Fed-Batch Biomolecule Production by Bacillus subtilis : A State of the Art Review

New insights into the efficient secretion of foreign protein in Bacillus subtilis via Ribo-seq and RNA-seq integrative analyses

BACKGROUND

As an important prokaryotic model organism, Bacillus subtilis has been widely used in the industrial production of a variety of target products. The efficient secretion of target products has always been the main purpose of industrial microbial technology. The modification of gene regulatory networks is an important technical means to construct a factory of microbial cells that efficiently secretes target products. However, the regulatory network of the efficient expression of foreign genes in B. subtilis has not been studied at the translation level.

RESULTS

In this study, Ribo-seq and RNA-seq technology were used to study the changes in differentially expressed genes during the efficient secretion of the protease PB92 by B. subtilis WB600, and the results revealed the gene regulatory network related to efficient secretion of foreign protein. The results revealed that the correlation between the differentially expressed genes of B. subtilis at the transcription and translation levels was only 0.5354. Forty-one common (transcription and translation) and 436 unique (translation) key differential gene sets that may be related to the efficient secretion of foreign proteins were revealed. KEGG enrichment analysis of these key gene sets revealed that they were involved mainly in the cell motility and central metabolic regulatory network of B. subtilis.

CONCLUSION

Our study provides important guidance for the construction of cell factories and metabolic networks for the efficient secretion of target products by B. subtilis.

An overview of engineering microbial production of nicotinamide mononucleotide

As the human body gradually ages, the cellular level of NAD+ will decline, which has been found to be related to a variety of age-related diseases. As a precursor of NAD+, NMN is able to effectively promote the synthesis of NAD+ with no significant side effects. Microbial production of NMN holds the potential to lower the production cost and facilitate its wide application. In this review, based on the metabolic pathway of NAD+, we summarize recent advances of metabolic engineering strategies for NMN biosynthesis. An outlook for future optimization to improve NMN production is also discussed.

Engineering the Tat-secretion pathway of Bacillus licheniformis for the secretion of cytoplasmic enzyme arginase

The industrial bacterium Bacillus licheniformis has long been used as a microbial factory for the production of enzymes due to its ability to secrete copious amounts of native extracellular proteins and its generally regarded as safe (GRAS) status. However, most attempts to use B. licheniformis to produce heterologous and cytoplasmic enzymes primarily via the general secretory (Sec) pathway have had limited success. The twin-arginine transport (Tat) pathway offers a promising alternative for the extracellular export of Sec-incompatible proteins because it transports full, correctly folded proteins. However, compared to the Sec pathway, the yields of the Tat pathway have historically been too low for commercial use. To improve the export efficiency of the Tat pathway, we identified the optimal Tat-dependent signal peptides and increased the abundance of the Tat translocases, the signal peptidase (SPase), and the intracellular chaperones. These strategic modifications significantly improved the Tat-dependent secretion of the cytoplasmic enzyme arginase into the culture medium using B. licheniformis. The extracellular enzymatic activity of arginase showed a 5.2-fold increase after these modifications. Moreover, compared to the start strain B. licheniformis 0F3, the production of extracellular GFP was improved by 3.8 times using the strategic modified strain B. licheniformis 0F13, and the extracellular enzymatic activity of SOX had a 1.3-fold increase using the strain B. licheniformis 0F14. This Tat-based production chassis has the potential for enhanced production of Sec-incompatible enzymes, therefore expanding the capability of B. licheniformis as an efficient cellular factory for the production of high-value proteins. KEY POINTS: • Systematic genetic modification of Tat-pathway in B. licheniformis. • Significant enhancement of the secretion capacity of Tat pathway for delivery the cytoplasmic enzyme arginase. • A new platform for efficient extracellular production of Sec-incompatible enzymes.

Creating Single-Cell Protein-Producing Bacillus subtilis Mutants Using Chemical Mutagen and Amino Acid Inhibitors

Due to population growth and climate changes, there is a rising need for alternative food and protein sources to reduce protein scarcity and the environmental impact of food industries. Single-cell proteins (SCPs) have the potential to partially or fully substitute plant- and animal-derived dietary proteins. Bacillus subtilis is an appealing bacterium for SCP production because of its fast growth and ability to obtain high protein and essential amino acid (AA) content in its biomass. It is also capable of utilizing a wide range of substrates. B. subtilis attractiveness and efficiency can be further enhanced using mutagenesis. In this study, a novel approach to creating mutant strains with enhanced protein and AA content was experimentally validated. The method is based on the application of AA inhibitors for selective pressure to ensure the growth of mutants with enhanced protein and/or AA synthesis capacity. For AA inhibitors, three herbicides were used: glufosinate-ammonium (GA), L-methionine sulfoximine (MSO), and S-(2-aminoethyl)-L-cysteine (AEC). Initially, AA inhibitor doses for the complete inhibition of wild-type (WT) B. subtilis strain were determined. Then, B. subtilis was treated with EMS chemical mutagen and created mutants were cultivated on a medium containing inhibitory dose of AA inhibitors. Growing samples were selected, analyzed, and compared. The optimal inhibitory concentrations of herbicides for mutant selection were 0.05-0.4 M for GA, 0.01-0.05 M for MSO, and 0.2 M for AEC. The best-performing mutants were selected when using GA-improvement of 7.1 times higher biomass content, 1.5 times higher protein concentration, 1.2 times higher AA content, and 1.2 times higher essential AA index was achieved in comparison with WT B. subtilis. Enhanced mutants were also successfully selected when using MSO and AEC. This study demonstrates the potential of using AA inhibitors for the selection of mutants with improved protein and AA profiles.

Improved taxadiene production by optimizing DXS expression and fusing short-chain prenyltransferases

This study highlights the significance of overexpressing 1-deoxy-d-xylulose-5-phosphate synthase (DXS) from the MEP (methylerythritol 4-phosphate) pathway, in addition to short-chain prenyltransferase fusions for the improved production of the diterpene, taxa-4,11-diene, the first committed intermediate in the production of anti-cancer drug paclitaxel. The results showed that the strain which has (i) the taxadiene synthase (txs) gene integrated into the genome, (ii) the MEP pathway genes overexpressed, (iii) the fpps-crtE prenyltransferases fusion protein and (iv) additional expression of 1-deoxy-d-xylulose-5-phosphate synthase (DXS), yielded the highest production of taxa-4,11-diene at 390 mg/L (26 mg/L/OD600). This represents a thirteen-fold increase compared to the highest reported concentration in B. subtilis. The focus on additional overexpression of DXS and utilizing short-chain prenyltransferase fusions underscores their pivotal role in achieving significant titer improvements in terpene biosynthesis.

