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

Metabolic engineering of Bacillus licheniformis DW2 for ectoine production

Ectoine is a high-value protective agent with extensive applications in the fields of fine chemicals and biopharmaceuticals, and it is naturally synthesized by Halomonas in extreme environment, however, the current production level cannot meet the growing market demand. In this study, we aimed to develop an efficient and environmentally friendly ectoine production process using Bacillus licheniformis as the host organism. Through introducing ectoine synthetase gene cluster ectABC from Halomonas elongate, as well as optimizing ectABCHs expression by promoter and 5'-UTR optimization, ectoine titer was increased to 0.55 g/L. Furthermore, subsequent introduction of exogenous phosphoenolpyruvate carboxylase PPCEC and down-regulated expression of phosphoenolpyruvate carboxykinase PCK optimized the carbon flux through C4 anaplerotic pathway, and further benefited ectoine synthesis. Furthermore, the carbon flux towards aspartic acid accumulation was increased through optimization of glyoxylate and TCA cycles, accompanied with introducing lysCT311ICg and asdCg, and blocking by-products pathways, ectoine titer produced by B. licheniformis ECT12 was 2.00 g/L. Moreover, NADPH supply was enhanced by overexpression of exogenous NADH kinase Pos5Sc, and ectoine transportation was improved by introducing compatible solute transporter ProP from Escherichia coli, and the resulting B. licheniformis ECT14 was able to produce 2.60 g/L ectoine. Last but not the least, the ectoine yield of 3.29 g/L was attained in a 5-L fermenter. Taken together, this study not only established B. licheniformis as a framework for sustainable production of ectoine, but also paved the way for achieving the industrial production of ectoine and aspartic acid derivatives in the future.

Advancing Bacillus licheniformis as a Superior Expression Platform through Promoter Engineering

Bacillus licheniformis is recognised as an exceptional expression platform in biomanufacturing due to its ability to produce high-value products. Consequently, metabolic engineering of B. licheniformis is increasingly pursued to enhance its utility as a biomanufacturing vehicle. Effective B. licheniformis cell factories require promoters that enable regulated expression of target genes. This review discusses recent advancements in the characterisation, synthesis, and engineering of B. licheniformis promoters. We highlight the application of constitutive promoters, quorum sensing promoters, and inducible promoters in protein and chemical synthesis. Additionally, we summarise efforts to expand the promoter toolbox through hybrid promoter engineering, transcription factor-based inducible promoter engineering, and ribosome binding site (RBS) engineering.

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.

Metabolic Engineering of Aspartic Acid Supply Modules for Enhanced Production of Bacitracin in Bacillus licheniformis

Bacitracin, a type of cyclic dodecapeptide antibiotic mainly produced by Bacillus, is widely used in fields of veterinary drug and feed additive. Modularization of metabolic pathways based on the concept of synthetic biology has been widely used in the efficient synthesis of target products. Here, we want to improve bacitracin production through strengthening aspartic acid (Asp) supply in B. licheniformis DW2. First, exogenous Asp addition assays implied that strengthening Asp supply benefited bacitracin production. Second, Asp synthetic pathways were strengthened via overexpressing aspartate dehydrogenase AspD and asparaginase AnsB, attaining recombinant strain DW2-ASP2, and bacitracin yield produced by DW2-ASP2 was 862.81 U/mL, increased by 14.05% compared with that of DW2 (756.49 U/mL). Then, to improve precursor oxaloacetate (OAA) accumulation for Asp synthesis, pyruvate carboxylase PycA and carbonic anhydrase EcaA were co-overexpressed in DW2-ASP2, and malic enzyme gene malS was deleted to weak overflow metabolism of tricarboxylic acid, and the attained strain DW2-ASP7 showed further increased bacitracin production from 862.81 to 989.23 U/mL. Subsequently, transporter YveA was identified as an Asp exporter, and bacitracin yield was increased to 1025.26 U/mL via deleting yveA, attaining strain DW2-ASP9. Finally, Asp ammonia-lyase gene aspA was disrupted to weaken Asp degradation, and bacitracin yield of attained strain DW2-ASP10 reached 1059.86 U/mL, increased by 40.10% compared to DW2. Taken together, this research demonstrated that metabolic engineering of Asp metabolic modules is an efficient strategy for enhancing bacitracin production, and these strategies could also be applied in the production of other peptide-related metabolites.

