17.30 mg/L in 163 (Lp_2642), which was 1.29-fold higher than that of the original strain. The regulation mechanism demonstrated that Lp_2642 can bind to three sites of plnA promoter, which enhances its transcription and expression, thereby increasing plantaricin EF production. Amino acids Asn-100, Asn-64, and Thr-69 may play a key role in the binding of Lp_2642. These results provide a novel strategy for mass production of plantaricin EF, which facilitates its large-scale production and application in the agriculture and food industries as a preservative.

Comments on the ochratoxin A degradation mechanism by Lysobacter sp. CW239 - Wei Wei et al. (2020)

This is a research comment on the ochratoxin A (OTA) degradation mechanism by Lysobacter sp. CW239 regarding the previous publication in Environmental Pollution (Wei et al., 2020). Three possible degradation mechanisms were discussed in the referred publication, but without definite evidences, it was not clear which one worked actually. Here, the gene cp4 deficient mutant CW239^Δcp4 was successfully constructed, and the carboxypeptidase CP4 role on OTA degradation in strain CW239 was validated in vivo. As a result, the mutant CW239^Δcp4 without gene cp4 showed less than 10% reduction of 24 hrs degradation ratio compared to wide-type strain CW239. After the gene cp4 complemented to CW239^Δcp4, the complementary strain (+)cp4 recovered the degradation ability to wide-type. The validation result indicated that the third degradation mechanism (i.e., OTA is degraded by joint action of multiple enzymes in CW239) proposed previous (Wei et al., 2020) was correct route for the degradation strain. This commentary was significant to the following studies on the pollutant detoxify strains with similar degradation characters between identified enzyme and the host strain.

CodY, ComA, DegU and Spo0A controlling lipopeptides biosynthesis in Bacillus amyloliquefaciens fmbJ

AIM

In the study, we investigated the regulatory effects of these genes (codY, comA, degU and spo0A) on the biosynthesis of three lipopeptides (bacillomycin D, fengycin and surfactin) in Bacillus amyloliquefaciens.

METHODS AND RESULTS

The codY, comA, degU and spo0A genes in B. amyloliquefaciens fmbJ were knocked out. The results showed that the productions of bacillomycin D were significantly reduced compared with that of fmbJ. Their deletion induced great changes in the levels of transcripts specifying metabolic pathways, quorum sensing system and substance transport system in fmbJ. Moreover, overexpression of these genes improved the productions of bacillomycin D. In particular, the overexpression of spo0A enhanced bacillomycin D yield up to 648·9 ± 60·9 mg l^-1 from 277·3 ± 30·5 mg l^-1 . In addition, the yields of surfactin in fmbJΔcodY and fmbJΔdegU were significantly improved, and the regulatory factor CodY had no significant effect on the synthesis of fengycin.

CONCLUSIONS

These genes positively regulated the expression of bacillomycin D and fengycin synthase genes in strain fmbJ. However, codY and degU negatively regulated surfactin biosynthesis. Moreover, it was found that CodY had a concentration dependence on bacillomycin D synthesis. Spo0A might play a direct regulatory role in the synthesis and secretion of bacillomycin D.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study indicated that genetic engineering of regulatory genes was an effective strategy to improve the yields of antimicrobial lipopeptides and provided promising strains for industrial production of lipopeptides.

Prebiotic, Probiotic, Antimicrobial, and Functional Food Applications of Bacillus amyloliquefaciens

Bacillus amyloliquefaciens belongs to the genus Bacillus and family Baciliaceae. It is ubiquitously found in food, plants, animals, soil, and in different environments. In this review, the application of B. amyloliquefaciens in probiotic and prebiotic microbes in fermentation, synthesis, and hydrolysis of food compounds is discussed as well as further insights into its potential application and gaps. B. amyloliquefaciens is also a potential microbe in the synthesis of bioactive compounds including peptides and exopolysaccharides. In addition, it can synthesize antimicrobial compounds (e.g., Fengycin, and Bacillomycin Lb), which makes its novelty in the food sector greater. Moreover, it imparts and improves the functional, sensory, and shelf life of the end products. The hydrolysis of complex compounds including insoluble proteins, carbohydrates, fibers, hemicellulose, and lignans also shows that B. amyloliquefaciens is a multifunctional and potential microbe which can be applied in the food industry and in functional food processing.

Exploration of production of C14 and C15 bacillomycin D homologues with enzymatic hydrolysis from maize straws using fed-batch fermentation by Bacillus subtilis NS-174

A strain with strong antifungal activity, Bacillus subtilis NS-174, was identified and the antifungal compounds were purified and structurally analyzed by high performance liquid chromatography-mass spectrometry/mass spectrometry (HPLC-MS/MS).