Engineering the cell wall reactive groups of Plant Growth Promoting Rhizobacteria by culture strategy for heavy metal removal

This research delved into the effects of nutrient limitation on the level of sporulation and the cadmium adsorption capacity of the bacterium Bacillus sp. isolated from the rhizosphere of endemic soils in the Region of Valparaiso, Chile. The bacteria were subjected to nitrogen limitation in fed-batch mode and were compared to bacteria grown in batch culture without nutrient limitation. The cultures were carried out in a 3 L bioreactor with an external nitrogen supply of ammonium at a flow of 0.123 L h-1. The specific maximum growth rate was 0.42 h-1 in batch and 0.45 h-1 in the exponential phase of the fed-batch. The analysis of sporulation did not show any significant difference between the biomass coming from the fed-batch and batch cultures. It was found that maximum cadmium adsorption capacity varied with culture strategy. The dry biomass grown without nutrient limitation exhibited a maximum adsorption capacity for cadmium of 65.0 mgCd g-1biomass. Conversely, the limited biomass achieved a lower cadmium adsorption capacity of approximately 36.0 mgCd g-1biomass. FTIR analysis showed that nitrogen limitation induced changes in the composition of the outer cell wall, specifically an increase of deacetlylated polysaccharides, reducing the relative amount of secondary amines and proteins from the peptidoglycan matrix. Amino groups from acetylated polysaccharides and proteins have been associated elsewhere with greater cadmium affinity, which could explain the poor results obtained with the nitrogen-restricted biomass. This study shows that new physiological states displaying different adsorption capabilities were effectively obtained by engineering the cell coverage of the bacteria using varying culture strategies. The fed-batch culture proved to be a valuable tool for studying PGPR strains for biosorption and other applications. Exploring diverse nutrient limitations and other pollutants in this bacterium and other members of the PGPR family offer great opportunities to tailor biosorption strategies based on specific conditions, ultimately contributing to sustainable environmental solutions.

Comparative evaluation of the extracellular production of a polyethylene terephthalate degrading cutinase by Corynebacterium glutamicum and leaky Escherichia coli in batch and fed-batch processes

BACKGROUND

With a growing global population, the generation of plastic waste and the depletion of fossil resources are major concerns that need to be addressed by developing sustainable and efficient plastic recycling methods. Biocatalytic recycling is emerging as a promising ecological alternative to conventional processes, particularly in the recycling of polyethylene terephthalate (PET). However, cost-effective production of the involved biocatalyst is essential for the transition of enzymatic PET recycling to a widely used industrial technology. Extracellular enzyme production using established organisms such as Escherichia coli or Corynebacterium glutamicum offers a promising way to reduce downstream processing costs.

RESULTS

In this study, we compared extracellular recombinant protein production by classical secretion in C. glutamicum and by membrane leakage in E. coli. A superior extracellular release of the cutinase ICCGDAQI was observed with E. coli in batch and fed-batch processes on a litre-scale. This phenomenon in E. coli, in the absence of a signal peptide, might be associated with membrane-destabilizing catalytic properties of the expressed cutinase. Optimisations regarding induction, expression temperature and duration as well as carbon source significantly enhanced extracellular cutinase activity. In particular, in fed-batch cultivation of E. coli at 30 °C with lactose as carbon source and inducer, a remarkable extracellular activity (137 U mL-1) and cutinase titre (660 mg L-1) were achieved after 48 h. Literature values obtained with other secretory organisms, such as Bacillus subtilis or Komagataella phaffii were clearly outperformed. The extracellular ICCGDAQI produced showed high efficacy in the hydrolysis of PET textile fibres, either chromatographically purified or unpurified as culture supernatant. In less than 18 h, 10 g L-1 substrate was hydrolysed using supernatant containing 3 mg cutinase ICCGDAQI at 70 °C, pH 9 with terephthalic acid yields of up to 97.8%.

CONCLUSION

Extracellular production can reduce the cost of recombinant proteins by simplifying downstream processing. In the case of the PET-hydrolysing cutinase ICCGDAQI, it was even possible to avoid chromatographic purification and still achieve efficient PET hydrolysis. With such production approaches and their further optimisation, enzymatic recycling of PET can contribute to a more efficient and environmentally friendly solution to the industrial recycling of plastics in the future.

High-Level Expression of Sucrose Isomerase in Bacillus subtilis Through Expression Element Optimization and Fermentation Optimization

Sucrose isomerase is an important food enzyme that catalyzes the isomerization of sucrose into isomaltulose, a functional sugar widely used in food industry, while the production level of sucrose isomerase in food safe host strains was much lower than industrial requirement. Bacillus subtilis is an excellent host strain for recombinant protein expression, which owns the characteristics of powerful secretory capability and generally recognized as safe state. In this study, the expression of sucrose isomerase in B. subtilis was improved through expression element optimization and fermentation optimization. Firstly, the extracellular chaperone PrsA was overexpressed to enhance extracellular folding of sucrose isomerase, which improved the recombinant expression level by 80.02%. Then, the protein synthesis level was optimized through promoter screening, improving the recombinant expression level by 60.40%. On the basis of strain modification, the fermentation conditions including nitrogen source, carbon source, metal ion, pH and temperature were optimized successively in shake-flask. Finally, the 3 L bioreactor cultivation condition was optimized and yielding a sucrose isomerase activity of 862.86 U/mL, the highest level among the food safety strains. This study provides an effective strategy to improve the expression level of food enzymes in B. subtilis.

Secretion of the cytoplasmic and high molecular weight β-galactosidase of Paenibacillus wynnii with Bacillus subtilis

BACKGROUND

The gram-positive bacterium Bacillus subtilis is widely used for industrial enzyme production. Its ability to secrete a wide range of enzymes into the extracellular medium especially facilitates downstream processing since cell disruption is avoided. Although various heterologous enzymes have been successfully secreted with B. subtilis, the secretion of cytoplasmic enzymes with high molecular weight is challenging. Only a few studies report on the secretion of cytoplasmic enzymes with a molecular weight > 100 kDa.

RESULTS

In this study, the cytoplasmic and 120 kDa β-galactosidase of Paenibacillus wynnii (β-gal-Pw) was expressed and secreted with B. subtilis SCK6. Different strategies were focused on to identify the best secretion conditions. Tailormade codon-optimization of the β-gal-Pw gene led to an increase in extracellular β-gal-Pw production. Consequently, the optimized gene was used to test four signal peptides and two promoters in different combinations. Differences in extracellular β-gal-Pw activity between the recombinant B. subtilis strains were observed with the successful secretion being highly dependent on the specific combination of promoter and signal peptide used. Interestingly, signal peptides of both the general secretory- and the twin-arginine translocation pathway mediated secretion. The highest extracellular activity of 55.2 ± 6 µkat/Lculture was reached when secretion was mediated by the PhoD signal peptide and expression was controlled by the PAprE promoter. Production of extracellular β-gal-Pw was further enhanced 1.4-fold in a bioreactor cultivation to 77.5 ± 10 µkat/Lculture with secretion efficiencies of more than 80%.

