A food-grade expression system for d-psicose 3-epimerase production in Bacillus subtilis using an alanine racemase-encoding selection marker

Reconstruction of a microbial TNT deep degradation system and its mechanism for reshaping microecology

This study is the first to use synthetic biological omics technology to analyze the molecular mechanism underlying deep degradation of TNT, to construct an artificial transformation system to create engineered Escherichia coli bacteria, and to use Bacillus subtilis as an expression host to explore the mechanism driving the reshaping of the deep degradation platform on microecology. Nitroreductase family protein, 2-oxoacid:acceptor oxidoreductase, NADPH-cytochrome P450 reductase, monooxygenase, ring-cleaving dioxygenase, and RraA family protein significantly participated in the reduction-hydroxylation-ring opening cleavage of TNT, achieving deep transformation of TNT to produce pyruvic acid and other products that entered the cellular metabolic cycle. The key toxic metabolic pathways of TNT, 2,4-diamino-6-nitrotoluene, 2,4,6-triaminotoluene, and 2,4,6-trihydroxytoluene are pantothenate and CoA biosynthesis. The engineered bacteria that impart TNT deep degradation ability regulate and optimize lipid, sugar, and amino acid metabolism to withstand stress. Engineered B. subtilis bacteria occupy ecological niches after repairing TNT-contaminated soil and water bodies while simultaneously recruiting a variety of microorganisms to reshape and positively regulate microecology. Key drivers for reshaping and optimization of microecological functions include ABC transporters and C/N/P/S functional cycles, together with a significant concomitant upregulation of the metabolic cycle of basic carbohydrates, nucleotides, and amino acids in the microecology.

High level food-grade expression of maltogenic amylase in Bacillus subtilis through genomic integration and comA overexpression

Maltogenic amylase AmyM can improve softness retention and extend shelf life of baked foods, while the low copy number of genomic integration and the limited, non-universal enhancement provided by existing heterologous protein synthesis-associated genes are the main constraints on achieving high food-grade expression levels of AmyM. In this study, we constructed a food-grade Bacillus subtilis strain that efficiently expressed AmyM by genomic multicopy integration and synthesis enhancer genes overexpression. Specifically, amyM (encoding AmyM) was sequentially integrated into 7 different sites of B. subtilis WS9C genome, yielding strain WS9C7. Then, transcriptome analysis of strains WS9C1 and WS9C7 was performed, and results showed that genes involved in iron ion homeostasis and amino acid metabolism were significantly changed. Twenty-six significant differentially expressed genes were chosen to be modified, and results showed that 9 genes had positive effect on AmyM expression. The best one, encoding the quorum-sensing regulator ComA, improved AmyM expression level by 1.55-fold reaching 10847 U/mL, which is currently the highest reported AmyM activity, and has been a novel modification target for higher recombinant expression.

Identification of a bacteria P450 enzyme from B. megaterium H-1 with vitamin D3 C-25 hydroxylation capabilities

Calcidiol (25(OH)VD3) and calcitriol (1α,25(OH)2VD3) are active vitamin D3 with high medicinal value, which can maintain calcium and phosphorus balance and treat vitamin D deficiency. Microbial synthesis is an important method to produce high-value-added compounds. It can produce active vitamin D3 through the hydroxylation reaction of P450, which can reduce the traditional chemical synthesis steps, and greatly improve the production efficiency and economic benefits. In this work, Bacillus megaterium H-1 was screened for its ability to produce 25(OH)VD3 and 1α,25(OH)2VD3 from vitamin D3. A new highly inducible vitamin D3 hydroxylase CYP109E1-H was identified from B. megaterium H-1 through searching for transcripts with cytochrome P450 structural domains, combining the transcriptome sequencing with functional expression in Bacillus subtilis WB600. Biotransformation in recombinant B. subtilis confirmed that CYP109E1-H has C-25 hydroxylase activity towards vitamin D3. CYP109E1-H is a natural mutant of CYP109E1 with greater stereoselectivity and it is a new vitamin D3 mono-hydroxylase. The cloning and characterization of the CYP109E1-H gene provide useful information on the structural basis for improving the regional and stereoselectivity of the CYP109E gene.