Optimization of enhanced microbial production of zinc bacitracin by submerged fermentation technology

Bacitracin is one of the most important antibiotics used in different biomedical fields. It helps to achieve sizeable amount of foreign exchange due to its use in the poultry feed. The cheap agricultural wastes are readily available for the preparation of fermentation media used for bacitracin production. The microorganisms could be mutated with different chemicals and UV radiation to improve bacitracin production. Thus, the current study was focused on the synthesis of low-cost and effective bacitracin by mutant strains of Bacillus licheniformis, employing the submerged fermentation technique. The bacteria were exposed to the UV irradiation for various time periods ranging from 5 to 40 min. These mutants were named as BLAA-5-BLAA-40. Mutant strain BLAA-25 produced maximum bacitracin, with significantly high activity (142.81 IU/mg) against Klebsiella pneumoniae but less activity against Escherichia coli (115.19 IU/mg). Several fermentation conditions were investigated to optimize bacitracin production. The highest bacitracin yield was obtained by an inoculum size of 10%, fermentation period 48 hr, pH 7, T = 37°C, using soybean meal as a substrate. Among all substrates, cucumber peel was the substrate showing the highest minimum inhibitory concentration (2.3 mg/ml and 2.7 mg/ml against K. pneumoniae and E. coli respectively). A comparison between commercial and experimentally produced Zn bacitracin showed that commercial bacitracin has a low activity (63.2 IU/mg) as compared with experimental bacitracin. Hence, the agro wastes and mutation could be used to increase the synthesis of Zn bacitracin in B. licheniformis.

Enhanced Bacitracin Production by Systematically Engineering S-Adenosylmethionine Supply Modules in Bacillus licheniformis

Bacitracin is a broad-spectrum veterinary antibiotic that widely used in the fields of veterinary drug and feed additive. S-Adenosylmethionine (SAM) is a critical factor involved in many biochemical reactions, especially antibiotic production. However, whether SAM affects bacitracin synthesis is still unknown. Here, we want to analyze the relationship between SAM supply and bacitracin synthesis, and then metabolic engineering of SAM synthetic pathway for bacitracin production in Bacillus licheniformis. Firstly, our results implied that SAM exogenous addition benefited bacitracin production, which yield was increased by 12.13% under the condition of 40 mg/L SAM addition. Then, SAM synthetases and Methionine (Met) synthetases from B. licheniformis, Corynebacterium glutamicum, and Saccharomyces cerevisiae were screened and overexpressed to improve SAM accumulation, and the combination of SAM synthetase from S. cerevisiae and Met synthetase from B. licheniformis showed the best performance, and 70.12% increase of intracellular SAM concentration (31.54 mg/L) and 13.08% increase of bacitraicn yield (839.54 U/mL) were achieved in resultant strain DW2-KE. Furthermore, Met transporters MetN and MetP were, respectively, identified as Met exporter and importer, and bacitracin yield was further increased by 5.94% to 889.42 U/mL via deleting metN and overexpressing metP in DW2-KE, attaining strain DW2-KENP. Finally, SAM nucleosidase gene mtnN and SAM decarboxylase gene speD were deleted to block SAM degradation pathways, and bacitracin yield of resultant strain DW2-KENPND reached 957.53 U/mL, increased by 28.97% compared to DW2. Collectively, this study demonstrated that SAM supply served as the critical role in bacitracin synthesis, and a promising strain B. licheniformis DW2-KENPND was attained for industrial production of bacitracin.