CONCLUSION

For the first time, the β-gal-Pw was efficiently secreted with B. subtilis SCK6, demonstrating the potential of this strain for secretory production of cytoplasmic, high molecular weight enzymes.

Bacillus subtilis stimulates plant growth and production of bioactive components in saffron

The effects of B. subtilis on the morphology and physiology of saffron were investigated using two types of soils. Three different bacterial suspensions were applied at 14-day intervals to treat saffron. Morphological attributes were recorded, and the amounts of α-crocin and safranal in the stigma extracts were quantified. The longest stigma, petal, and leaf were observed in the treated groups with 105 and 108 cfu/ml. The highest weight of stigma per corm belonged to the treated groups with 102 cfu/ml in unsterile soil and 105 and 108 cfu/ml in sterile soil. Treatment with 102 and 108 cfu/ml caused a significant increase in safranal production in sterile and unsterile peat/perlite. While treatment with 105 and 108 cfu/ml in sterile peat/perlite and exposure to 102 cfu/ml in unsterile peat/perlite soil resulted in an increase in α-crocin. The data showed that B. subtlis triggers the morphological and physiological processes in saffron.

Efficient production of single cell protein from biogas slurry using screened alkali-salt-tolerant Debaryomyces hansenii

Production of single cell protein (SCP) by recovering ammonia nitrogen from biogas slurry shows great potential against protein scarcity and unsustainable production of plant and animal proteins. Herein, a high-alkali-salt-tolerant yeast strain, Debaryomyces hansenii JL8-0, was isolated and demonstrated for high-efficient SCP production. This strain grew optimally at pH 8.50 and 2500 mg/L NH4+-N, and it could efficiently utilize acetate as the additional carbon source. Under optimal conditions, SCP biomass of 32.21 g/L and productivity of 0.32 g/L·h-1 were obtained in fed-batch fermentation. Remarkably, nearly complete (97.40 %) ammonia nitrogen from biogas slurry was recovered, probably due to its high affinity for NH4+-N. Altogether, this strain showed advantages in terms of cell biomass titer, productivity, and yield. A cultivation strategy was proposed by co-culturing D. hansenii with other compatible yeast strains to achieve high-efficient SCP production from biogas slurry, which could be a promising alternative technology for biogas slurry treatment.

Engineering Bacillus subtilis J46 for efficient utilization of galactose through adaptive laboratory evolution

Efficient utilization of galactose by microorganisms can lead to the production of valuable bio-products and improved metabolic processes. While Bacillus subtilis has inherent pathways for galactose metabolism, there is potential for enhancement via evolutionary strategies. This study aimed to boost galactose utilization in B. subtilis using adaptive laboratory evolution (ALE) and to elucidate the genetic and metabolic changes underlying the observed enhancements. The strains of B. subtilis underwent multiple rounds of adaptive laboratory evolution (approximately 5000 generations) in an environment that favored the use of galactose. This process resulted in an enhanced specific growth rate of 0.319 ± 0.005 h-1, a significant increase from the 0.03 ± 0.008 h-1 observed in the wild-type strains. Upon selecting the evolved strain BSGA14, a comprehensive whole-genome sequencing revealed the presence of 63 single nucleotide polymorphisms (SNPs). Two of them, located in the coding sequences of the genes araR and glcR, were found to be the advantageous mutations after reverse engineering. The strain with these two accumulated mutations, BSGALE4, exhibited similar specific growth rate on galactose to the evolved strain BSGA14 (0.296 ± 0.01 h-1). Furthermore, evolved strain showed higher productivity of protease and β-galactosidase in mock soybean biomass medium. ALE proved to be a potent tool for enhancing galactose metabolism in B. subtilis. The findings offer valuable insights into the potential of evolutionary strategies in microbial engineering and pave the way for industrial applications harnessing enhanced galactose conversion.

Production of dehairing protease by Bacillus cereus VITSN04: a model cradle-to-cradle approach for sustainable greener production of leathers

Despite several attempts over decades, process scalability and sustainability remain a challenge to produce an environmental-friendly enzyme to gain industrial attention. In the present study, microbial degradation of chrome shavings (chromium-collagen leather waste) and the resulting collagen hydrolysate for producing the dehairing protease by Bacillus cereus VITSN04 were investigated in a lab-scale fermentor. Scale-up degradation of shavings resulted in higher recovery of collagen hydrolysate (76%) within 72 h compared to shake flasks (68% in 120 h). Earlier achieved medium composition of collagen hydrolysate (12 g L-1) and molasses (15 g L-1) appeared to induce amylase at the high rate, despite the maximal production of protease (203.8 ± 0.18 U mL-1), which was analysed by ANS fluorescence spectroscopy. Optimization of the media containing collagen hydrolysate (12 g L-1) and molasses (5 g L-1) was effective in producing protease (170.6 ± 0.1 U mL-1) and reduced the co-synthesis of amylase (48.2 ± 0.09 U mL-1). The controlled fermentation process by feeding molasses during the exponential growth phase had enhanced the dehairing protease production (∼2.96 fold). The produced protease then partitioned through the biphasic system and showed significant dehairing of goat skins on the pilot scale. Thus, the scalability of the process to produce dehairing enzymes using waste, generated at the site of its use, offers hope for sustainable greener production of leathers.

Functional small peptides for enhanced protein delivery, solubility, and secretion in microbial biotechnology

In microbial biotechnology, there is a constant demand for functional peptides to give new functionality to engineered proteins to address problems such as direct delivery of functional proteins into bacterial cells, enhanced protein solubility during the expression of recombinant proteins, and efficient protein secretion from bacteria. To tackle these critical issues, we selected three types of functional small peptides: cell-penetrating peptides (CPPs) enable the delivery of diverse cargoes into bacterial cytoplasm for a variety of purposes, protein-solubilizing peptide tags demonstrate remarkable efficiency in solubilizing recombinant proteins without folding interference, and signal peptides play a key role in enabling the secretion of recombinant proteins from bacterial cells. In this review, we introduced these three functional small peptides that offer effective solutions to address emerging problems in microbial biotechnology. Additionally, we summarized various engineering efforts aimed at enhancing the activity and performance of these peptides, thereby providing valuable insights into their potential for further applications.

