Efficient Biosynthesis of Low-Molecular-Weight Poly-γ-glutamic Acid by Stable Overexpression of PgdS Hydrolase in Bacillus amyloliquefaciens NB

Molecular weight control of poly-γ-glutamic acid reveals novel insights into extracellular polymeric substance synthesis in Bacillus licheniformis

BACKGROUND

The structural diversity of extracellular polymeric substances produced by microorganisms is attracting particular attention. Poly-gamma-glutamic acid (γ-PGA) is a widely studied extracellular polymeric substance from Bacillus species. The function of γ-PGA varies with its molecular weight (Mw).

RESULTS

Herein, different endogenous promoters in Bacillus licheniformis were selected to regulate the expression levels of pgdS, resulting in the formation of γ-PGA with Mw values ranging from 1.61 × 103 to 2.03 × 104 kDa. The yields of γ-PGA and exopolysaccharides (EPS) both increased in the pgdS engineered strain with the lowest Mw and viscosity, in which the EPS content was almost tenfold higher than that of the wild-type strain. Subsequently, the compositions of EPS from the pgdS engineered strain also changed. Metabolomics and RT-qPCR further revealed that improving the transportation efficiency of EPS and the regulation of carbon flow of monosaccharide synthesis could affect the EPS yield.

CONCLUSIONS

Here, we present a novel insight that increased pgdS expression led to the degradation of γ-PGA Mw and changes in EPS composition, thereby stimulating EPS and γ-PGA production. The results indicated a close relationship between γ-PGA and EPS in B. licheniformis and provided an effective strategy for the controlled synthesis of extracellular polymeric substances.

Genomic characterization and related functional genes of γ- poly glutamic acid producing Bacillus subtilis

γ- poly glutamic acid (γ-PGA), a high molecular weight polymer, is synthesized by microorganisms and secreted into the extracellular space. Due to its excellent performance, γ-PGA has been widely used in various fields, including food, biomedical and environmental fields. In this study, we screened natto samples for two strains of Bacillus subtilis N3378-2at and N3378-3At that produce γ-PGA. We then identified the γ-PGA synthetase gene cluster (PgsB, PgsC, PgsA, YwtC and PgdS), glutamate racemase RacE, phage-derived γ-PGA hydrolase (PghB and PghC) and exo-γ-glutamyl peptidase (GGT) from the genome of these strains. Based on these γ-PGA-related protein sequences from isolated Bacillus subtilis and 181 B. subtilis obtained from GenBank, we carried out genotyping analysis and classified them into types 1-5. Since we found B. amyloliquefaciens LL3 can produce γ-PGA, we obtained the B. velezensis and B. amyloliquefaciens strains from GenBank and classified them into types 6 and 7 based on LL3. Finally, we constructed evolutionary trees for these protein sequences. This study analyzed the distribution of γ-PGA-related protein sequences in the genomes of B. subtilis, B. velezensis and B. amyloliquefaciens strains, then the evolutionary diversity of these protein sequences was analyzed, which provided novel information for the development and utilization of γ-PGA-producing strains.

Engineering functional homopolymeric amino acids: from biosynthesis to design

Homopolymeric amino acids (HPAs) are a class of microbial polymers that can be classified into two categories: anionic and cationic HPAs. Notable examples include γ-poly-glutamic acid (γ-PGA) and ε-poly-L-lysine (ε-PL) that have wide-ranging applications in medicine, food, and agriculture. The primary method of manufacture is through microbial synthesis. In recent decades significant efforts have been made to enhance the production of HPAs, specifically focusing on γ-PGA and ε-PL. We comprehensively review current advances in understanding the synthetic mechanisms as well as metabolic engineering and fermentation process techniques to improve the production of HPAs. In addition, we discuss the major challenges and solutions associated with desired structure regulation of HPAs and the development of novel structures.

Advanced strategies for metabolic engineering of Bacillus to produce extracellular polymeric substances

Extracellular polymeric substances are mainly synthesized via a variety of biosynthetic pathways in bacteria. Bacilli-sourced extracellular polymeric substances, such as exopolysaccharides (EPS) and poly-γ-glutamic acid (γ-PGA), can serve as active ingredients and hydrogels, and have other important industrial applications. However, the functional diversity and widespread applications of these extracellular polymeric substances, are hampered by their low yields and high costs. Biosynthesis of extracellular polymeric substances is very complex in Bacillus, and there is no detailed elucidation of the reactions and regulations among various metabolic pathways. Therefore, a better understanding of the metabolic mechanisms is required to broaden the functions and increase the yield of extracellular polymeric substances. This review systematically summarizes the biosynthesis and metabolic mechanisms of extracellular polymeric substances in Bacillus, providing an in-depth understanding of the relationships between EPS and γ-PGA synthesis. This review provides a better clarification of Bacillus metabolic mechanisms during extracellular polymeric substance secretion and thus benefits their application and commercialization.

