Advances on systems metabolic engineering of Bacillus subtilis as a chassis cell

Recent advances in microbial synthesis of free heme

Heme is an iron-containing porphyrin compound widely used in the fields of healthcare, food, and medicine. Compared to animal blood extraction, it is more advantageous to develop a microbial cell factory to produce heme. However, heme biosynthesis in microorganisms is tightly regulated, and its accumulation is highly cytotoxic. The current review describes the biosynthetic pathway of free heme, its fermentation production using different engineered bacteria constructed by metabolic engineering, and strategies for further improving heme synthesis. Heme synthetic pathway in Bacillus subtilis was modified utilizing genome-editing technology, resulting in significantly improved heme synthesis and secretion abilities. This technique avoided the use of multiple antibiotics and enhanced the genetic stability of strain. Hence, engineered B. subtilis could be an attractive cell factory for heme production. Further studies should be performed to enhance the expression of heme synthetic module and optimize the expression of heme exporter and fermentation processes, such as iron supply. KEY POINTS: • Strengthening the heme biosynthetic pathway can significantly increase heme production. • Heme exporter overexpression helps to promote heme secretion, thereby further promoting excessive heme synthesis. • Engineered B. subtilis is an attractive alternative for heme production.

Molecular strategies to enhance the keratinase gene expression and its potential implications in poultry feed industry

The tons of keratin waste are produced by the poultry and meat industry which is an insoluble and protein-rich material found in hair, feathers, wool, and some epidermal wastes. These waste products could be degraded and recycled to recover protein, which can save our environment. One of the potential strategy to achieve this target is use of microbial biotreatment which is more convenient, cost-effective, and environment-friendly by formulating hydrolysate complexes that could be administered as protein supplements, bioactive peptides, or animal feed ingredients. Keratin degradation shows great promise for long-term protein and amino acid recycling. According to the MEROPS database, known keratinolytic enzymes currently belong to at least 14 different protease families, including S1, S8, S9, S10, S16, M3, M4, M14, M16, M28, M32, M36, M38, and M55. In addition to exogenous attack (proteases from families S9, S10, M14, M28, M38, and M55), the various keratinolytic enzymes also function via endo-attack (proteases from families S1, S8, S16, M4, M16, and M36). Biotechnological methods have shown great promise for enhancing keratinase expression in different strains of microbes and different protein engineering techniques in genetically modified microbes such as bacteria and some fungi to enhance keratinase production and activity. Some microbes produce specific keratinolytic enzymes that can effectively degrade keratin substrates. Keratinases have been successfully used in the leather, textile, and pharmaceutical industries. However, the production and efficiency of existing enzymes need to be optimized before they can be used more widely in other processes, such as the cost-effective pretreatment of chicken waste. These can be improved more effectively by using various biotechnological applications which could serve as the best and novel approach for recycling and degrading biomass. This paper provides practical insights about molecular strategies to enhance keratinase expression to effectively utilize various poultry wastes like feathers and feed ingredients like soybean pulp. Furthermore, it describes the future implications of engineered keratinases for environment friendly utilization of wastes and crop byproducts for their better use in the poultry feed industry.

Efficient expression of γ-glutamyl transpeptidase in Bacillus subtilis via CRISPR/Cas9n and its immobilization

In this study, we successfully applied the strategy of combining tandem promoters and tandem signal peptides with overexpressing signal peptidase to efficiently express and produce γ-glutamyl peptidase (GGT) enzymes (BsGGT, BaGGT, and BlGGT) from Bacillus subtilis, Bacillus amyloliquefaciens, and Bacillus licheniformis in Bacillus subtilis ATCC6051Δ5. In order to avoid the problem of instability caused by duplicated strong promoters, we assembled tandem promoters of different homologous genes from different species. To achieve resistance marker-free enzyme in the food industry, we first removed the replication origin and corresponding resistance marker of Escherichia coli from the expression vector. The plasmid was then transformed into the B. subtilis host, and the Kan resistance gene in the expression plasmid was directly edited and silenced using the CRISPR/Cas9n-AID base editing system. As a result, a recombinant protein expression carrier without resistance markers was constructed, and the enzyme activity of the BlGGT strain during shake flask fermentation can reach 53.65 U/mL. The recombinant BlGGT was immobilized with epoxy resin and maintained 82.8% enzyme activity after repeated use for 10 times and 87.36% enzyme activity after storage at 4 °C for 2 months. The immobilized BlGGT enzyme was used for the continuous synthesis of theanine with a conversion rate of 65.38%. These results indicated that our approach was a promising solution for improving enzyme production efficiency and achieving safe production of enzyme preparations in the food industry. KEY POINTS: • Efficient expression of recombinant proteins by a combination of dual promoter and dual signal peptide. • Construction of small vectors without resistance markers in B. subtilis using CRISPR/Cas9n-AID editing system. • The process of immobilizing BlGGT with epoxy resin was optimized.