Enhanced extracellular production of raw starch-degrading α-amylase in Bacillus subtilis through expression regulatory element modification and fermentation optimization

BACKGROUND

Raw starch-degrading α-amylase (RSDA) can hydrolyze raw starch at moderate temperatures, thus contributing to savings in starch processing costs. However, the low production level of RSDA limits its industrial application. Therefore, improving the extracellular expression of RSDA in Bacillus subtilis, a commonly used industrial expression host, has great value.

RESULTS

In this study, the extracellular production level of Pontibacillus sp. ZY raw starch-degrading α-amylase (AmyZ1) in B. subtilis was enhanced by expression regulatory element modification and fermentation optimization. As an important regulatory element of gene expression, the promoter, signal peptide, and ribosome binding site (RBS) sequences upstream of the amyZ1 gene were sequentially optimized. Initially, based on five single promoters, the dual-promoter P_veg-P_ylB was constructed by tandem promoter engineering. Afterward, the optimal signal peptide SP_NucB was obtained by screening 173 B. subtilis signal peptides. Then, the RBS sequence was optimized using the RBS Calculator to obtain the optimal RBS1. The resulting recombinant strain WBZ-VY-B-R1 showed an extracellular AmyZ1 activity of 4824.2 and 41251.3 U/mL during shake-flask cultivation and 3-L fermenter fermentation, which were 2.6- and 2.5-fold greater than those of the original strain WBZ-Y, respectively. Finally, the extracellular AmyZ1 activity of WBZ-VY-B-R1 was increased to 5733.5 U/mL in shake flask by optimizing the type and concentration of carbon source, nitrogen source, and metal ions in the fermentation medium. On this basis, its extracellular AmyZ1 activity was increased to 49082.1 U/mL in 3-L fermenter by optimizing the basic medium components as well as the ratio of carbon and nitrogen sources in the feed solution. This is the highest production level reported to date for recombinant RSDA production.

CONCLUSIONS

This study represents a report on the extracellular production of AmyZ1 using B. subtilis as a host strain, and achieved the current highest expression level. The results of this study will lay a foundation for the industrial application of RSDA. In addition, the strategies employed here also provide a promising way for improving other protein production in B. subtilis.

Autoinduction AND Gate Inhibits Cell Lysis to Enhance Protein Production in Bacillus subtilis Controlled by Population Density and Cell Physiological State

The extracellular protease-deficient strain Bacillus subtilis WB600 is commonly used as a chassis cell for the production of industrial proteins. However, B. subtilis WB600 exhibits an increased susceptibility to cell lysis and a reduction in biomass. Inhibition of cell lysis by knocking out lytic genes will impair physiological function. Here, we dynamically inhibited cell lysis in B. subtilis WB600 to balance the impairment of physiological function with the accumulation of biomass. First, the inducible protein degradation systems (IPDSs) were constructed and used to investigate the effects of inhibiting cell lysis on biomass, cell morphology, and protein production at different times (using pullulanase as a test). The highest pullulanase activity was obtained at 20 h of inhibiting cell lysis, 184.8 U/mL, which was 44% higher than the activity of B. subtilis WB600. Then, to avoid addition of inducers, we introduced orthogonal quorum sensing and constructed autoinduction protein degradation systems (AIPDSs). The optimized AIPDS showed similar pullulanase activity to the optimal IPDS (20 h), 181.3 U/mL. Next, we constructed dual-signal input autoinduction protein degradation systems (DSI-AIPDSs) via AND gate to further address two deficiencies of AIPDS, one-time activation and damage to new cells. These DSI-AIPDSs were controlled by quorum sensing and stationary phase promoters that respond to population density and single-cell physiological state, respectively. Finally, the OD₆₀₀ and pullulanase activity of the strain with optimal DSI-AIPDS were 51% and 115% higher than those of B. subtilis WB600 in pullulanase production, respectively. We provided a B. subtilis chassis strain with considerable potential for biomass accumulation and enhanced protein production.

Autoinduction Expression Modules for Regulating Gene Expression in Bacillus subtilis

Although quorum sensing (QS) promoters that can autonomously activate gene expression have been identified and engineered in Bacillus subtilis, researchers focus on quantifying individual promoters while ignoring the interaction between other genetic regulatory elements. Here, we constructed the autoinduction expression modules consisting of promoters responsive to QS ComQXPA, ribosome binding sites (RBSs), and terminators. Using superfolder green fluorescent protein (sfGFP) as a reporter gene, three individual element libraries were generated from 945 promoters, 12,000 RBSs, and 425 terminators by random mutation, de novo design, and database mining strategies, respectively. Then, the efficiency of three libraries in regulating gene expression was further enhanced by engineering the core region of each optimal element. After hybridizing the element libraries, the generated expression modules exhibited a 627-fold range in regulating gene expression without significantly affecting the autoinduction initiation. Here, the hybrid modules with broad expression strength may benefit the application of QS-based autoinduction systems in B. subtilis.

Development and application of CRISPR-based genetic tools in Bacillus species and Bacillus phages

Recently, the clustered regularly interspaced short palindromic repeats (CRISPR) system has been developed into a precise and efficient genome editing tool. Since its discovery as an adaptive immune system in prokaryotes, it has been applied in many different research fields including biotechnology and medical sciences. The high demand for rapid, highly efficient and versatile genetic tools to thrive in bacteria-based cell factories accelerates this process. This review mainly focuses on significant advancements of the CRISPR system in Bacillus subtilis, including the achievements in gene editing, and on problems still remaining. Next, we comprehensively summarize this genetic tool's up-to-date development and utilization in other Bacillus species, including B. licheniformis, B. methanolicus, B. anthracis, B. cereus, B. smithii and B. thuringiensis. Furthermore, we describe the current application of CRISPR tools in phages to increase Bacillus hosts' resistance to virulent phages and phage genetic modification. Finally, we suggest potential strategies to further improve this advanced technique and provide insights into future directions of CRISPR technologies for rendering Bacillus species cell factories more effective and more powerful.

Strategies for improving antimicrobial peptide production

Antimicrobial peptides (AMPs) found in a wide range of animal, insect, and plant species are host defense peptides forming an integral part of their innate immunity. Although the exact mode of action of some AMPs is yet to be deciphered, many exhibit membrane lytic activity or interact with intracellular targets. The ever-growing threat of antibiotic resistance has brought attention to research on AMPs to enhance their clinical use as a therapeutic alternative. AMPs have several advantages over antibiotics such as broad range of antimicrobial activities including anti-fungal, anti-viral and anti-bacterial, and have not reported to contribute to resistance development. Despite the numerous studies to develop efficient production methods for AMPs, limitations including low yield, degradation, and loss of activity persists in many recombinant approaches. In this review, we outline available approaches for AMP production and various expression systems used to achieve higher yield and quality. In addition, recent advances in recombinant strategies, suitable fusion protein partners, and other molecular engineering strategies for improved AMP production are surveyed.