High level food-grade expression of maltogenic amylase in Bacillus subtilis through dal gene auxotrophic selection marker

As a food-safe microorganism, Bacillus subtilis has been widely utilized in the production of food enzyme, where a food-grade expression system without antibiotic is required. However, there is no mature system for such expression, since the recombinant plasmid in existing food-grade expression system is unstable especially in high-density fermentation. In this study, we constructed a food-grade expression system based on the dal gene auxotrophic selection marker. Specifically, maltogenic amylase (AmyM) was expressed in dal deletion strain without antibiotic, yielding an activity of 519 U/mL. To increase the expression of AmyM, the promoter of amyM (gene encoding AmyM) was optimized. Furthermore, we found that excessive expression of dal gene was detrimental to the stability of plasmid, and the ribosome binding site (RBS) of dal was mutated with the reduced synthesis of D-alanine. After that, AmyM activity increased to 1364 U/mL with the 100 % stability of plasmid. The 3-L fermentor cultivation was performed with the highest value ever reported in food-grade microorganisms, an activity of 2388 U/mL, showing the scale-up production capability of this system. Besides, it is also able to apply the system for other food enzymes, which indicating the great generalizability of this system for different application.

Produce D-allulose from non-food biomass by integrating corn stalk hydrolysis with whole-cell catalysis

D-allulose is a high-value rare sugar with many health benefits. D-allulose market demand increased dramatically after approved as generally recognized as safe (GRAS). The current studies are predominantly focusing on producing D-allulose from either D-glucose or D-fructose, which may compete foods against human. The corn stalk (CS) is one of the main agricultural waste biomass in the worldwide. Bioconversion is one of the promising approach to CS valorization, which is of significance for both food safety and reducing carbon emission. In this study, we tried to explore a non-food based route by integrating CS hydrolysis with D-allulose production. Firstly we developed an efficient Escherichia coli whole-cell catalyst to produce D-allulose from D-glucose. Next we hydrolyzed CS and achieved D-allulose production from the CS hydrolysate. Finally we immobilized the whole-cell catalyst by designing a microfluidic device. Process optimization improved D-allulose titer by 8.61 times, reaching 8.78 g/L from CS hydrolysate. With this method, 1 kg CS was finally converted to 48.87 g D-allulose. This study validated the feasibility of valorizing corn stalk by converting it to D-allulose.

Overexpression of Bacillus circulans alkaline protease in Bacillus subtilis and its potential application for recovery of protein from soybean dregs

Proteases are important for decomposition of proteins to generate peptides or amino acids and have a broad range of applications in different industries. Herein, a gene encoding an alkaline protease (AprBcp) from Bacillus circulans R1 was cloned and bioinformatics analyzed. In addition, a series of strategies were applied to achieve high-level expression of AprBcp in Bacillus subtilis. The maximum activity of AprBcp reached 165,870 U/ml after 60 h fed-batch cultivation in 50 l bioreactor. The purified recombinant AprBcp exhibited maximum activity at 60°C and pH 10.0, and remained stable in the range from pH 8.0 to 11.0 and 30 to 45°C. Metal ions Ca²⁺, Mn²⁺, and Mg²⁺ could improve the stability of AprBcp. Furthermore, the recombinant AprBcp displayed great potential application on the recovery of protein from soybean dregs. The results of this study will provide an effective method to prepare AprBcp in B. subtilis and its potential application on utilization of soybean dregs.

A 4-α-Glucanotransferase from Thermus thermophilus HB8: Secretory Expression and Characterization

4-α-glucanotransferase (4GT, EC 2.4.1.25) catalyzes the breakdown of the α-1,4 glycosidic bonds of the starch main chain and forms new α-1,4 glycosidic bonds in the side chain, which is often used to optimize the physical and chemical properties of starch and to improve the quality of starch-based food. However, the low enzyme activity of 4GT limits its production and widespread application. Herein, the 4GT gene encoding 500 amino acids from Thermus thermophilus HB8 was cloned and expressed in Escherichia coli. The purified 4GT exhibited maximum activity at pH 7.0 and 60 °C and had a good stability at pH 6.0-8.0 and 30-60 °C. It was confirmed that 4GT possessed the catalytic function of extending the branch length of potato starch. Furthermore, the 4GT gene was successfully expressed extracellularly in Bacillus subtilis. Then, the enzyme yield of 4GT increased by 4.1 times through screening of different plasmids and hosts. Additionally, the fermentation conditions were optimized to enhance 4GT extracellular enzyme yield. Finally, a recombinant Bacillus subtilis with 299.9 U/mL enzyme yield of 4GT was obtained under the optimized fermentation process. In conclusion, this study provides a valuable reference for characterization and expression of food-grade enzymes.

D-allulose, a versatile rare sugar: recent biotechnological advances and challenges

D-Allulose is the C-3 epimer of D-fructose, and widely regarded as a promising substitute for sucrose. It's an excellent low-calorie sweetener, with 70% sweetness of sucrose, 0.4 kcal/g dietary energy, and special physiological functions. It has been approved as GRAS by the U.S. Food and Drug Administration, and is allowed to be excluded from total and added sugar counts on the food labels. Therefore, D-allulose gradually attracts more public attention. Owing to scarcity in nature, the bioproduction of D-allulose by using ketose 3-epimerase (KEase) has become the research hotspot. Herein, we give a summary of the physicochemical properties, physiological function, applications, and the chemical and biochemical synthesis methods of D-allulose. In addition, the recent progress in the D-allulose bioproduction using KEases, and the possible solutions for existing challenges in the D-allulose industrial production are comprehensively discussed, focusing on the molecular modification, immobilization, food-grade expression, utilizing low-cost biomass as feedstock, overcoming thermodynamic limitation, as well as the downstream separation and purification. Finally, Prospects for further development are also proposed.