Development of a Conjugation-Based Genome Editing System in an Undomesticated Bacillus subtilis Strain for Poly-γ-glutamic Acid Production with Diverse Molecular Masses

Poly-γ-glutamic acid (γ-PGA) is a biodegradable polymer produced by microorganisms. Biosynthesizing γ-PGA with diverse molecular masses (M_w) is an urgent industrial technical problem to be solved. Bacillus subtilis KH2, a high-M_w γ-PGA producer, is an ideal candidate for de novo production of γ-PGA with diverse M_w values. However, the inability to transfer DNA to this strain has limited its industrial use. In this study, a conjugation-based genetic operating system was developed in strain KH2. This system enabled us to modify the promoter of γ-PGA hydrolase PgdS in strain KH2 chromosome to de novo biosynthesize γ-PGA with diverse M_ws. The conjugation efficiency was improved to 1.23 × 10^-4 by establishing a plasmid replicon sharing strategy. A further increase to 3.15 × 10^-3 was achieved after knocking out two restriction endonucleases. To demonstrate the potential of our newly established system, the pgdS promoter was replaced by different phase-dependent promoters. A series of strains producing γ-PGA with specific M_ws of 411.73, 1356.80, 2233.30, and 2411.87 kDa, respectively, were obtained. The maximum yield of γ-PGA was 23.28 g/L. Therefore, we have successfully constructed ideal candidate strains for efficient γ-PGA production with a specific M_w value, which provides an important research basis for sustainable production of desirable γ-PGA.

Efficient molasses utilization for low-molecular-weight poly-γ-glutamic acid production using a novel Bacillus subtilis stain

Background

Poly-γ-glutamic acid (γ-PGA) is a biopolymer and has various applications based on its biocompatibility, non-toxicity, and edibility. Low-molecular-weight (Mw)-γ-PGA has promising applications in agriculture and pharmaceuticals. It is traditionally produced by enzymatic hydrolysis. Cost-effective bioproduction of low-Mw-γ-PGA is essential for commercial application of γ-PGA.

Results

Bacillus subtilis 242 is a newly isolated low-Mw-γ-PGA-producing strain. To develop cost-effective production of γ-PGA using this newly isolated strain, cane molasses and corn steep liquor were used to produce γ-PGA. The concentration of cane molasses was optimized and 100 g/L cane molasses resulted in high γ-PGA production. The effects of yeast extract and corn steep liquor on γ-PGA yield were investigated. High concentration of γ-PGA was obtained in the medium with corn steep liquor. A concentration of 32.14 g/L γ-PGA was achieved in fed-batch fermentation, with a productivity of 0.67 g/L/h and a percentage yield (g_γ-PGA/g_glutamate) of 106.39%. The Mw of γ-PGA was 27.99 kDa.

Conclusion

This study demonstrated the potential application of B. subtilis 242 for cost-effective production of low-Mw-γ-PGA from cane molasses.

Metabolic Engineering of Bacillus amyloliquefaciens to Efficiently Synthesize L-Ornithine From Inulin

Bacillus amyloliquefaciens is the dominant strain used to produce γ-polyglutamic acid from inulin, a non-grain raw material. B. amyloliquefaciens has a highly efficient tricarboxylic acid cycle metabolic flux and glutamate synthesis ability. These features confer great potential for the synthesis of glutamate derivatives. However, it is challenging to efficiently convert high levels of glutamate to a particular glutamate derivative. Here, we conducted a systematic study on the biosynthesis of L-ornithine by B. amyloliquefaciens using inulin. First, the polyglutamate synthase gene pgsBCA of B. amyloliquefaciens NB was knocked out to hinder polyglutamate synthesis, resulting in the accumulation of intracellular glutamate and ATP. Second, a modular engineering strategy was applied to coordinate the degradation pathway, precursor competition pathway, and L-ornithine synthesis pathway to prompt high levels of intracellular precursor glutamate for l-ornithine synthesis. In addition, the high-efficiency L-ornithine transporter was further screened and overexpressed to reduce the feedback inhibition of L-ornithine on the synthesis pathway. Combining these strategies with further fermentation optimizations, we achieved a final L-ornithine titer of 31.3 g/L from inulin. Overall, these strategies hold great potential for strengthening microbial synthesis of high value-added products derived from glutamate.