Aliivibrio fischeri L-Asparaginase production by engineered Bacillus subtilis: a potential new biopharmaceutical

L-Asparaginase (L-ASNase) is an enzyme applied in the treatment of lymphoid malignancies. However, an innovative L-ASNase with high yield and lower side effects than the commercially available preparations are still a market requirement. Here, a new-engineered Bacillus subtilis strain was evaluated for Aliivibrio fischeri L-ASNase II production, being the bioprocess development and the enzyme characterization studied. The pBS0E plasmid replicative in Bacillus sp and containing PxylA promoter inducible by xylose and its repressive molecule sequence (XylR) was used for the genetic modification. Initially, cultivations were carried out in orbital shaker, and then the process was scaled up to stirred tank bioreactor (STB). After the bioprocess, the cells were recovered and submitted to ultrasound sonication for cells disruption and intracellular enzyme recovery. The enzymatic extract was characterized to assess its biochemical, kinetic and thermal properties using L-Asparagine and L-Glutamine as substrates. The results indicated the potential enzyme production in STB achieving L-ASNase activity up to 1.539 U mL^-1. The enzymatic extract showed an optimum pH of 7.5, high L-Asparagine affinity (K_m = 1.2275 mmol L^-1) and low L-Glutaminase activity (0.568-0.738 U mL^-1). In addition, thermal inactivation was analyzed by two different Kinect models to elucidate inactivation mechanisms, low kinetic thermal inactivation constants for 25 ºC and 37 ºC (0.128 and 0.148 h^-1, respectively) indicate an elevated stability. The findings herein show that the produced recombinant L-ASNase has potential to be applied for pharmaceutical purposes.

Recombinant Protein Technology in the Challenging Era of Coronaviruses

Coronaviruses have caused devastation in both human and animal populations, affecting both health and the economy. Amidst the emergence and re-emergence of coronaviruses, humans need to surmount the health and economic threat of coronaviruses through science and evidence-based approaches. One of these approaches is through biotechnology, particularly the heterologous production of biopharmaceutical proteins. This review article briefly describes the genome, general virion morphology, and key structural proteins of different coronaviruses affecting animals and humans. In addition, this review paper also presents the different systems in recombinant protein technology such as bacteria, yeasts, plants, mammalian cells, and insect/insect cells systems used to express key structural proteins in the development of countermeasures such as diagnostics, prophylaxis, and therapeutics in the challenging era of coronaviruses.

Control algorithms and strategies of feeding for fed-batch fermentation of Escherichia coli: a review of 40 years of experience

Fed-batch cultivation is a well-known type of submerged fermentation that is frequently used in manufacture of recombinant proteins and various kinds of enzymes, owing to its ability to produce products with high concentrations and high efficiency. In fed-batch culture, several issues must be considered; most of them are also presented in batch culture. However, feed flow rate calculation only corresponds to fed-batch fermentation and its value has a significant impact on productivity, efficiency, final concentration of product, formation of by-products, and viscosity of the culture. From this background, the present review article is an effort to gather the information on feeding strategies for fed-batch cultivation of Escherichia coli, which is a well-known microorganism in the production of recombinant proteins and industrial enzymes, especially for therapeutic applications. Moreover, this review is an aid to comprehend and compare the fundamental concept of different feeding strategies and their advantages and drawbacks.

Inducible Population Quality Control of Engineered Bacillus subtilis for Improved N-Acetylneuraminic Acid Biosynthesis

Biosynthesis by microorganisms using renewable feedstocks is an important approach for realizing sustainable chemical manufacturing. However, cell-to-cell variation in biosynthesis capability during fermentation restricts the robustness and efficiency of bioproduction, hampering the industrialization of biosynthesis. Herein, we developed an inducible population quality control system (iPopQC) for dynamically modulating the producing and nonproducing subpopulations of engineered Bacillus subtilis, which was constructed via inducible promoter- and metabolite-responsive biosensor-based genetic circuit for regulating essential genes. Moreover, iPopQC achieved a 1.97-fold increase in N-acetylneuraminic acid (NeuAc) titer by enriching producing cell subpopulation during cultivation, representing 52% higher than that of previous PopQC. Strains with double-output iPopQC cocoupling the expression of double essential genes with NeuAc production improved production robustness further, retaining NeuAc production throughout 96 h of fermentation, upon which the strains cocoupling one essential gene expression with NeuAc production abolished the production ability.

An overview and future prospects of recombinant protein production in Bacillus subtilis

Bacillus subtilis is a well-characterized Gram-positive bacterium and a valuable host for recombinant protein production because of its efficient secretion ability, high yield, and non-toxicity. Here, we comprehensively review the recent studies on recombinant protein production in B. subtilis to update and supplement other previous reviews. We have focused on several aspects, including optimization of B. subtilis strains, enhancement and regulation of expression, improvement of secretion level, surface display of proteins, and fermentation optimization. Among them, optimization of B. subtilis strains mainly involves undirected chemical/physical mutagenesis and selection and genetic manipulation; enhancement and regulation of expression comprises autonomous plasmid and integrated expression, promoter regulation and engineering, and fine-tuning gene expression based on proteases and molecular chaperones; improvement of secretion level predominantly involves secretion pathway and signal peptide screening and optimization; surface display of proteins includes surface display of proteins on spores or vegetative cells; and fermentation optimization incorporates medium optimization, process condition optimization, and feeding strategy optimization. Furthermore, we propose some novel methods and future challenges for recombinant protein production in B. subtilis.Key points• A comprehensive review on recombinant protein production in Bacillus subtilis.• Novel techniques facilitate recombinant protein expression and secretion.• Surface display of proteins has significant potential for different applications.

Halomonas as a chassis

With the rapid development of systems and synthetic biology, the non-model bacteria, Halomonas spp., have been developed recently to become a cost-competitive platform for producing a variety of products including polyesters, chemicals and proteins owing to their contamination resistance and ability of high cell density growth at alkaline pH and high salt concentration. These salt-loving microbes can partially solve the challenges of current industrial biotechnology (CIB) which requires high energy-consuming sterilization to prevent contamination as CIB is based on traditional chassis, typically, Escherichia coli, Bacillus subtilis, Pseudomonas putida and Corynebacterium glutamicum. The advantages and current status of Halomonas spp. including their molecular biology and metabolic engineering approaches as well as their applications are reviewed here. Moreover, a systematic strain engineering streamline, including product-based host development, genetic parts mining, static and dynamic optimization of modularized pathways and bioprocess-inspired cell engineering are summarized. All of these developments result in the term called next-generation industrial biotechnology (NGIB). Increasing efforts are made to develop their versatile cell factories powered by synthetic biology to demonstrate a new biomanufacturing strategy under open and continuous processes with significant cost-reduction on process complexity, energy, substrates and fresh water consumption.