Identification and engineering of the aprE regulatory region and relevant regulatory proteins in Bacillus licheniformis 2709

Bacillus licheniformis 2709 is the main industrial producer of alkaline protease (AprE), but its biosynthesis is strictly controlled by a highly sophisticated transcriptional network. In this study, the UP elements of aprE located 74-98, 98-119 and 140-340 bp upstream of the transcriptional start site (TSS) were identified, which presented obvious effects on the transcription of aprE. To further analyze the transcriptional mechanism, the specific proteins binding to the approximately 500-bp DNA sequences were subsequently captured by reverse-chromatin immunoprecipitation (reverse-ChIP) and DNA pull-down (DPD) assays, which captured the transcriptional factors CggR, FruR, and YhcZ. The study demonstrated that CggR, FruR and YhcZ had no significant effect on cell growth and aprE expression. Then, aprE expression was significantly enhanced by deleting a potential negative regulatory factor binding site in the genome. The AprE enzyme activity in shake flasks of the genomic mutant BL ∆1 was 47% higher than in the original strain, while the aprE transcription level increased 3.16 times. The protocol established in this study provides a valuable reference for the high-level production of proteins in other Bacillus species. At the same time, it will help reveal the molecular mechanism of the transcriptional regulatory network of aprE and provide important theoretical guidance for further enhancing the yield of AprE.

Whole genome sequencing and the lignocellulose degradation potential of Bacillus subtilis RLI2019 isolated from the intestine of termites

BACKGROUND

Lignocellulosic biomass is the most abundant and renewable terrestrial raw material for conversion into bioproducts and biofuels. However, the low utilization efficiency of lignocellulose causes environmental pollution and resource waste, which limits the large-scale application of bioconversion. The degradation of lignocellulose by microorganisms is an efficient and cost-effective way to overcome the challenge of utilizing plant biomass resources. This work aimed to screen valuable cellulolytic bacteria, explore its molecular mechanism from genomic insights, and investigate the ability of the strain to biodegrade wheat straw.

RESULTS

Bacillus subtilis (B. subtilis) RLI2019 was isolated from the intestine of Reticulitermes labralis. The strain showed comprehensive enzyme activities related to lignocellulose degradation, which were estimated as 4.06, 1.97, 4.12, 0.74, and 17.61 U/mL for endoglucanase, β-glucosidase, PASC enzyme, filter paper enzyme, and xylanase, respectively. Whole genome sequencing was performed to better understand the genetic mechanism of cellulose degradation. The genome size of B. subtilis RLI2019 was 4,195,306 bp with an average GC content of 43.54%, and the sequence characteristics illustrated an extremely high probability (99.41%) as a probiotic. The genome contained 4,381 protein coding genes with an average GC content of 44.20%, of which 145 genes were classified into six carbohydrate-active enzyme (CAZyme) families and 57 subfamilies. Eight cellulose metabolism enzyme-related genes and nine hemicellulose metabolism enzyme-related genes were annotated by the CAZyme database. The starch and sucrose metabolic pathway (ko00500) was the most enriched with 46 genes in carbohydrate metabolism. B. subtilis RLI2019 was co-cultured with wheat straw for 7 days of fermentation, the contents of neutral detergent fiber, acid detergent fiber, hemicellulose, and lignin were significantly reduced by 5.8%, 10.3%, 1.0%, and 4.7%, respectively. Moreover, the wheat straw substrate exhibited 664.9 μg/mL of reducing sugars, 1.22 U/mL and 6.68 U/mL of endoglucanase and xylanase activities, respectively. Furthermore, the fiber structures were effectively disrupted, and the cellulose crystallinity was significantly reduced from 40.2% to 36.9%.

CONCLUSIONS

The complex diversity of CAZyme composition mainly contributed to the strong cellulolytic attribute of B. subtilis RLI2019. These findings suggest that B. subtilis RLI2019 has favorable potential for biodegradation applications, thus it can be regarded as a promising candidate bacterium for lignocellulosic biomass degradation.