One-step construction of a food-grade expression system based on the URA3 gene in Kluyveromyces lactis

Proteins from food-grade expression systems can be used in food products and medical applications. Herein, we describe a one-step method of constructing an expression vector in Kluyveromyces lactis by combining a URA3-deficient strain and a plasmid vector with no drug-resistant selection. Adjacent DNA elements of the vector were assembled in a targeted manner through a reaction with a special recombinase to form a plasmid vector using a one-step reaction. The unnecessary fragments containing the pUC origin and the ampicillin resistance gene were removed, and the vector was isolated and purified before transformation. A single transformation of the vector can produce a URA3-deficient strain. PCR assay, sequencing, and western blot analysis all indicated that the method of vector construction and target protein expression (mCherry and human serum albumin) were successful. This method may potentially be applied to any species containing the URA3 gene; this system has the potential to become a safe and powerful tool for promoting protein expression in food-safe species.

Developing rapid growing Bacillus subtilis for improved biochemical and recombinant protein production

Bacillus subtilis is a model Gram-positive bacterium, which has been widely used as industrially important chassis in synthetic biology and metabolic engineering. Rapid growth of chassis is beneficial for shortening the fermentation period and enhancing production of target product. However, engineered B. subtilis with faster growth phenotype is lacking. Here, fast-growing B. subtilis were constructed through rational gene knockout and adaptive laboratory evolution using wild type strain B. subtilis 168 (BS168) as starting strain. Specifically, strains BS01, BS02, and BS03 were obtained through gene knockout of oppD, hag, and flgD genes, respectively, resulting 15.37%, 24.18% and 36.46% increases of specific growth rate compared with BS168. Next, strains A28 and A40 were obtained through adaptive laboratory evolution, whose specific growth rates increased by 39.88% and 43.53% compared to BS168, respectively. Then these two methods were combined via deleting oppD, hag, and flgD genes respectively on the basis of evolved strain A40, yielding strain A4003 with further 7.76% increase of specific growth rate, reaching 0.75 h^-1 in chemical defined M9 medium. Finally, bioproduction efficiency of intracellular product (ribonucleic acid, RNA), extracellular product (acetoin), and recombinant proteins (green fluorescent protein (GFP) and ovalbumin) by fast-growing strain A4003 was tested. And the production of RNA, acetoin, GFP, and ovalbumin increased 38.09%, 5.40%, 9.47% and 19.79% using fast-growing strain A4003 as chassis compared with BS168, respectively. The developed fast-growing B. subtilis strains and strategies used for developing these strains should be useful for improving bioproduction efficiency and constructing other industrially important bacterium with faster growth phenotype.

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Fast-growing Bacillus subtilis were constructed through rational gene knockout and adaptive laboratory evolution.

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Specific growth rate of engineered B. subtilis ​increased 53.06% compared with ​B. subtilis 168, reaching 0.75 h^-1 ​in M9 medium.

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Production of RNA, acetoin, and ovalbumin increased 38.09%, 5.40%, and 19.79% using fast-growing strain as chassis.

Functionalized polyhydroxyalkanoate nano-beads as a stable biocatalyst for cost-effective production of the rare sugar d-allulose

d-Allulose is a promising low-calorie sweetener especially for diabetes and obesity patients. The functionalized polyhydroxyalkanoate (PHA) nano-beads decorated with d-tagatose 3-epimerase (DTE) was produced in recombinant endotoxin-free ClearColi, whereby the expression, purification, and immobilization of the active DTE were efficiently combined into one step. The immobilized DTE exhibited remarkable enzyme activity of 649.3 U/g beads and extremely high stability at a harsh working condition (pH 7.0-8.0, 65 °C). When DTE-PHA beads were subjected to enzymatic synthesis of d-allulose, a maximum conversion rate of 33% can be achieved at pH 7.0 and 65 °C for 3 h, and DTE-PHA beads retained about 80% of its initial activity after 8 continuous cycles. Moreover, the d-allulose/d-fructose binary mixture can be simply separated by a single cation exchange resin-equipped chromatography. Taken together, DTE-PHA beads are promising and robust nano-biocatalysts that will remarkably simplify the production procedures of d-allulose, contributing to its cost-effective production.