Biochemical characterization of a novel bifunctional chitosanase from Paenibacillus barengoltzii for chitooligosaccharide production

A novel chitosanase gene, designated as PbCsn8, was cloned from Paenibacillus barengoltzii. It shared the highest identity of 73% with the glycoside hydrolase (GH) family 8 chitosanase from Bacillus thuringiensis JAM-GG01. The gene was heterologously expressed in Bacillus subtilis as an extracellular protein, and the highest chitosanase yield of 1, 108 U/mL was obtained by high-cell density fermentation in a 5-L fermentor. The recombinant chitosanase (PbCsn8) was purified to homogeneity and biochemically characterized. PbCsn8 was most active at pH 5.5 and 70 °C, respectively. It was stable in a wide pH range of 5.0-11.0 and up to 55 °C. PbCsn8 was a bifunctional enzyme, exhibiting both chitosanase and glucanase activities, with the highest specificity towards chitosan (360 U/mg), followed by barley β-glucan (72 U/mg) and lichenan (13 U/mg). It hydrolyzed chitosan to release mainly chitooligosaccharides (COSs) with degree of polymerization (DP) 2-3, while hydrolyzed barley β-glucan to yield mainly glucooligosaccharides with DP > 5. PbCsn8 was further applied in COS production, and the highest COS yield of 79.3% (w/w) was obtained. This is the first report on a GH family 8 chitosanase from P. barengoltzii. The high yield and remarkable hydrolysis properties may make PbCsn8 a good candidate in industrial application.

Bacilysin within the Bacillus subtilis group: gene prevalence versus antagonistic activity against Gram-negative foodborne pathogens

The Bacillus subtilis group comprises species known for their ability to produce a wide variety of antimicrobial peptides. This work focuses on bacilysin, a broad-spectrum active dipeptide, and its prevalence in the B. subtilis group. In silico genome analysis of strains from Bacillus amyloliquefaciens, Bacillus velezensis, Bacillus licheniformis, Bacillus pumilus and B. subtilis subspecies inaquosorum, spizizenii and subtilis revealed that the bacilysin gene cluster is present in all species except for B. licheniformis. This observation was corroborated by PCR detection of the bacilysin genetic determinants on a collection of 168 food and environmental strains from the B. subtilis group. Phylogenetic analyses also demonstrated that the bacilysin gene cluster sequence showed more than 80 % identity within each species of the B. subtilis group. An in vitro screening of the strain collection was performed against foodborne pathogens. Twenty-three strains were selected for their ability of their Cell-Free Supernatant to inhibit foodborne pathogens. After an ammonium sulphate precipitation of their supernatant, eight strains, all belonging to B. velezensis, exhibited antimicrobial activity against Gram-negative pathogens. Using Ultra High Performance Liquid Chromatography - Mass Spectrometry, the presence of bacilysin was confirmed in these eight precipitates. These findings provide evidence that bacilysin is a major player in the antagonistic activity of B. velezensis against Gram-negative foodborne pathogens.

A General Process-Based Model for Describing the Metabolic Shift in Microbial Cell Cultures

The metabolic shift between respiration and fermentation at high glucose concentration is a widespread phenomenon in microbial world, and it is relevant for the biotechnological exploitation of microbial cell factories, affecting the achievement of high-cell-densities in bioreactors. Starting from a model already developed for the yeast Saccharomyces cerevisiae, based on the System Dynamics approach, a general process-based model for two prokaryotic species of biotechnological interest, such as Escherichia coli and Bacillus subtilis, is proposed. The model is based on the main assumption that glycolytic intermediates act as central catabolic hub regulating the shift between respiratory and fermentative pathways. Furthermore, the description of a mixed fermentation with secondary by-products, characteristic of bacterial metabolism, is explicitly considered. The model also represents the inhibitory effect on growth and metabolism of self-produced toxic compounds relevant in assessing the late phases of high-cell density culture. Model simulations reproduced data from experiments reported in the literature with different strains of non-recombinant and recombinant E. coli and B. subtilis cultured in both batch and fed-batch reactors. The proposed model, based on simple biological assumptions, is able to describe the main dynamics of two microbial species of relevant biotechnological interest. It demonstrates that a reductionist System Dynamics approach to formulate simplified macro-kinetic models can provide a robust representation of cell growth and accumulation in the medium of fermentation by-products.

Cell-free synthesis system-assisted pathway bottleneck diagnosis and engineering in Bacillus subtilis

Metabolic engineering is a key technology for cell factories construction by rewiring cellular resources to achieve efficient production of target chemicals. However, the existence of bottlenecks in synthetic pathway can seriously affect production efficiency, which is also one of the core issues for metabolic engineers to solve. Therefore, developing an approach for diagnosing potential metabolic bottlenecks in a faster and simpler manner is of great significance to accelerate cell factories construction. The cell-free reaction system based on cell lysates can transfer metabolic reactions from in vivo to in vitro, providing a flexible access to directly change protein and metabolite variables, thus provides a potential solution for rapid identification of bottlenecks. Here, bottleneck diagnosis of the N-acetylneuraminic acid (NeuAc) biosynthesis pathway in industrially important chassis microorganism Bacillus subtilis was performed using cell-free synthesis system. Specifically, a highly efficient B. subtilis cell-free system for NeuAc de novo synthesis was firstly constructed, which had a 305-fold NeuAc synthesis rate than that in vivo and enabled fast pathway dynamics analysis. Next, through the addition of all potential key intermediates in combination with substrate glucose respectively, it was found that insufficient phosphoenolpyruvate supply was one of the NeuAc pathway bottlenecks. Rational in vivo metabolic engineering of NeuAc-producing B. subtilis was further performed to eliminate the bottleneck. By down-regulating the expression level of pyruvate kinase throughout the growth phase or only in the stationary phase using inhibitory N-terminal coding sequences (NCSs) and growth-dependent regulatory NCSs respectively, the maximal NeuAc titer increased 2.0-fold. Our study provides a rapid method for bottleneck diagnosis, which may help to accelerate the cycle of design, build, test and learn cycle for metabolic engineering.