Rational engineering of cofactor specificity of glutamate dehydrogenase for poly-γ-glutamic acid synthesis in Bacillus licheniformis

Poly-γ-glutamic acid (γ-PGA) is a multifunctional biopolymer mainly produced by Bacillus. The cofactor specificity of enzymes plays a critical role in regulating metabolic process and metabolite production. Here, we present a novel approach for switching cofactor specificity of glutamate dehydrogenase RocG from nicotinamide adenine dinucleotide phosphate (NADPH) to nicotinamide adenine dinucleotide (NADH) to improve γ-PGA production. Firstly, 3D structural modeling and molecular docking were performed to predict the binding modes of NADH and NADPH. Several site-specific mutants based on the conventional and Random Accelerated Molecular Dynamics simulations were obtained to alter cofactor specificity. Then, the effects of RocG variants overexpressions on γ-PGA production were evaluated. Compared to the wild-type, the mutant RocG^D276E showed highest increase in γ-PGA yield, increased by 40.50%. Meanwhile, yields of main by-products acetoin and 2,3-butandieol were decreased by 21.70% and 16.53%, respectively. Finally, the results of enzymatic properties confirmed that glutamate dehydrogenase mutant RocG^D276E exhibited the higher affinity for NADH, caused a shift in coenzyme preference from NADPH to NADH, with a catalytic efficiency comparable with NADPH-dependent RocG. Taken together, this research demonstrated that switching the cofactor preference of glutamate dehydrogenase via rational design was an effective strategy for high-level production of γ-PGA in Bacillus licheniformis.

Epsilon-poly-L-lysine: Recent Advances in Biomanufacturing and Applications

ε-poly-L-lysine (ε-PL) is a naturally occurring poly(amino acid) of varying polymerization degree, which possesses excellent antimicrobial activity and has been widely used in food and pharmaceutical industries. To provide new perspectives from recent advances, this review compares several conventional and advanced strategies for the discovery of wild strains and development of high-producing strains, including isolation and culture-based traditional methods as well as genome mining and directed evolution. We also summarize process engineering approaches for improving production, including optimization of environmental conditions and utilization of industrial waste. Then, efficient downstream purification methods are described, including their drawbacks, followed by the brief introductions of proposed antimicrobial mechanisms of ε-PL and its recent applications. Finally, we discuss persistent challenges and future perspectives for the commercialization of ε-PL.

Current advances in the biosynthesis of hyaluronic acid with variable molecular weights

Hyaluronic acid (HA) is a naturally formed acidic mucopolysaccharide, with excellent moisturising properties and used widely in the medicine, cosmetics, and food industries. The industrial production of specific molecular weight HA has become imperative. Different biological activities and physiological functions of HA mainly depend on the degree of polymerisation. This article reviews the research status and development prospects of the green biosynthesis and molecular weight regulation of HA. There is an application-based prerequisite of specific molecular weight of HA that could be regulated either during the fermentation process or via a controlled HA degradation process. This work provides an important theoretical basis for the downstream efficient production of diversified HA, which will further accelerate the research applications of HA and provide a good scientific basis and method reference for the study of the molecular weight regulation of similar biopolymers.

Bio-synthesis of food additives and colorants-a growing trend in future food

Food additives and colorants are extensively used in the food industry to improve food quality and safety during processing, storage and packing. Sourcing of these molecules is predominately through three means: extraction from natural sources, chemical synthesis, and bio-production, with the first two being the most utilized. However, growing demands for sustainability, safety and "natural" products have renewed interest in using bio-based production methods. Likewise, the move to more cultured foods and meat alternatives requires the production of new additives and colorants. The production of bio-based food additives and colorants is an interdisciplinary research endeavor and represents a growing trend in future food. To highlight the potential of microbial hosts for food additive and colorant production, we focus on current advances for example molecules based on their utilization stage and bio-production yield as follows: (I) approved and industrially produced with high titers; (II) approved and produced with decent titers (in the g/L range), but requiring further engineering to reduce production costs; (III) approved and produced with very early stage titers (in the mg/L range); and (IV) new/potential candidates that have not been approved but can be sourced through microbes. Promising approaches, as well as current challenges and future directions will also be thoroughly discussed for the bioproduction of these food additives and colorants.

