Enhanced production of heterologous proteins by Bacillus licheniformis with defective d-alanylation of lipoteichoic acid

Inactivation of the conserved protease LonA increases production of xylanase and amylase in Bacillus subtilis

BACKGROUND

Bacillus subtilis is widely used for industrial enzyme production due to its capacity to efficiently secrete proteins. However, secretion efficiency of enzymes varies widely, and optimizing secretion is crucial to make production commercially viable. Previously, we have shown that overexpression of the xylanase XynA lowers expression of Clp protein chaperones, and that inactivation of CtsR, which regulates and represses clp transcription, increases the production of XynA. In the current study, we examined whether the same is the case for overexpression of the α-amylase AmyM from Geobacillus stearothermophilus by B. subtilis, and why XynA shows a different timing of secretion compared to AmyM.

RESULTS

Transcriptome analyses revealed that B. subtilis cells overexpressing AmyM exhibited a distinct profile compared to XynA overexpressing cells, however there were also similarities and in both cases expression of CtsR controlled genes was downregulated. In contrast to XynA, inactivation of CtsR did not improve AmyM production. Upregulation of other protein chaperones, including GroEL/ES and DnaJ/K, by inactivating their transcriptional repressor HrcA, had almost no effect on XynA yields and in fact considerably lowered that of AmyM. Despite using the same promoter, the production of XynA peaks well before AmyM reaches its optimal secretion rate. Transcriptome and ribosome profiling indicated that this is neither related to transcription nor to translation regulation. We show that the reduced secretion in the stationary phase is partially due to the activity of secreted proteases, but also due to the activity of the intracellular protease LonA. The absence of this protein resulted in a 140% and 20% increased production for XynA and AmyM, respectively.

CONCLUSION

The combination of transcriptome and ribosome profiling offered important information to determine at which cellular level production bottlenecks occurred. This helped us to identify LonA protease as an important factor influencing enzyme production yields in B. subtilis.

Design-build-test of recombinant Bacillus subtilis chassis cell by lifespan engineering for robust bioprocesses

Microbial cell factories utilize renewable raw materials for industrial chemical production, providing a promising path for sustainable development. Bacillus subtilis is widely used in industry for its food safety properties, but challenges remain in the limitations of microbial fermentation. This study proposes a novel strategy based on lifespan engineering to design robust B. subtilis chassis cells to supplement traditional metabolic modification strategies that can alleviate cell autolysis, tolerate toxic substrates, and get a higher mass transfer efficiency. The modified chassis cells could produce high levels of l-glutaminase, and tolerate hydroquinone to produce α-arbutin efficiently. In a 5 L bioreactor, the l-glutaminase enzyme activity of the final strain CRE15TG was increased to 2817.4 ± 21.7 U mL-1, about 1.98-fold compared with that of the wild type. The α-arbutin yield of strain CRE15A was increased to 134.7 g L-1, about 1.34-fold compared with that of the WT. To our knowledge, both of the products in this study performed the highest yields reported so far. The chassis modification strategy described in this study can Improve the utilization efficiency of chassis cells, mitigate the possible adverse effects caused by excessive metabolic modification of engineered strains, and provide a new idea for the future design of microbial cell factories.

Phenotypic and genomic insights into mutant with high nattokinase-producing activity induced by carbon ion beam irradiation of Bacillus subtilis

Nattokinase (NK) is found in fermented foods and has high fibrinolytic activity, which makes it promising for biological applications. In this study, a mutant strain (Bacillus subtilis ZT-S1, 5529.56 ± 183.59 U/mL) with high NK-producing activity was obtained using 12C6+ heavy ion beam mutagenesis for the first time. The surface morphology of B. subtilis is also altered by changes in functional groups caused by heavy ion beams. Furthermore, B. subtilis ZT-S1 required more carbon and nitrogen sources and reached stabilization phase later. Comparative genome analysis revealed that most of the mutant implicated genes (oppA, appA, kinA, spoIIP) were related to spore formation. And the affected rpoA is related to the synthesis of the NK-coding gene aprE. In addition, the B. subtilis ZT-S1 obtained by mutagenesis had good genetic stability. This study further explores the factors affecting NK activity and provides a promising microbial resource for NK production in commercial applications.

