Poly-γ-Glutamic Acid Production by Engineering a DegU Quorum-Sensing Circuit in Bacillus subtilis

Engineering a PhrC-RapC-SinR quorum sensing molecular switch for dynamic fine-tuning of menaquinone-7 synthesis in Bacillus subtilis

BACKGROUND

Menaquinone-7 (MK-7) is a valuable vitamin K2 produced by Bacillus subtilis. Although many strategies have been adopted to increase the yield of MK-7 in B. subtilis, the effectiveness of these common approaches is not high because long metabolic synthesis pathways and numerous bypass pathways competing for precursors with MK-7 synthesis. Regarding the modification of bypass pathways, studies of common static metabolic engineering method such as knocking out genes involved in side pathway have been reported previously. Since byproductsphenylalanine(Phe), tyrosine (Tyr), tryptophan (Trp), folic acid, dihydroxybenzoate, hydroxybutanone in the MK-7 synthesis pathway are indispensable for cell growth, the complete knockout of the bypass pathway restricts cell growth, resulting in limited increase in MK-7 synthesis. Dynamic regulation via quorum sensing (QS) provides a cost-effective strategy to harmonize cell growth and product synthesis, eliminating the need for pricey inducers. SinR, a transcriptional repressor, is crucial in suppressing biofilm formation, a process closely intertwined with MK-7 biosynthesis. Given this link, we targeted SinR to construct a dynamic regulatory system, aiming to modulate MK-7 production by leveraging SinR's regulatory influence.

RESULTS

A modular PhrC-RapC-SinR QS system is developed to dynamic regulate side pathway of MK-7. In this study, first, we analyzed the SinR-based gene expression regulation system in B. subtilis 168 (BS168). We constructed a promoter library of different abilities, selected suitable promoters from the library, and performed mutation screening on the selected promoters. Furthermore, we constructed a PhrC-RapC-SinR QS system to dynamically control the synthesis of Phe, Tyr, Trp, folic acid, dihydroxybenzoate, hydroxybutanone in MK-7 synthesis in BS168. Cell growth and efficient synthesis of the MK-7 production can be dynamically balanced by this QS system. Using this system to balance cell growth and product fermentation, the MK-7 yield was ultimately increased by 6.27-fold, from 13.95 mg/L to 87.52 mg/L.

CONCLUSION

In summary, the PhrC-RapC-SinR QS system has been successfully integrated with biocatalytic functions to achieve dynamic metabolic pathway control in BS168, which has potential applicability to a large number of microorganisms to fine-tune gene expression and enhance the production of metabolites.

Development and construction of a novel Bacillus subtilis autoinducible extracellular expression system based on a LuxI/R device

BACKGROUND

Microbial chassis expression systems are valuable tools in biotechnology and synthetic biology, and Bacillus subtilis is an important industrial microbial chassis. Quorum sensing (QS)-based dynamic regulation is widely used to automatically activate gene expression in response to changes in cell density. The main bottleneck currently limiting the use of exogenous QS systems in B. subtilis for efficient autoinducible extracellular expression of recombinant proteins is their low level of autoinducible expression.

RESULTS

A novel B. subtilis autoinducible extracellular expression system based on the LuxI/R-type QS system (lux system) of Vibrio fischeri was developed in which the autoinducible expression of the lux system was enhanced by engineering the sensing module and response module promoters. By engineering the sensing module promoter SPluxI core region (- 10 and - 35 elements) and critical region (UP and spacer elements), and the response module promoter RPluxIR6 core region and lux box copy number in the original LuxI/R device (S0-R0), the high-expression Sc-R2 construct was obtained. After shake flask and 3-L fermenter fermentation, the extracellular amylase activity obtained with Sc-R2 was 2.7- and 3.1-fold greater, respectively, than that obtained with the well-characterized promoter Pveg. Sc-R2 achieved 2.6-fold greater extracellular activity than S0-R0 when either levansucrase or invertase was used as a reporter protein. Overall, the B. subtilis autoinducible extracellular expression system developed in this study showed good generalizability and application potential for industrial-scale fermentation.