Synergistic Degradation of Pyrethroids by the Quorum Sensing-Regulated Carboxylesterase of Bacillus subtilis BSF01

The well-studied quorum sensing (QS) mechanism has established a complex knowledge system of how microorganisms behave collectively in natural ecosystems, which contributes to bridging the gap between the ecological functions of microbial communities and the molecular mechanisms of cell-to-cell communication. In particular, the ability of agrochemical degradation has been one most attractive potential of functional bacteria, but the interaction and mutual effects of intracellular degradation and intraspecific behavior remained unclear. In this study, we establish a connection between QS regulation and biodegradation by harnessing the previously isolated Bacillus subtilis BSF01 as a template which degrades various pyrethroids. First, we characterize the genetic and transcriptional basis of comA-involved QS system in B. subtilis BSF01 since the ComQXPA circuit coordinates group behaviors in B. subtilis isolates. Second, the genetic and transcriptional details of pyrethroid-degrading carboxylesterase CesB are defined, and its catalytic capacity is evaluated under different conditions. More importantly, we adopt DNA pull-down and yeast one-hybrid techniques to reveal that the enzymatic degradation of pyrethroids is initiated through QS signal regulator ComA binding to carboxylesterase gene cesB, highlighting the synergistic effect of QS regulation and pyrethroid degradation in B. subtilis BSF01. Taken together, the elucidated mechanism provides novel details on the intercellular response of functional bacteria against xenobiotic exposure, which opens up possibilities to facilitate the in-situ contaminant bioremediation via combining the QS-mediated strategies.

Engineering the gut microbiota to treat chronic diseases

Gut microbes play vital roles in host health and disease. A number of commensal bacteria have been used as vectors for genetic engineering to create living therapeutics. This review highlights recent advances in engineering gut bacteria for the treatment of chronic diseases such as metabolic diseases, cancer, inflammatory bowel diseases, and autoimmune disorders. KEY POINTS: • Bacterial homing to tumors has been exploited to deliver therapeutics in mice models. • Engineered bacteria show promise in mouse models of metabolic diseases. • Few engineered bacterial treatments have advanced to clinical studies.

Strategies for recombinant production of antimicrobial peptides with pharmacological potential

INTRODUCTION

The need to develop new drugs for the control of pathogenic microorganisms has redoubled efforts to prospect for antimicrobial peptides (AMPs) from natural sources and to characterize its structure and function. These molecules present a broad spectrum of action against different microorganisms and frequently present promiscuous action, with anticancer and immunomodulatory activities. Furthermore, AMPs can be used as biopharmaceuticals in the treatment of hospital-acquired infections and other serious diseases with relevant social and economic impacts.Areas covered: The low yield and the therefore difficult extraction and purification process in AMPs are problems that limit their industrial application and scientific research. Thus, optimized heterologous expression systems were developed to significantly boost AMP yields, allow high efficiency in purification and structural optimization for the increase of therapeutic activity.Expert opinion: This review provides an update on recent developments in the recombinant production of ribosomal and non-ribosomal synthesis of AMPs and on strategies to increase the expression of genes encoding AMPs at the transcriptional and translational levels and regulation of the post-translational modifications. Moreover, there are detailed reports of AMPs that have already reached marketable status or are in the pipeline under advanced stages of preclinical testing.

Use of Bacillus subtilis PB6 enriched with choline to improve growth performance, immune status, histological parameters and intestinal microbiota of broiler chickens

Context Probiotics used in poultry nutrition may promote the propagation of beneficial bacteria and limit the growth of pathogens, improving the body’s resistance to disease. Aims The aim of the study was to establish the dose and timing of administration of a probiotic preparation containing live cultures of Bacillus subtilis PB6 and choline that would have the most beneficial effect on histological parameters and microbiological status of the intestine, immune status, and growth performance of broiler chickens. Methods In total, 980 one-day-old Ross 308 male chickens, divided into seven groups of 140 (each group with seven replications of 20 individuals), were used in the experiment. The birds were reared until Day 42 of life. In the control group, birds received water without addition of the probiotic preparation. In three continuous treatments, birds received the probiotic preparation in their water at doses of 0.05, 0.1 or 0.25 g/L from Day 1 to Day 42 of rearing. In three periodic treatments, birds received the same doses of the probiotic preparation, but only during Days 1–7, 15–21 and 29–35 of rearing. Key results Addition of the probiotic preparation to the drinking water of broiler chickens increased the total number of aerobic bacteria as well as the length of the intestinal villi and the depth of the crypts. It also reduced the number of fungi and coliform bacteria. In addition, increases were noted in the lysozyme content, the phagocytic index, and the level of immunoglobulin A. Conclusions The probiotic preparation containing B. subtilis and choline administered continuously at a dose of 0.25 g/L in water throughout the rearing period had the most beneficial effect on the composition of the microbiome, and improved the mucous membrane structure of the intestine (increasing villus length and intestinal crypt depth), immunity, and growth performance of the broiler chickens. Implications The use of probiotics in poultry nutrition improves the health of animals and makes breeding more profitable. Administration of this probiotic improves disease resistance, jejunal histological parameters, and intestinal microflora of broiler chickens.

Optimization of heterotrophic cultivation of Chlorella sp. HS2 using screening, statistical assessment, and validation

The heterotrophic cultivation of microalgae has a number of notable advantages, which include allowing high culture density levels as well as enabling the production of biomass in consistent and predictable quantities. In this study, the full potential of Chlorella sp. HS2 is explored through optimization of the parameters for its heterotrophic cultivation. First, carbon and nitrogen sources were screened in PhotobioBox. Initial screening using the Plackett-Burman design (PBD) was then adopted and the concentrations of the major nutrients (glucose, sodium nitrate, and dipotassium phosphate) were optimized via response surface methodology (RSM) with a central composite design (CCD). Upon validation of the model via flask-scale cultivation, the optimized BG11 medium was found to result in a three-fold improvement in biomass amounts, from 5.85 to 18.13 g/L, in comparison to a non-optimized BG11 medium containing 72 g/L glucose. Scaling up the cultivation to a 5-L fermenter resulted in a greatly improved biomass concentration of 35.3 g/L owing to more efficient oxygenation of the culture. In addition, phosphorus feeding fermentation was employed in an effort to address early depletion of phosphate, and a maximum biomass concentration of 42.95 g/L was achieved, with biomass productivity of 5.37 g/L/D.

Establishing a Fed-Batch Process for Protease Expression with Bacillus licheniformis in Polymer-Based Controlled-Release Microtiter Plates

Introducing fed-batch mode in early stages of development projects is crucial for establishing comparable conditions to industrial fed-batch fermentation processes. Therefore, cost efficient and easy to use small-scale fed-batch systems that can be integrated into existing laboratory equipment and workflows are required. Recently, a novel polymer-based controlled-release fed-batch microtiter plate is described. In this work, the polymer-based controlled-release fed-batch microtiter plate is used to investigate fed-batch cultivations of a protease producing Bacillus licheniformis culture. Therefore, the oxygen transfer rate (OTR) is online-monitored within each well of the polymer-based controlled-release fed-batch microtiter plate using a µRAMOS device. Cultivations in five individual polymer-based controlled-release fed-batch microtiter plates of two production lots show good reproducibility with a mean coefficient of variation of 9.2%. Decreasing initial biomass concentrations prolongs batch phase while simultaneously postponing the fed-batch phase. The initial liquid filling volume affects the volumetric release rate, which is directly translated in different OTR levels of the fed-batch phase. An increasing initial osmotic pressure within the mineral medium decreases both glucose release and protease yield. With the volumetric glucose release rate as scale-up criterion, microtiter plate- and shake flask-based fed-batch cultivations are highly comparable. On basis of the small-scale fed-batch cultivations, a mechanistic model is established and validated. Model-based simulations coincide well with the experimentally acquired data.