Integrated Genomics and Transcriptomics Provide Insights into Salt Stress Response in Bacillus subtilis ACP81 from Moso Bamboo Shoot (Phyllostachys praecox) Processing Waste

Salt stress is detrimental to the survival of microorganisms, and only a few bacterial species produce hydrolytic enzymes. In this study, we investigated the expression of salt stress-related genes in the salt-tolerant bacterial strain Bacillus subtilis ACP81, isolated from bamboo shoot processing waste, at the transcription level. The results indicate that the strain could grow in 20% NaCl, and the sub-lethal concentration was 6% NaCl. Less neutral protease and higher cellulase and β-amylase activities were observed for B. subtilis ACP81 under sub-lethal concentrations than under the control concentration (0% NaCl). Transcriptome analysis showed that the strain adapted to high-salt conditions by upregulating the expression of genes involved in cellular processes (membrane synthesis) and defense systems (flagellar assembly, compatible solute transport, glucose metabolism, and the phosphotransferase system). Interestingly, genes encoding cellulase and β-amylase-related (malL, celB, and celC) were significantly upregulated and were involved in starch and sucrose metabolic pathways, and the accumulated glucose was effective in mitigating salt stress. RT-qPCR was performed to confirm the sequencing data. This study emphasizes that, under salt stress conditions, ACP81 exhibits enhanced cellulase and β-amylase activities, providing an important germplasm resource for saline soil reclamation and enzyme development.

Microbial nattokinase: from synthesis to potential application

Nattokinase (NK) is an alkaline serine protease with strong thrombolytic activity produced by Bacillus spp. or Pseudomonas spp. It is a potential therapeutic agent for thrombotic diseases because of its safety, economy, and lack of side effects. Herein, a comprehensive summary and analysis of the reports surrounding NK were presented, and the physical-chemical properties and producers of NK were first described. The process and mechanism of NK synthesis were summarized, but these are vague and not specific enough. Further results may be achieved if detection techniques such as multi-omics are used to explore the process of NK synthesis. The purification of NK has problems such as a complicated operation and low recovery rate, which were found when summarizing the techniques to improve the quality of finished products. If multiple simple and efficient precipitation methods and purification materials are combined to purify NK, it may be possible to solve the current challenges. Additionally, the application potential of NK in biomedicine was reviewed, but functional foods with NK are challenging for acceptance in daily life due to their unpleasant odor. Accordingly, multi-strain combination fermentation or food flavoring agents can improve the odor of fermented foods and increase people's acceptance of them. Finally, the possible future directions focused on NK studies were proposed and provided suggestions for subsequent researchers.

Research Progress on the Effect of Autolysis to Bacillus subtilis Fermentation Bioprocess

Bacillus subtilis is a gram-positive bacterium, a promising microorganism due to its strong extracellular protein secretion ability, non-toxic, and relatively mature industrial fermentation technology. However, cell autolysis during fermentation restricts the industrial application of B. subtilis. With the fast advancement of molecular biology and genetic engineering technology, various advanced procedures and gene editing tools have been used to successfully construct autolysis-resistant B. subtilis chassis cells to manufacture various biological products. This paper first analyses the causes of autolysis in B. subtilis from a mechanistic perspective and outlines various strategies to address autolysis in B. subtilis. Finally, potential strategies for solving the autolysis problem of B. subtilis are foreseen.

Occurrence and potential mechanism of holin-mediated non-lytic protein translocation in bacteria

Holins are generally believed to generate large membrane lesions that permit the passage of endolysins across the cytoplasmic membrane of prokaryotes, ultimately resulting in cell wall degradation and cell lysis. However, there are more and more examples known for non-lytic holin-dependent secretion of proteins by bacteria, indicating that holins somehow can transport proteins without causing large membrane lesions. Phage-derived holins can be used for a non-lytic endolysin translocation to permeabilize the cell wall for the passage of secreted proteins. In addition, clostridia, which do not possess the Tat pathway for transport of folded proteins, most likely employ non-lytic holin-mediated transport also for secretion of toxins and bacteriocins that are incompatible with the general Sec pathway. The mechanism for non-lytic holin-mediated transport is unknown, but the recent finding that the small holin TpeE mediates a non-lytic toxin secretion in Clostridium perfringens opened new perspectives. TpeE contains only one short transmembrane helix that is followed by an amphipathic helix, which is reminiscent of TatA, the membrane-permeabilizing component of the Tat translocon for folded proteins. Here we review the known cases of non-lytic holin-mediated transport and then focus on the structural and functional comparison of TatA and TpeE, resulting in a mechanistic model for holin-mediated transport. This model is strongly supported by a so far not recognized naturally occurring holin-endolysin fusion protein.

Microbial cell surface engineering for high-level synthesis of bio-products

Microbial cell surface layers, which mainly include the cell membrane, cell wall, periplasmic space, outer membrane, capsules, S-layers, pili, and flagella, control material exchange between the cell and the extracellular environment, and have great impact on production titers and yields of various bio-products synthesized by microbes. Recent research work has made exciting achievements in metabolic engineering using microbial cell surface components as novel regulation targets without direct modifications of the metabolic pathways of the desired products. This review article will summarize the accomplishments obtained in this emerging field, and will describe various engineering strategies that have been adopted in bacteria and yeasts for the enhancement of mass transfer across the cell surface, improvement of protein expression and folding, modulation of cell size and shape, and re-direction of cellular resources, all of which contribute to the construction of more efficient microbial cell factories toward the synthesis of a variety of bio-products. The existing problems and possible future directions will also be discussed.