CONCLUSIONS

To our knowledge, this is the first study to report enhanced autoinducible expression of the lux system in B. subtilis by engineering the sensing module promoter SPluxI sequence and the lux box copy number of the response module promoter RPluxIR6. This study further expands the application potential of the B. subtilis expression system in synthetic biology.

Analysis of glutamate-dependent mechanism and optimization of fermentation conditions for poly-gamma-glutamic acid production by Bacillus subtilis SCP017-03

Poly-gamma-glutamic acid (γ-PGA) is mainly synthesized by glutamate-dependent strains in the manufacturing industry. Therefore, understanding glutamate-dependent mechanisms is imperative. In this study, we first systematically analyzed the response of Bacillus subtilis SCP017-03 to glutamate addition by comparing transcriptomics and proteomics. The introduction of glutamate substantially altered gene expression within the central metabolic pathway of cellular carbon. Most genes in the pentose phosphate pathway (PPP), tricarboxylic acid (TCA) cycle, and energy-consuming phase of the glycolysis pathway (EMP) were down-regulated, whereas those in the energy-producing phase of glycolysis and those responsible for γ-PGA synthesis were up-regulated. Based on these findings, the fermentation conditions were optimized, and γ-PGA production was improved by incorporating oxygen carriers. In a batch-fed fermentor with glucose, the γ-PGA production reached 95.2 g/L, demonstrating its industrial production potential. This study not only elucidated the glutamate dependence mechanism of Bacillus subtilis but also identified a promising metabolic target for further enhancing γ-PGA production.

Efficient Autoinducible Expression of Recombinant Proteins via the DegSU Quorum Sensing System in a Robust Bacillus subtilis

DegSU quorum sensing (QS) system enables autoinducible expression of recombinant proteins in Bacillus subtilis . However, insufficient promoter strength and a complex regulatory circuit limit its practical application. Here, the QS-responsive promoter PaprE was modified by core region mutation, upstream truncation, and addition of activating binding sites, yielding PE742 with a 118.3% increase in strength. A mathematical model was developed to accurately quantify the regulatory process from a comprehensive perspective. Guided by this model, the DegSU QS system was further optimized in a robust B. subtilis by knocking out competitive target genes sacB and amyE, operons pgs and srfA, introducing variants degUL113F and degQ36Hy, and increasing regulatory strength by 84.0%. A 52.5% increase in acetoin titer and a 65.9% increase in extracellular carboxypeptidase activity validated the industrial value of this study. Overall, this study addresses the limitations of the DegSU QS system in practical application and demonstrates its potential for high-level recombinant protein production.

Building electrode/electrolyte interphases in aqueous zinc batteries via self-polymerization of electrolyte additives

Aqueous zinc batteries offer promising prospects for large-scale energy storage, yet their application is limited by undesired side reactions at the electrode/electrolyte interface. Here, we report a universal approach for the in situ building of an electrode/electrolyte interphase (EEI) layer on both the cathode and the anode through the self-polymerization of electrolyte additives. In an exemplified Zn||V2O5·nH2O cell, we reveal that the glutamate additive undergoes radical-initiated electro-polymerization on the cathode and polycondensation on the anode, yielding polyglutamic acid-dominated EEI layers on both electrodes. These EEI layers effectively mitigate undesired interfacial side reactions while enhancing reaction kinetics, enabling Zn||V2O5·nH2O cells to achieve a high capacity of 387 mAh g-1 at 0.2 A g-1 and maintain >96.3% capacity retention after 1500 cycles at 1 A g-1. Moreover, this interphase-forming additive exhibits broad applicability to varied cathode materials, encompassing VS2, VS4, VO2, α-MnO2, β-MnO2 and δ-MnO2. The methodology of utilizing self-polymerizable electrolyte additives to construct robust EEI layers opens a novel pathway in interphase engineering for electrode stabilization in aqueous batteries.