Screening and identification of genes involved in β-alanine biosynthesis in Bacillus subtilis

β-alanine is the only naturally occurring β-amino acid, which is widely used in medicine, food, and feed fields, and generally produced through synthetic biological methods based on engineered strains of Escherichia coli or Corynebacterium glutamicum. However, the β-alanine biosynthesis in Bacillus subtilis, a traditional industrial model microorganism of food safety grade, has not been thoroughly explored. In this study, the native l-aspartate-α-decarboxylase was overexpressed in B. subtilis 168 to obtain an increase of 842% in β-alanine production. A total of 16 single-gene knockout strains were constructed to block the competitive consumption pathways to identify a total of 6 genes (i.e., ptsG, fbp, ydaP, yhfS, mmgA, and pckA) involved in β-alanine synthesis, while the multigene knockout of these 6 genes obtained an increased β-alanine production by 40.1%. Ten single-gene suppression strains with the competitive metabolic pathways inhibited revealed that the inhibited expressions of genes glmS, accB, and accA enhanced the β-alanine production. The introduction of heterologous phosphoenolpyruvate carboxylase increased the β-alanine production by 81.7%, which was 17-fold higher than that of the original strain. This was the first study using multiple molecular strategies to investigate the biosynthetic pathway of β-alanine in B. subtilis and to identify the genetic factors limiting the excessive synthesis of β-alanine by microorganisms.

Toward implementation of carbon-conservation networks in nonmodel organisms

Decarboxylation - the release of carbon dioxide (CO₂) from a substrate - reduces the carbon yield of bioproduced chemicals. When overlaid onto central carbon metabolism, carbon-conservation networks (CCNs) that reroute flux around CO₂ release can theoretically achieve higher carbon yields for products derived from intermediates that traditionally require CO₂ release, such as acetyl-CoA. Recently, CCNs have started to be implemented in model organisms to produce compounds at higher carbon yields. However, implementation of CCNs in nonmodel hosts may have the greatest impact given their ability to assimilate a larger array of feedstocks, greater environmental tolerance, and unique biosynthetic pathways, ultimately enabling access to a wider range of products. Here, we review recent advances in CCNs with a focus on their application to nonmodel organisms. The differences in central carbon metabolism among different nonmodel hosts reveal opportunities to engineer and apply new CCNs.

Potent IPTG-inducible integrative expression vectors for production of recombinant proteins in Bacillus subtilis

The IPTG-inducible promoter family, Pgrac, allows high protein expression levels in an inducible manner. In this study, we constructed IPTG-inducible expression vectors containing strong Pgrac promoters that allow integration of the transgene at either the amyE or lacA locus or both loci in Bacillus subtilis. Our novel integrative expression vectors based on Pgrac promoters could control the repression of protein production in the absence and the induction in the presence of an inducer, IPTG. The β-galactosidase (BgaB) protein levels were 9.0%, 15% and 30% of the total cellular protein in the B. subtilis strains carrying single cassettes with the Pgrac01, Pgrac100 or Pgrac212 promoters, respectively. The maximal induction ratio of Pgrac01-bgaB was 35.5 while that of Pgrac100-bgaB was 7.5 and that of Pgrac212-bgaB was 9. The inducible expression of GFP and BgaB protein was stably maintained for 24 h, with the highest yield of GFP being 24% of cell total protein while the maximum amount of BgaB was found to be 38%. A dual integration of two copies of the gfp⁺ gene into the B. subtilis genome at the lacA and amyE loci resulted in a yield of about 40% of total cellular protein and a 1.74-fold increase in GFP compared with single-integrated strains containing the same Pgrac212 promoter. The capability of protein production from low to high levels of these inducible integrative systems is useful for fundamental and applied research in B. subtilis.

Design and genome engineering of microbial cell factories for efficient conversion of lignocellulose to fuel

The gradually increasing need for fossil fuels demands renewable biofuel substitutes. This has fascinated an increasing investigation to design innovative energy fuels that have comparable Physico-chemical and combustion characteristics with fossil-derived fuels. The efficient microbes for bioenergy synthesis desire the proficiency to consume a large quantity of carbon substrate, transfer various carbohydrates through efficient metabolic pathways, capability to withstand inhibitory components and other degradation compounds, and improve metabolic fluxes to synthesize target compounds. Metabolically engineered microbes could be an efficient methodology for synthesizing biofuel from cellulosic biomass by cautiously manipulating enzymes and metabolic pathways. This review offers a comprehensive perspective on the trends and advances in metabolic and genetic engineering technologies for advanced biofuel synthesis by applying various heterologous hosts. Probable technologies include enzyme engineering, heterologous expression of multiple genes, CRISPR-Cas technologies for genome editing, and cell surface display.