Wall teichoic acids: physiology and applications

Wall teichoic acids (WTAs) are charged glycopolymers containing phosphodiester-linked polyol units and represent one of the major components of Gram-positive cell envelope. WTAs have important physiological functions in cell division, gene transfer, surface adhesion, drug resistance and biofilm formation, and are critical virulence factors and vital determinants in mediating cell interaction with and tolerance to environmental factors. Here, we first briefly introduce WTA structure, biosynthesis and its regulation, and then summarize in detail four major physiological roles played by WTAs, i.e. WTA-mediated resistance to antimicrobials, virulence to mammalian cells, interaction with bacteriolytic enzymes and regulation of cell metabolism. We also review the applications of WTAs in these fields that are closely related to the human society, including antibacterial drug discovery targeting WTA biosynthesis, development of vaccines and antibodies regarding WTA-mediated pathogenicity, specific and sensitive detection of pathogens in food using WTAs as a surface epitope and regulation of WTA-related pathways for efficient microbial production of useful compounds. We also point out major problems remaining in these fields, and discuss some possible directions in the future exploration of WTA physiology and applications.

Enhanced production of heterologous proteins via engineering the cell surface of Bacillus licheniformis

Cell surface engineering was proven as the efficient strategy for enhanced production of target metabolites. In this study, we want to improve the yield of target protein by engineering cell surface in Bacillus licheniformis. First, our results confirmed that deletions of d-alanyl-lipoteichoic acid synthetase gene dltD, cardiolipin synthase gene clsA and CDP-diacylglycerol-serine O-phosphatidyltransferase gene pssA were not conducive to cell growth, and the biomass of gene deletion strains were, respectively, decreased by 10.54 ± 1.43%, 14.17 ± 1.51%, and 17.55 ± 1.28%, while the concentrations of total extracellular proteins were improved, due to the increases of cell surface net negative charge and cell membrane permeability. In addition, the activities of target proteins, nattokinase, and α-amylase were also improved significantly in gene deletion strains. Furthermore, the triplicate gene (dltD, clsA, and pssA) deletion strain was constructed, which further led to the 45.71 ± 2.43% increase of cell surface net negative charge and 26.45 ± 2.31% increase of cell membrane permeability, and the activities of nattokinase and α-amylase reached 37.15 ± 0.89 FU/mL and 305.3 ± 8.4 U/mL, increased by 46.09 ± 3.51% and 96.34 ± 7.24%, respectively. Taken together, our results confirmed that cell surface engineering via deleting dltD, clsA, and pssA is an efficient strategy for enhanced production of target proteins, and this research provided a promising host strain of B. licheniformis for efficient protein expression.

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.

13C-Metabolic Flux Analysis Reveals the Metabolic Flux Redistribution for Enhanced Production of Poly-γ-Glutamic Acid in dlt Over-Expressed Bacillus licheniformis

Poly-γ-glutamic acid (γ-PGA) is an anionic polymer with various applications. Teichoic acid (TA) is a special component of cell wall in gram-positive bacteria, and its D-alanylation modification can change the net negative charge of cell surface, autolysin activity and cationic binding efficiency, and might further affect metabolic production. In this research, four genes (dltA, dltB, dltC, and dltD) of dlt operon were, respectively, deleted and overexpressed in the γ-PGA producing strain Bacillus licheniformis WX-02. Our results implied that overexpression of these genes could all significantly increase γ-PGA synthetic capabilities, among these strains, the dltB overexpression strain WX-02/pHY-dltB owned the highest γ-PGA yield (2.54 g/L), which was 93.42% higher than that of the control strain WX-02/pHY300 (1.31 g/L). While, the gene deletion strains produced lower γ-PGA titers. Furthermore, ¹³C-Metabolic flux analysis was conducted to investigate the influence of dltB overexpression on metabolic flux redistribution during γ-PGA synthesis. The simulation data demonstrated that fluxes of pentose phosphate pathway and tricarboxylic acid cycle in WX-02/pHY-dltB were 36.41 and 19.18 mmol/g DCW/h, increased by 7.82 and 38.38% compared to WX-02/pHY300 (33.77 and 13.86 mmol/g DCW/h), respectively. The synthetic capabilities of ATP and NADPH were also increased slightly. Meanwhile, the fluxes of glycolytic and by-product synthetic pathways were all reduced in WX-02/pHY-dltB. All these above phenomenons were beneficial for γ-PGA synthesis. Collectively, this study clarified that overexpression of dltB strengthened the fluxes of PPP pathway, TCA cycle and energy metabolism for γ-PGA synthesis, and provided an effective strategy for enhanced production of γ-PGA.