Efficient biodegradation of organic matter using a thermophilic bacterium and development of a cost-effective culture medium for industrial use

Microorganisms with efficient organic matter degradation ability are essential for organic waste treatment. In this study, a thermophilic bacterium, Bacillus thermoliquefaciens, was identified to have excellent cellulase, amylase, and protease activity, and provided efficient degradation of food waste. This is the first report on the organic matter degradation potential of B. thermoliquefaciens. Using a "one-variable-at-a-time" approach and response surface methodology, the optimal culture conditions for B. thermoliquefaciens were determined to be a 5% inoculation level, 50 °C culture temperature, 25 mL filling volumes in 250 mL flasks, and 180 rpm shaking for 24 h. The optimized medium was formulated as 1 g Na₂HPO₄, 1 g KH₂PO₄, 0.05 g MgSO₄, 3 g NaCl, 0.05 g CaCl₂, 11.44 g wheat bran powder, 4.92 g soybean meal, and 1 L distilled water at pH 7.12. The maximum biomass attained was 1.57 ± 0.153 × 10⁹ CFU/mL. The cost of this medium was 4.18 times less than that before optimization. This promising result lays a foundation for future industrial application of this bacterium to the degradation of organic waste.

Improving the utilization rate of soybean meal for efficient production of bacitracin and heterologous proteins in the aprA-deficient strain of Bacillus licheniformis

Soybean meal is commonly applied as the raw material in the bio-fermentation industry, and bacitracin is a widely used feed additive in the feed industry. In this study, we investigated the influence of subtilisin enhancement on soybean meal utilization and bacitracin production in Bacillus licheniformis DW2, an industrial strain for bacitracin production. Firstly, blocking sRNA aprA expression benefited bacitracin synthesis, and the bacitracin yield produced by aprA-deficient strain DW2△PaprA reached 931.43 U/mL, 18.92% higher than that of DW2 (783.25 U/mL). The bacitracin yield was reduced by 14.27% in the aprA overexpression strain. Furthermore, our results showed that deficiency of aprA led to a 6.54-fold increase of the aprE transcriptional level and a 1.84-fold increase of subtilisin activity, respectively, which led to the increases of soybean meal utilization rate (28.86%) and precursor amino acid supplies for bacitracin synthesis. Additionally, strengthening the utilization rate of soybean meal also benefited heterologous protein production, and the α-amylase and nattokinase activities were respectively enhanced by 59.81% and 50.53% in aprA-deficient strains. Collectively, this research demonstrated that strengthening subtilisin production could improve the utilization rate of soybean meal and thereby enhance bacitracin and target protein production; also, this strategy would be useful for the improvement of protein/peptide production using soybean meal as the main nitrogen source in the fermentation process.

Metabolic Engineering of Main Transcription Factors in Carbon, Nitrogen, and Phosphorus Metabolisms for Enhanced Production of Bacitracin in Bacillus licheniformis

Primary metabolism plays a key role in the synthesis of secondary metabolite. In this study, the main transcription factors in carbon, nitrogen, and phosphorus metabolisms (CcpA, CcpC, CcpN, CodY, TnrA, GlnR, and PhoP) were engineered to improve bacitracin yield in Bacillus licheniformis DW2, an industrial strain for bacitracin production. First, our results demonstrated that deletions of ccpC and ccpN improved ATP and NADPH supplies, and the bacitracin yields were respectively increased by 14.02% and 16.06% compared with that of DW2, while it was decreased significantly in ccpA deficient strain DW2ΔccpA. Second, excessive branched chain amino acids (BCAAs) were accumulated in codY, tnrA, and glnR deletion strains DW2ΔcodY, DW2ΔtnrA, and DW2ΔglnR, which resulted in the nitrogen catabolite repressions and reductions of bacitracin yields. Moreover, overexpression of these regulators improved intracellular BCAA supplies, and further enhanced bacitracin yields by 14.17%, 12.98%, and 16.20%, respectively. Furthermore, our results confirmed that phosphate addition reduced bacitracin synthesis capability, and bacitracin yield was improved by 15.71% in gene phop deletion strain. On the contrary, overexpression of PhoP led to a 19.40% decrease of bacitracin yield. Finally, a combinatorial engineering of these above metabolic manipulations was applied, and bacitracin yield produced by the final strain DW2-CNCTGP (Simultaneously deleting ccpC, ccpN, phop and overexpressing glnR, codY, and tnrA in DW2) reached 1014.38 U/mL, increased by 35.72% compared to DW2, and this yield was the highest bacitracin yield currently reported. Taken together, this study implied that metabolic engineering of carbon, nitrogen, and phosphorus metabolism regulators is an efficient strategy to enhance bacitracin production, and provided a promising B. licheniformis strain for industrial production of bacitracin.