Microbial synthesis of poly-γ-glutamic acid (γ-PGA) with fulvic acid powder, the waste from yeast molasses fermentation

BACKGROUND

Molasses is a wildly used feedstock for fermentation, but it also poses a severe wastewater-disposal problem worldwide. Recently, the wastewater from yeast molasses fermentation is being processed into fulvic acid (FA) powder as a fertilizer for crops, but it consequently induces a problem of soil acidification after being directly applied into soil. In this study, the low-cost FA powder was bioconverted into a value-added product of γ-PGA by a glutamate-independent producer of Bacillus velezensis GJ11.

RESULTS

FA power could partially substitute the high-cost substrates such as sodium glutamate and citrate sodium for producing γ-PGA. With FA powder in the fermentation medium, the amount of sodium glutamate and citrate sodium used for producing γ-PGA were both decreased around one-third. Moreover, FA powder could completely substitute Mg²⁺, Mn²⁺, Ca²⁺, and Fe³⁺ in the fermentation medium for producing γ-PGA. In the optimized medium with FA powder, the γ-PGA was produced at 42.55 g/L with a productivity of 1.15 g/(L·h), while only 2.87 g/L was produced in the medium without FA powder. Hydrolyzed γ-PGA could trigger induced systemic resistance (ISR), e.g., H₂O₂ accumulation and callose deposition, against the pathogen's infection in plants. Further investigations found that the ISR triggered by γ-PGA hydrolysates was dependent on the ethylene (ET) signaling and nonexpressor of pathogenesis-related proteins 1 (NPR1).

CONCLUSIONS

To our knowledge, this is the first report to use the industry waste, FA powder, as a sustainable substrate for microbial synthesis of γ-PGA. This bioprocess can not only develop a new way to use FA powder as a cheap feedstock for producing γ-PGA, but also help to reduce pollution from the wastewater of yeast molasses fermentation.

CRISPRi-Based Dynamic Regulation of Hydrolase for the Synthesis of Poly-γ-Glutamic Acid with Variable Molecular Weights

Poly-γ-glutamic acid (γ-PGA) is a decomposable polymer and has been useful in various industries. The biological functions of γ-PGA are closely linked with its molecular weight (MW). In this study, we established an efficient method to produce variable MWs of γ-PGA from renewable biomass (Jerusalem artichoke) by Bacillus amyloliquefaciens. First, a systematic engineering strategy was proposed in B. amyloliquefaciens to construct an optimal platform for γ-PGA overproduction, in which 24.95 g/L γ-PGA generation was attained. Second, 27.12 g/L γ-PGA with an MW of 20-30 kDa was obtained by introducing a γ-PGA hydrolase (pgdS) into the platform strain constructed above, which reveals a potential correlation between the expression level of pgdS and MW of γ-PGA. Then, a Clustered Regularly Interspaced Short Palindromic Repeats interference (CRISPRi) system was further designed to regulate pgdS expression levels, resulting in γ-PGA with variable MWs. Finally, a combinatorial approach based on three sgRNAs with different repression efficiencies was developed to achieve the dynamic regulation of pgdS and obtain tailor-made γ-PGA production in the MW range of 50-1400 kDa in one strain. This study illustrates a promising approach for the sustainable making of biopolymers with diverse molecular weights in one strain through the controllable expression of hydrolase using the CRISPRi system.

Engineering Expression Cassette of pgdS for Efficient Production of Poly-γ-Glutamic Acids With Specific Molecular Weights in Bacillus licheniformis

Poly-γ-glutamic acid (γ-PGA) is an emerging biopolymer with various applications and γ-PGAs with different molecular weights exhibit distinctive properties. However, studies on the controllable molecular weights of biopolymers are limited. The purpose of this study is to achieve production of γ-PGAs with a wide range of molecular weights through manipulating the expression of γ-PGA depolymerase (PgdS) in Bacillus licheniformis WX-02. Firstly, the expression and secretion of PgdS were regulated through engineering its expression elements (four promoters and eight signal peptides), which generated γ-PGAs with molecular weights ranging from 6.82 × 10⁴ to 1.78 × 10⁶ Da. Subsequently, through combination of promoters with signal peptides, the production of γ-PGAs with a specific molecular weight could be efficiently obtained. Interestingly, the γ-PGA yield increased with the reduced molecular weight in flask cultures (Pearson correlation coefficient of −0.968, P < 0.01). Finally, in batch fermentation, the highest yield of γ-PGA with a weight-average molecular weight of 7.80 × 10⁴ Da reached 39.13 g/L under glutamate-free medium. Collectively, we developed an efficient strategy for one-step production of γ-PGAs with specific molecular weights, which have potential application for industrial production of desirable γ-PGAs.