Recombinant protein expression in biofilms

Biofilm research is usually focused on the prevention or control of biofilm formation. Recently, the significance of the biofilm mode of growth in biotechnological applications received increased attention. Since biofilm reactors show many advantages over suspended cell reactors, especially in their higher biomass density and operational stability, bacterial biofilms have emerged as an interesting approach for the expression of specific proteins. Despite the potential of biofilm systems, recombinant protein production using biofilms has been scarcely investigated for the past 25 years. Our group has demonstrated that E. coli biofilms were able to produce a model recombinant protein, the enhanced green fluorescent protein (eGFP), at much higher levels than their planktonic counterparts. Even without optimization of cultivation conditions, an attractive productivity was obtained, indicating that biofilm cultures can be used as an alternative form of high cell density cultivation (HCDC). E. coli remains one of the favorite hosts for recombinant protein production and it has been successfully used in metabolic engineering for the synthesis of high value products. This review presents the advantages and concerns of using biofilms for the production of recombinant proteins and summarizes the different biofilm systems which have been described for this purpose. The relative advantages and disadvantages of the four microbial hosts tested for recombinant protein production in biofilms (two bacteria and two filamentous fungi) are also discussed.

Introducing substrate limitations to overcome catabolite repression in a protease producing Bacillus licheniformis strain using membrane-based fed-batch shake flasks

To overcome catabolite repression, industrial fermentation processes are usually operated in substrate-limited fed-batch mode. Therefore, the implementation of such an operating mode at small scale is crucial to maintain comparable process conditions. In this study, Bacillus licheniformis, a well-known producer of proteases, was cultivated with carbon (glucose)- and nitrogen (ammonium)-limited fed-batch conditions using the previously introduced membrane-based fed-batch shake flasks. A repression of protease production by glucose and ammonium was thus avoided and yields increased 1.5- and 2.1-fold relative to batch, respectively. An elevated feeding rate of glucose caused depletion of ammonium, which was recognizable within the oxygen transfer rate (OTR) signal measured with the Respiration Activity MOnitoring System (RAMOS). Ammonium limitation was prevented by feeding ammonium simultaneously with glucose. The OTR signal clearly indicated the initiation of the fed-batch phase and gave direct feedback on the nutrient release kinetics. Increased feeding rates of glucose and ammonium led to an elevated protease activity without affecting the protease yield (Y_P/Glu ). In addition to Y_P/Glu , protease yields were determined based on the metabolized amount of oxygen ( Y P / O 2 ) . The results showed that the protease production correlated with the amount of consumed glucose as well as with the amount of consumed oxygen. The membrane-based fed-batch shake flask in combination with the RAMOS device is a powerful combination to investigate the effect of substrate-limited fed-batch conditions.

The YoaW signal peptide directs efficient secretion of different heterologous proteins fused to a StrepII-SUMO tag in Bacillus subtilis

Background

Heterologous gene expression is well established for various prokaryotic model systems. However, low yield, incorrect folding and instability still impede the production of soluble, bioactive proteins. To improve protein production with the Gram-positive host Bacillus subtilis, a secretory expression system was designed that enhances translocation, folding and stability of heterologous proteins, and simplifies purification. Based on the theta-replication plasmid pHT01, a B. subtilis secretory expression vector was constructed that encodes a fusion protein consisting of a signal peptide and a StrepII-tag linked to a SUMO-tag serving as a folding catalyst. The gene of a protein of interest can be translationally fused to the SUMO cassette and an additional 6xHis-tag encoding region. In order to maximize secretory expression of the construct by fitting the signal peptide to the StrepII-SUMO part of the fusion protein, a B. subtilis signal-peptide library was screened with the Escherichia coli alkaline phosphatase PhoA as a reporter.

Results

The YoaW signal peptide-encoding region (SPyoaW) was identified with highest secretory expression capacity in context with the StrepII-SUMO-tag fusion in a B. subtilis eightfold extracellular protease deletion strain. PhoA activity and fusion protein production was elevated by a factor of approximately five when compared to an α-amylase (AmyQ) signal peptide construct. Replacement of PhoA with a single-chain variable fragment antibody specific for GFP or the B. amyloliquefaciens RNase barnase, respectively, resulted in a similar enhancement of secretory expression, demonstrating universality of the YoaW signal peptide-StrepII-SUMO encoding cassette for secretory expression in B. subtilis. Optimisation of codon usage and culture conditions further increased GFP-specific scFv fusion-protein production, and a simple affinity purification strategy from culture supernatant with removal of the StrepII-SUMO-tag by SenP-processing yielded 4 mg of pure, soluble and active GFP-specific scFv from 1 l of culture under standard laboratory conditions.

Conclusions

The new expression system employing a YoaW signal peptide-StrepII-SUMO fusion will simplify secretory protein production and purification with B. subtilis. It can obviate the need for time consuming individual signal-peptide fitting to maximize yield for many different heterologous proteins of interest.

Electronic supplementary material

The online version of this article (10.1186/s12934-019-1078-0) contains supplementary material, which is available to authorized users.

Development and benefit evaluation of fermentation strategies for poly(malic acid) production from malt syrup by Aureobasidium melanogenum GXZ-6

Malt syrup, as a low-cost substrate without any pretreatment, was proved to be able to replace maltose for ploymalic acid (PMA) production by Aureobasidium melanogenum GXZ-6. The PMA titer of 55.53 ± 1.72 g/L was obtained by batch fermentation in a 10-L fermentor with addition of malate, citrate and sodium malonate. Then, a higher PMA titer of 124.07 ± 2.28 g/L was obtained in fed-batch fermentation, which increased by 123.43% than that from batch fermentation. Moreover, repeated-batch fermentation with three batches gave a PMA titer of 64.06 g/L on average with a higher yield of 0.81 g/g and productivity of 0.56 g/L·h. Fermentation process and economics analysis were performed by SuperPro Designer for a 2000 metric tons plant. Results showed that PMA production cost was as low as $ 1.716/kg by fed-batch fermentation, which provides an economical strategy for large-scale PMA production.