Enhancement of precursor amino acid supplies for improving bacitracin production by activation of branched chain amino acid transporter BrnQ and deletion of its regulator gene lrp in Bacillus licheniformis

Bacitracin, a new type of cyclic peptide antibiotic, is widely used as the feed additive in feed industry. Branched chain amino acids (BCAAs) are the key precursors for bacitracin synthesis. In this research, soybean meal was served as the raw material to supply precursor amino acids for bacitracin synthesis, and enhanced production of bacitracin was attempted by engineering BCAA transporter BrnQ and its regulator Lrp in the bacitracin industrial production strain Bacillus licheniformis DW2. Firstly, our results confirmed that Lrp negatively affected bacitracin synthesis in DW2, and deletion of lrp improved intracellular BCAA accumulations, as well as the expression level of BCAA transporter BrnQ, which further led to a 14.71% increase of bacitracin yield, compared with that of DW2. On the contrary, overexpression of Lrp decreased bacitracin yield by 12.28%. Secondly, it was suggested that BrnQ acted as a BCAA importer in DW2, and overexpression of BrnQ enhanced the intracellular BCAA accumulations and 10.43% of bacitracin yield. While, the bacitracin yield decreased by 18.27% in the brnQ deletion strain DW2△brnQ. Finally, BrnQ was further overexpressed in lrp deletion strain DW2△lrp, and bacitracin yield produced by the final strain DW2△lrp::BrnQ was 965.34 U/mL, increased by 22.42% compared with that of DW2 (788.48 U/mL). Collectively, this research confirmed that Lrp affected bacitracin synthesis via regulating the expression of BCAA transporter BrnQ and BCAA distributions, and provided a promising strain for industrial production of bacitracin.

Enhancement of Bacitracin Production by NADPH Generation via Overexpressing Glucose-6-Phosphate Dehydrogenase Zwf in Bacillus licheniformis

Bacitracin, a kind of cyclic peptide antibiotic mainly produced by Bacillus, has wide ranges of applications. NADPH generation plays an important role in amino acid synthesis, which might influence precursor amino acid supply for bacitracin production. In this study, we want to improve bacitracin yield by enhancing intracellular precursor amino acids via strengthening NAPDH generation pathways in the bacitracin industrial production strain Bacillus licheniformis DW2. Based on our results, strengthening of NADPH pathway genes (zwf, gnd, ppnk, pntAB, and udhA) could all improve bacitracin yields in DW2, and the glucose-6-phosphate dehydrogenase Zwf overexpression strain DW2::Zwf displayed the best performance, the yield of which (886.43 U/mL) was increased by 12.43% compared to DW2 (788.40 U/mL). Then, the zwf transcriptional level and Zwf activity of DW2::Zwf were increased by 12.24-fold and 1.57-fold; NADPH and NADPH/NADH were enhanced by 61.24% and 90.63%, compared with those of DW2, respectively. Moreover, the concentrations of intracellular precursor amino acids (isoleucine, leucine, cysteine, ornithine, lysine, glutamic acid) were all enhanced obviously for bacitracin production in DW2::Zwf. Collectively, this research constructed a promising B. licheniformis strain for industrial production of bacitracin, more importantly, which revealed that strengthening of NADPH generation is an efficient strategy to improve precursor amino acid supplies for bacitracin production.

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.