Efficient Biosynthesis of Low-Molecular-Weight Poly-γ-glutamic Acid Based on Stereochemistry Regulation in Bacillus amyloliquefaciens

Low-molecular-weight poly-γ-glutamic acid (LMW-γ-PGA) has attracted much attention because of its many potential applications in food, agriculture, medicine, and cosmetics. Enzymatic degradation is an efficient way for the synthesis of LMW-γ-PGA. However, the stereochemistry of γ-PGA limits the degradation of γ-PGA. This study identifies the role of γ-PGA synthase (pgsA) and glutamate racemase (racE) in the regulation of γ-PGA stereochemistry and demonstrates their combinational use for LMW-γ-PGA synthesis. First, the expression of pgsA and racE was enhanced, leading to improvements both in the molecular weight (Mw) and the d-glutamate proportion of γ-PGA. Then, an optimal combination of pgsA, racE, and γ-PGA hydrolase pgdS was constructed by exchanging the gene origins for the synthesis of LMW-γ-PGA. Finally, the Mw of γ-PGA was decreased to 6-8 kDa, which was much lower compared with the case without stereochemistry switching (20-30 kDa). This study provides a novel strategy to control the Mw of γ-PGA based on stereochemistry regulation and lays a solid foundation for synthesis of LMW-γ-PGA.

A Dual Network Hydrogel Sunscreen Based on Poly-γ-glutamic Acid/Tannic Acid Demonstrates Excellent Anti-UV, Self-Recovery, and Skin-Integration Capacities

Novel sunscreen products based on bioadhesive/gel systems that can prevent the skin penetration behaviors of UV filters have attracted increasing attention in recent years. However, integration is very difficult to achieve and control on the wet surface of the skin under sweaty/dynamic physiological conditions, resulting in functional failure. Herein, we demonstrated the fabrication of a novel dual-network hydrogel sunscreen (DNHS) based on poly-γ-glutamic acid (γ-PGA) and tannic acid (TA), which demonstrated prominent UV protection properties across broad UVA and UVB regions (360-275 nm). Due to a three-dimensional network microstructure and a highly hydrated nature that mimics the extracellular matrix of natural skin, DNHS can perfectly match the skin surface without irritation and sensitization. In addition, the intermolecular hydrogen bond interactions of γ-PGA and TA provide an important driving force for coacervation, which endows the DNHS with remarkable self-recovery properties (within 60 s). Moreover, due to the multiple interfacial interactions between γ-PGA/TA and the protein-rich skin tissue surfaces, DNHS simultaneously possesses excellent skin-integration and water-resistance capacities, and it can be readily removed on demand. Our results highlight the potential of the DNHS to be used in next-generation sunscreens by providing long-term and stable UV protection functions even under sweaty/dynamic physiological conditions.

Engineering Corynebacterium glutamicum for the de novo biosynthesis of tailored poly-γ-glutamic acid

γ-Polyglutamic acid (γ-PGA) is a biodegradable polymer naturally produced by Bacillus spp. that has wide applications. Fermentation of γ-PGA using Bacillus species often requires the supplementation of L-glutamic acid, which greatly increases the overall cost. Here, we report a metabolically engineered Corynebacterium glutamicum capable of producing γ-PGA from glucose. The genes encoding γ-PGA synthase complex from B. subtilis (pgsB, C, and A) or B. licheniformis (capB, C, and A) were expressed under inducible promoter P_tac in a L-glutamic acid producer C. glutamicum ATCC 13032, which led to low levels of γ-PGA production. Subsequently, C. glutamicum F343 with a strong L-glutamic acid production capability was tested. C. glutamicum F343 carrying capBCA produced γ-PGA up to 11.4 g/L, showing a higher titer compared with C. glutamicum F343 expressing pgsBCA. By introducing B. subtilis glutamate racemase gene racE under P_tac promoter mutants with different expression strength, the percentage of L-glutamic acid units in γ-PGA could be adjusted from 97.1% to 36.9%, and stayed constant during the fermentation process, while the γ-PGA titer reached 21.3 g/L under optimal initial glucose concentrations. The molecular weight (M_w) of γ-PGA in the engineered strains ranged from 2000 to 4000 kDa. This work provides a foundation for the development of sustainable and cost-effective de novo production of γ-PGA from glucose with customized ratios of L-glutamic acid in C. glutamicum.