Engineering of global transcription factors in Bacillus, a genetic tool for increasing product yields: a bioprocess overview

Transcriptional factors are well studied in bacteria for their global interactions and the effects they produce at the phenotypic level. Particularly, Bacillus subtilis has been widely employed as a model Gram-positive microorganism used to characterize these network interactions. Bacillus species are currently used as efficient commercial microbial platforms to produce diverse metabolites such as extracellular enzymes, antibiotics, surfactants, industrial chemicals, heterologous proteins, among others. However, the pleiotropic effects caused by the genetic modification of specific genes that codify for global regulators (transcription factors) have not been implicated commonly from a bioprocess point of view. Recently, these strategies have attracted the attention in Bacillus species because they can have an application to increase production efficiency of certain commercial interest metabolites. In this review, we update the recent advances that involve this trend in the use of genetic engineering (mutations, deletion, or overexpression) performed to global regulators such as Spo0A, CcpA, CodY and AbrB, which can provide an advantage for the development or improvement of bioprocesses that involve Bacillus species as production platforms. Genetic networks, regulation pathways and their relationship to the development of growth stages are also discussed to correlate the interactions that occur between these regulators, which are important to consider for application in the improvement of commercial-interest metabolites. Reported yields from these products currently produced mostly under laboratory conditions and, in a lesser extent at bioreactor level, are also discussed to give valuable perspectives about their potential use and developmental level directed to process optimization at large-scale.

Influence of N-terminal His-tags on the production of recombinant proteins in the cytoplasm of Bacillus subtilis

The influence of fusion tags to produce recombinant proteins in the cytoplasm of Bacillus subtilis is not well-studied as in E. coli. This study aimed to investigate the influence of His-tags with different codons on the protein production levels of the high expression gene (gfp+) and low expression gene (egfp) in the cytoplasm of B. subtilis cells. We used three different N-terminal His-tags, M-6xHis, MRGS-8xHis and MEA-8xHis, to investigate their effects on the production levels of GFP variants under the control of the Pgrac212 in B. subtilis. The fusions of His-tags with GFP+ caused a reduction compared to the construct without His-tag. When three His-tags fused with egfp, the EGFP production levels were significantly increased up to 3.5-, 12-, and 15-fold. This study suggested that His-tag at the N-terminus could enhance the protein production for the low expression gene and reduce that of the high expression gene in B. subtilis.

Production of 5-aminolevulinic acid from hydrolysates of cassava residue and fish waste by engineered Bacillus cereus PT1

The economical production of 5-aminolevulinic acid (ALA) has recently received increasing attention for its extensive use in agriculture. In this study, a strain of Bacillus cereus PT1 could initially produce ALA at a titre of 251.72 mg/L by using a hydrolysate mixture of low-cost cassava residue and fish waste. The integration of endogenous hemA encoding glutamyl-tRNA reductase led to a 39.30% increase in ALA production. Moreover, improving cell permeability by deletion of the LytR-CpsA-Psr (LCP) family gene tagU led to a further increase of 59.73% in ALA production. Finally, the engineered strain B. cereus PT1-hemA-ΔtagU produced 2.62 g/L of ALA from the previously mentioned hydrolysate mixture in a 7-L bioreactor. In a pot experiment, foliar spray of the ALA produced by B. cereus PT1-hemA-ΔtagU from the hydrolysates increased salt tolerance of cucumber by improving chlorophyll content and catalase activity, while decreasing malondialdehyde content. Overall, this study demonstrated an economic way to produce ALA using a microbial platform and evidenced the potential of ALA in agricultural application.