Synergistic Effect of Combined Application of a New Fungicide Fluopimomide with a Biocontrol Agent Bacillus methylotrophicus TA-1 for Management of Gray Mold in Tomato

Gray mold caused by Botrytis cinerea can be a severe disease of tomato infecting leaves and fruits of tomato plants. Chemical control is currently the most effective and reliable method; however, application of fungicides has many drawbacks. The combination of biological control agents with newly developed fungicides may be a practicable method to control B. cinerea. Fluopimomide is a newly developed fungicide with a novel mode of action. Bacillus methylotrophicus TA-1, isolated from rhizosphere soil of tomato, is a bacterial strain with a broad spectrum of antimicrobial activities. Little information is currently available about the effect of fluopimomide and its integrated effect on B. cinerea. Therefore, laboratory, pot, and field experiments were carried out to determine the effects of fluopimomide alone and in combination with B. methylotrophicus TA-1 against gray mold on tomato. The in vitro growth of B. methylotrophicus TA-1 was unaffected by 100 mg liter^-1 fluopimomide. Inhibition of B. cinerea mycelial growth was significantly increased under combined treatment of fluopimomide and B. methylotrophicus TA-1. In greenhouse experiments, efficacy against gray mold was significantly greater by an integration of fluopimomide and B. methylotrophicus TA-1 than by either alone; control efficacy of fluopimomide at 50 and 100 g ha^-1 in combination with B. methylotrophicus TA-1 at 10⁸ colony-forming units (cfu) ml^-1 reached 70.16 and 69.32%, respectively, compared with the untreated control. In both field trials during 2017 and 2018, control efficacy was significantly higher for the combination of fluopimomide at 50 and 100 g ha^-1 in combination with B. methylotrophicus TA-1 than for either treatment alone. The results from this study indicated that integration of the new fungicide fluopimomide with the biocontrol agent B. methylotrophicus TA-1 synergistically increased control efficacy of the fungicide against gray mold of tomato.

A comprehensive genomic and growth proteomic analysis of antitumor lipopeptide bacillomycin Lb biosynthesis in Bacillus amyloliquefaciens X030

Lipopeptides (such as iturin, fengycin, and surfactin) from Bacillus possess antibacterial, antifungal, and antiviral activities and have important application in agriculture and pharmaceuticals. Although unremitting efforts have been devoted to improve lipopeptide production by designing gene regulatory circuits or optimizing fermentation process, little attention has been paid to utilizing multi-omics for systematically mining core genes and proteins during the bacterial growth cycle. Here, lipopeptide bacillomycin Lb from new Bacillus amyloliquefaciens X030 was isolated and first found to have anticancer activity in various cancer cells (such as SMMC-7721 and MDA-MB-231). A comprehensive genomic and growth proteomic analysis of X030 revealed bacillomycin Lb biosynthetic gene cluster, key enzymes and potential regulatory proteins (PerR, PhoP, CcpA, and CsfB), and novel links between primary metabolism and bacillomycin Lb production in X030. The antitumor activity of the fermentation supernatant supplemented with amino acids (such as glutamic acid) and sucrose was significantly increased, verifying the role of key metabolic switches in the metabolic regulatory network. Quantitative real-time PCR analysis confirmed that 7 differential expressed genes exhibited a positive correlation between changes at transcriptional and translational levels. The study not only will stimulate the deeper and wider antitumor study of lipopeptides but also provide a comprehensive database, which promotes an in-depth analysis of pathways and networks for complex events in lipopeptide biosynthesis and regulation and gives great help in improving the yield of bacillomycin Lb (media optimization, genetic modification, or pathway engineering).

Engineered biosynthesis of cyclic lipopeptide locillomycins in surrogate host Bacillus velezensis FZB42 and derivative strains enhance antibacterial activity

Locillomycins are cyclic lipononapeptides assembled by a nonlinear hexamodular NRPS and have strong antibacterial activity. In this study, we genetically engineered Bacillus velezensis FZB42 as a surrogate host for the heterologous expression of the loc gene cluster for locillomycins. The fosmid N13 containing whole loc gene cluster was screened from the B. velezensis 916 genomic library. Subsequently, a spectinomycin resistance cassette, and the cassette fused with an IPTG inducible promoter Pspac, was introduced in the fosmid N13 using λ Red recombination system, respectively. The resulting fosmids, designated N13+Spec and N13+PSSpec, were used for the transformation of B. velezensis FZB42 to obtain derivative strains FZBNPLOC and FZBPSLOC. RT-PCR and qRT-PCR results revealed the efficient heterologous expression of the loc gene cluster in both derivative strains. Particularly, there was positive correlation between the derivative FZBPSLOC strain and the enhanced production of locillomycins upon addition of the inducer IPTG with the highest production of locillomycins at 15-fold more than that of B. velezensis 916. This overproduction of locillomycins was also related to the enhancement of antibacterial activity against methicillin-resistant Staphylococcus aureus, and exhibited moderate changes in its hemolytic activity. Together our findings demonstrate that the nonlinear hexamodular NRPS, encoded by the loc gene cluster from B. velezensis 916, is sufficient for the biosynthesis of cyclic lipononapeptide locillomycins in the surrogate host B. velezensis FZB42. Moreover, the FZBPSLOC strain will also be useful for further development of novel locillomycins derivatives with improved antibacterial activity.