Delaying production with prokaryotic inducible expression systems

BACKGROUND

Engineering bacteria with the purpose of optimizing the production of interesting molecules often leads to a decrease in growth due to metabolic burden or toxicity. By delaying the production in time, these negative effects on the growth can be avoided in a process called a two-stage fermentation.

MAIN TEXT

During this two-stage fermentation process, the production stage is only activated once sufficient cell mass is obtained. Besides the possibility of using external triggers, such as chemical molecules or changing fermentation parameters to induce the production stage, there is a renewed interest towards autoinducible systems. These systems, such as quorum sensing, do not require the extra interference with the fermentation broth to start the induction. In this review, we discuss the different possibilities of both external and autoinduction methods to obtain a two-stage fermentation. Additionally, an overview is given of the tuning methods that can be applied to optimize the induction process. Finally, future challenges and prospects of (auto)inducible expression systems are discussed.

CONCLUSION

There are numerous methods to obtain a two-stage fermentation process each with their own advantages and disadvantages. Even though chemically inducible expression systems are well-established, an increasing interest is going towards autoinducible expression systems, such as quorum sensing. Although these newer techniques cannot rely on the decades of characterization and applications as is the case for chemically inducible promoters, their advantages might lead to a shift in future inducible expression systems.

Enhanced Iturin A Production of Engineered Bacillus amyloliquefaciens by Knockout of Endogenous Plasmid and Rap Phosphatase Genes

Iturin A biosynthesis has garnered considerable interest, yet bottlenecks persist in its low productivity in wild strains and the ability to engineer Bacillus amyloliquefaciens producers. This study reveals that deleting the endogenous plasmid, plas1, from the wild-type B. amyloliquefaciens HM618 notably enhances iturin A synthesis, likely related to the effect of the Rap phosphatase gene within plas1. Furthermore, inactivating Rap phosphatase-related genes (rapC, rapF, and rapH) in the genome of the strain also improved the iturin A level and specific productivity while reducing cell growth. Strategic rap genes and plasmid elimination achieved a synergistic balance between cell growth and iturin A production. Engineered strain HM-DR13 exhibited an increase in iturin A level to 849.9 mg/L within 48 h, significantly shortening the production period. These insights underscore the critical roles of endogenous plasmids and Rap phosphatases in iturin A biosynthesis, presenting a novel engineering strategy to optimize iturin A production in B. amyloliquefaciens.

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.

Enhanced poly-γ-glutamic acid synthesis in Corynebacterium glutamicum by reconstituting PgsBCA complex and fermentation optimization

Previously, a novel Corynebacterium glutamicum strain for the de novo biosynthesis of tailored poly-γ-glutamic acid (γ-PGA) has been constructed by our group. The strain was based on the γ-PGA synthetase complex, PgsBCA, which is the only polyprotein complex responsible for γ-PGA synthesis in Bacillus spp. In the present study, PgsBCA was reconstituted and overexpressed in C. glutamicum to further enhance γ-PGA synthesis. First, we confirmed that all the components (PgsB, PgsC, and PgsA) of γ-PGA synthetase derived from B. licheniformis are necessary for γ-PGA synthesis, and γ-PGA was detected only when PgsB, PgsC, and PgsA were expressed in combination in C. glutamicum. Next, the expression level of each pgsB, pgsC, and pgsA was tuned in order to explore the effect of expression of each of the γ-PGA synthetase subunits on γ-PGA production. Results showed that increasing the transcription levels of pgsB or pgsC and maintaining a medium-level transcription level of pgsA led to 35.44% and 76.53% increase in γ-PGA yield (γ-PGA yield-to-biomass), respectively. Notably, the expression level of pgsC had the greatest influence (accounting for 68.24%) on γ-PGA synthesis, followed by pgsB. Next, genes encoding for PgsC from four different sources (Bacillus subtilis, Bacillus anthracis, Bacillus methylotrophicus, and Bacillus amyloliquefaciens) were tested in order to identify the influence of PgsC-encoding orthologues on γ-PGA production, but results showed that in all cases the synthesis of γ-PGA was significantly inhibited. Similarly, we also explored the influence of gene orthologues encoding for PgsB on γ-PGA production, and found that the titer increased to 17.14 ± 0.62 g/L from 8.24 ± 0.10 g/L when PgsB derived from B. methylotrophicus replaced PgsB alone in PgsBCA from B. licheniformis. The resulting strain was chosen for further optimization, and we achieved a γ-PGA titer of 38.26 g/L in a 5 L fermentor by optimizing dissolved oxygen level. Subsequently, by supplementing glucose, γ-PGA titer increased to 50.2 g/L at 48 h. To the best of our knowledge, this study achieved the highest titer for de novo production of γ-PGA from glucose, without addition of L-glutamic acid, resulting in a novel strategy for enhancing γ-PGA production.