Enhancing the Activity of Carboxymethyl Cellulase Enzyme Using Highly Stable Selenium Nanoparticles Biosynthesized by Bacillus paralicheniformis Y4

The inorganic selenium is absorbed and utilized inefficiently, and the range between toxicity and demand is narrow, so the application is strictly limited. Selenium nanoparticles have higher bioactivity and biosafety properties, including increased antioxidant and anticancer properties. Thus, producing and applying eco-friendly, non-toxic selenium nanoparticles in feed additives is crucial. Bacillus paralicheniformis Y4 was investigated for its potential ability to produce selenium nanoparticles and the activity of carboxymethyl cellulases. The selenium nanoparticles were characterized using zeta potential analyses, Fourier transform infrared (FTIR) spectroscopy, and scanning electron microscopy (SEM). Additionally, evaluations of the anti-α-glucosidase activity and the antioxidant activity of the selenium nanoparticles and the ethyl acetate extracts of Y4 were conducted. B. paralicheniformis Y4 exhibited high selenite tolerance of 400 mM and the selenium nanoparticles had an average particle size of 80 nm with a zeta potential value of −35.8 mV at a pH of 7.0, suggesting that the particles are relatively stable against aggregation. After 72 h of incubation with 5 mM selenite, B. paralicheniformis Y4 was able to reduce it by 76.4%, yielding red spherical bio-derived selenium nanoparticles and increasing the carboxymethyl cellulase activity by 1.49 times to 8.96 U/mL. For the first time, this study reports that the carboxymethyl cellulase activity of Bacillus paralicheniforis was greatly enhanced by selenite. The results also indicated that B. paralicheniformis Y4 could be capable of ecologically removing selenite from contaminated sites and has great potential for producing selenium nanoparticles as feed additives to enhance the added value of agricultural products.

Recent Advances in Nattokinase-Enriched Fermented Soybean Foods: A Review

With the dramatic increase in mortality of cardiovascular diseases (CVDs) caused by thrombus, this has sparked an interest in seeking more effective thrombolytic drugs or dietary nutriments. The dietary consumption of natto, a traditional Bacillus-fermented food (BFF), can reduce the risk of CVDs. Nattokinase (NK), a natural, safe, efficient and cost-effective thrombolytic enzyme, is the most bioactive ingredient in natto. NK has progressively been considered to have potentially beneficial cardiovascular effects. Microbial synthesis is a cost-effective method of producing NK. Bacillus spp. are the main production strains. While microbial synthesis of NK has been thoroughly explored, NK yield, activity and stability are the critical restrictions. Multiple optimization strategies are an attempt to tackle the current problems to meet commercial demands. We focus on the recent advances in NK, including fermented soybean foods, production strains, optimization strategies, extraction and purification, activity maintenance, biological functions, and safety assessment of NK. In addition, this review systematically discussed the challenges and prospects of NK in actual application. Due to the continuous exploration and rapid progress of NK, NK is expected to be a natural future alternative to CVDs.

In vivo, in vitro and in silico: an open space for the development of microbe-based applications of synthetic biology

Living systems are studied using three complementary approaches: living cells, cell-free systems and computer-mediated modelling. Progresses in understanding, allowing researchers to create novel chassis and industrial processes rest on a cycle that combines in vivo, in vitro and in silico studies. This design-build-test-learn iteration loop cycle between experiments and analyses combines together physiology, genetics, biochemistry and bioinformatics in a way that keeps going forward. Because computer-aided approaches are not directly constrained by the material nature of the entities of interest, we illustrate here how this virtuous cycle allows researchers to explore chemistry which is foreign to that present in extant life, from whole chassis to novel metabolic cycles. Particular emphasis is placed on the importance of evolution.

Expression of SARS-CoV-2 Spike Protein Receptor Binding Domain on Recombinant B. subtilis on Spore Surface: A Potential COVID-19 Oral Vaccine Candidate

Various types of vaccines, such as mRNA, adenovirus, and inactivated virus by injection, have been developed to prevent SARS-CoV-2 infection. Although some of them have already been approved under the COVID-19 pandemic, various drawbacks, including severe side effects and the requirement for sub-zero temperature storage, may hinder their applications. Bacillus subtilis (B. subtilis) is generally recognized as a safe and endotoxin-free Gram-positive bacterium that has been extensively employed as a host for the expression of recombinant proteins. Its dormant spores are extraordinarily resistant to the harsh environment in the gastrointestinal tract. This feature makes it an ideal carrier for oral administration in resisting this acidic environment and for release in the intestine. In this study, an engineered B. subtilis spore expressing the SARS-CoV-2 spike protein receptor binding domain (sRBD) on the spore surface was developed. In a pilot test, no adverse health event was observed in either mice or healthy human volunteers after three oral courses of B. subtilis spores. Significant increases in neutralizing antibody against sRBD, in both mice and human volunteers, after oral administration were also found. These findings may enable the further clinical developments of B. subtilis spores as an oral vaccine candidate against COVID-19 in the future.

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.

The multifunctionality of expression systems in Bacillus subtilis: Emerging devices for the production of recombinant proteins

Bacillus subtilis is a successful host for producing recombinant proteins. Its GRAS (generally recognized as safe) status and its remarkable innate ability to absorb and incorporate exogenous DNA into its genome make this organism an ideal platform for the heterologous expression of bioactive substances. The factors that corroborate its value can be attributed to the scientific knowledge obtained from decades of study regarding its biology that has fostered the development of several genetic engineering strategies, such as the use of different plasmids, engineering of constitutive or double promoters, chemical inducers, systems of self-inducing expression with or without a secretion system that uses a signal peptide, and so on. Tools that enrich the technological arsenal of this expression platform improve the efficiency and reduce the costs of production of proteins of biotechnological importance. Therefore, this review aims to highlight the major advances involving recombinant expression systems developed in B. subtilis, thus sustaining the generation of knowledge and its application in future research. It was verified that this bacterium is a model in constant demand and studies of the expression of recombinant proteins on a large scale are increasing in number. As such, it represents a powerful bacterial host for academic research and industrial purposes.

Biodegradation of aromatic pollutants meets synthetic biology

Ubiquitously distributed microorganisms are natural decomposers of environmental pollutants. However, because of continuous generation of novel recalcitrant pollutants due to human activities, it is difficult, if not impossible, for microbes to acquire novel degradation mechanisms through natural evolution. Synthetic biology provides tools to engineer, transform or even re-synthesize an organism purposefully, accelerating transition from unable to able, inefficient to efficient degradation of given pollutants, and therefore, providing new solutions for environmental bioremediation. In this review, we described the pipeline to build chassis cells for the treatment of aromatic pollutants, and presented a proposal to design microbes with emphasis on the strategies applied to modify the target organism at different level. Finally, we discussed challenges and opportunities for future research in this field.

Production of proteins and commodity chemicals using engineered Bacillus subtilis platform strain

Currently, increasing demand of biochemicals produced from renewable resources has motivated researchers to seek microbial production strategies instead of traditional chemical methods. As a microbial platform, Bacillus subtilis possesses many advantages including the generally recognized safe status, clear metabolic networks, short growth cycle, mature genetic editing methods and efficient protein secretion systems. Engineered B. subtilis strains are being increasingly used in laboratory research and in industry for the production of valuable proteins and other chemicals. In this review, we first describe the recent advances of bioinformatics strategies during the research and applications of B. subtilis. Secondly, the applications of B. subtilis in enzymes and recombinant proteins production are summarized. Further, the recent progress in employing metabolic engineering and synthetic biology strategies in B. subtilis platform strain to produce commodity chemicals is systematically introduced and compared. Finally, the major limitations for the further development of B. subtilis platform strain and possible future directions for its research are also discussed.

Anodic electro-fermentation: Empowering anaerobic production processes via anodic respiration

In nature as well as in industrial microbiology, all microorganisms need to achieve redox balance. Their redox state and energy conservation highly depend on the availability of a terminal electron acceptor, for example oxygen in aerobic production processes. Under anaerobic conditions in the absence of an electron acceptor, redox balance is achieved via the production of reduced carbon-compounds (fermentation). An alternative strategy to artificially stabilize microbial redox and energy state is the use of anodic electro-fermentation (AEF). This emerging biotechnology empowers respiration under anaerobic conditions using the anode of a bioelectrochemical system as an undepletable terminal electron acceptor. Electrochemical control of redox metabolism and energy conservation via AEF can steer the carbon metabolism towards a product of interest and avoid the need for continuous and cost-inefficient supply of oxygen as well as the production of mixed reduced by-products, as is the case in aerobic production and fermentation processes, respectively. The great challenge for AEF is to establish efficient extracellular electron transfer (EET) from the microbe to the anode and link it to central carbon metabolism to enhance the synthesis of a target product. This article reviews the advantages and challenges of AEF, EET mechanisms, microbial energy gain, and discusses the rational choice of substrate-product couple as well as the choice of microbial catalyst. Besides, it discusses the potential of the industrial model-organism Bacillus subtilis as a promising candidate for AEF, which has not been yet considered for such an application. This prospective review contributes to a better understanding of how industrial microbiology can benefit from AEF and analyses key-factors required to successfully implement AEF processes. Overall, this work aims to advance the young research field especially by critically revisiting the fundamental aspects of AEF.