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.

Quorum Sensing as a Trigger That Improves Characteristics of Microbial Biocatalysts

Quorum sensing (QS) of various microorganisms (bacteria, fungi, microalgae) today attracts the attention of researchers mainly from the point of view of clarifying the biochemical basics of this general biological phenomenon, establishing chemical compounds that regulate it, and studying the mechanisms of its realization. Such information is primarily aimed at its use in solving environmental problems and the development of effective antimicrobial agents. This review is oriented on other aspects of the application of such knowledge; in particular, it discusses the role of QS in the elaboration of various prospective biocatalytic systems for different biotechnological processes carried out under aerobic and anaerobic conditions (synthesis of enzymes, polysaccharides, organic acids, etc.). Particular attention is paid to the biotechnological aspects of QS application and the use of biocatalysts, which have a heterogeneous microbial composition. The priorities of how to trigger a quorum response in immobilized cells to maintain their long-term productive and stable metabolic functioning are also discussed. There are several approaches that can be realized: increase in cell concentration, introduction of inductors for synthesis of QS-molecules, addition of QS-molecules, and provoking competition between the participants of heterogeneous biocatalysts, etc.).

Application of Quorum Sensing in Metabolic Engineering

Metabolic engineering is widely utilized in the food and other fields and has the benefits of low-cost substrates, eco-friendly fermentation processes, and efficient substrate synthesis. Microbial synthesis by metabolic engineering requires maintaining the productive capacity of the microorganism. Moreover, economic reasons limit the use of inducers in the exogenous synthesis pathway. Most unicellular microorganisms can interact by emitting signaling molecules; this mechanism, known as quorum sensing (QS), is an autoinduced system of microorganisms. With the deepening research on QS systems of different microorganisms, its components are widely used to regulate the metabolic synthesis of microorganisms as a dynamic regulatory system. In this Review, we described the typical bacterial QS mechanisms. Then, we summarized various regulatory strategies for QS and their applications to metabolic engineering. Finally, we underlined the potential for QS modularity in future metabolic engineering and suggested stimulating research on fungal QS systems.

Spatiotemporal Gene Expression by a Genetic Circuit for Chemical Production in Escherichia coli

Gene expression in spatiotemporal distribution improves the ability of cells to respond to changing environments. For microbial cell factories in artificial environments, reconstruction of the target compound's biosynthetic pathway in a new spatiotemporal dimension/scale promotes the production of chemicals. Here, a genetic circuit based on the Esa quorum sensing and lac operon was designed to achieve the dynamic temporal gene expression. Meanwhile, the pathway was regulated by an l-cysteine-specific sensor and relocalized to the plasma membrane for further flux enhancement to l-cysteine and toxicity reduction on a spatial scale. Finally, the integrated spatiotemporal regulation circuit for l-cysteine biosynthesis enabled a 14.16 g/L l-cysteine yield in Escherichia coli. Furthermore, this spatiotemporal regulation circuit was also applied in our previously constructed engineered strain for pantothenic acid, methionine, homoserine, and 2-aminobutyric acid production, and the titer increased by 29, 33, 28, and 41%, respectively. These results highlighted the applicability of our spatiotemporal regulation circuit to enhance the performance of microbial cell factories.