Identification of unstructured model for subtilin production through Bacillus subtilis using hybrid genetic algorithm

Subtilin production is favorable when Bacillus subtilis 168 is subjected to stress condition such as nutrient scarcity. A mathematical model underlying such growth process has immense applicability in determining the optimal operating conditions at industrial scale. We present this work with multiple objectives of a) selection of a substrate for creating the minimal nutrient media for B. subtilis thereby enhancing subtilin production, b) experimental study of the growth along with morphological characteristics of B. subtilis and product profile in nutrient scarcity condition and c) identification of an optimal unstructured model for subtilin production using a computational framework. First, we show that subtilin can be produced while B. subtilis is grown using galactose and B. subtilis undergoes morphological changes and takes filamentous shape. We then constructed a series of plausible models and used a hybrid method combining Genetic Algorithm and gradient based search methodologies, for model selection. The estimated kinetic parameters and the stoichiometric analysis indicate that the B. subtilis growth/death, product profile and respiratory mechanism undergo specific modifications in galactose as an adaptive response. Current study provides an inexpensive platform to produce subtilin and the predictive framework presented here has potential applications for large scale production of subtilin.     

Novel extremely acidic lipases produced from Bacillus species using oil substrates

The extremely acidophilic microorganisms Bacillus pumilus and Bacillus subtilis were isolated from soil collected from the commercial edible oil and fish oil extraction industry. Optimization of conditions for acidic lipase production from B. pumilus and B. subtilis using palm oil and fish oil, respectively, was carried out using response surface methodology. The extremely acidic lipases, thermo-tolerant acidic lipase (TAL) and acidic lipase (AL), were produced by B. pumilus and B. subtilis, respectively. The optimum conditions for B. pumilus obtaining the maximum activity (1,100 U/mL) of TAL were fermentation time, 96 h; pH, 1; temperature, 50 °C; concentration of palm oil, 50 g/L. After purification, a 7.1-fold purity of lipase with specific activity of 5,173 U/mg protein was obtained. The molecular weight of the TAL was 55 kDa. The AL from B. subtilis activity was 214 U/mL at a fermentation time of 72 h; pH, 1; temperature, 35 °C; concentration of fish oil, 30 g/L; maltose concentration, 10 g/L. After purification, an 11.4-fold purity of lipase with specific activity of 2,189 U/mg protein was obtained. The molecular weight of the extremely acidic lipase was 22 kDa. The functional groups of lipases were determined by Fourier transform-infrared (FT-IR) spectroscopy.     

Proteome analysis for antifungal effects of Bacillus subtilis KB-1122 on Magnaporthe grisea P131

Rice blast, caused by Magnaporthe grisea threatens rice production worldwide. It is important to develop novel and environment-safe strategies to control the fungus. Here we reported that Bacillus subtilis KB-1122 could strikingly inhibit the growth of M. grisea P131 in agar diffusion assays. To further understand the molecular mechanism on the suppressive role of B. subtilis on M. grisea, the antagonist–pathogen interaction of the two strains was studied by using comparative proteome analysis in this report. The cellular and culture supernatant (CSN) proteins were prepared from co-culture and subjected to two-dimensional polyacrylamide gel electrophoresis. Proteome analysis revealed 33 cellular and 18 CSN proteins showing changes upon co-culture respectively. Importantly, down-regulated cellular proteins came from M. grisea, whereas up-regulated proteins derived from B. subtilis. Results suggested that glyceraldehyde-3-phosphate dehydrogenase and serine protein kinase might contribute to antifungal activity of B. subtilis KB-1122. Of CSN proteins identified, the endo-1,4-beta-glucanase (involved in degradation of polysaccharides) was up-regulated consistently at different times of incubation. This suggests that this enzyme plays an important role in the interaction between B. subtilis KB-1122 with M. grisea P131.     

Optimization of flocculation conditions for Botryococcus braunii using response surface methodology

Biodiesel from microalgae is recognized as a desirable, renewable biofuel to replace petroleum-derived transport fuels. However, the efficient harvesting of microalgae is a major hurdle for commercialization. Therefore, the development of a cost-effective harvesting method is essential to reduce production cost. A partial factorial design was used to screen the main factors involved, which were the concentration of FeCl₃, the bioflocculant, and the time of slow mixing. Response surface methodology (RSM) was used to further investigate the optimal conditions for these factors on flocculation of Botryococcus braunii. Analysis of variance and other relevant tests confirmed the validity of the suggested model. The optimal conditions inferred from the obtained equation were 0.79 mM FeCl₃, 0.58 % (v/v) bioflocculant, and 180 sec of slow mixing for 1.1 g DCW L^?1 of B. braunii. The flocculating activity under these conditions was 90.6 %. By using RSM, the optimal conditions for flocculation of B. braunii could be reached more quickly and efficiently.     

Metabolic engineering of Bacillus subtilis fueled by systems biology: Recent advances and future directions

By combining advanced omics technology and computational modeling, systems biologists have identified and inferred thousands of regulatory events and system-wide interactions of the bacterium Bacillus subtilis, which is commonly used both in the laboratory and in industry. This dissection of the multiple layers of regulatory networks and their interactions has provided invaluable information for unraveling regulatory mechanisms and guiding metabolic engineering. In this review, we discuss recent advances in the systems biology and metabolic engineering of B. subtilis and highlight current gaps in our understanding of global metabolism and global pathway engineering in this organism. We also propose future perspectives in the systems biology of B. subtilis and suggest ways that this approach can be used to guide metabolic engineering. Specifically, although hundreds of regulatory events have been identified or inferred via systems biology approaches, systematic investigation of the functionality of these events in vivo has lagged, thereby preventing the elucidation of regulatory mechanisms and further rational pathway engineering. In metabolic engineering, ignoring the engineering of multilayer regulation hinders metabolic flux redistribution. Post-translational engineering, allosteric engineering, and dynamic pathway analyses and control will also contribute to the modulation and control of the metabolism of engineered B. subtilis, ultimately producing the desired cellular traits. We hope this review will aid metabolic engineers in making full use of available systems biology datasets and approaches for the design and perfection of microbial cell factories through global metabolism optimization.     

Diverse LXG toxin and antitoxin systems specifically mediate intraspecies competition in Bacillus subtilis biofilms

Biofilms are multispecies communities, in which bacteria constantly compete with one another for resources and niches. Bacteria produce many antibiotics and toxins for competition. However, since biofilm cells exhibit increased tolerance to antimicrobials, their roles in biofilms remain controversial. Here, we showed that Bacillus subtilis produces multiple diverse polymorphic toxins, called LXG toxins, that contain N-terminal LXG delivery domains and diverse C-terminal toxin domains. Each B. subtilis strain possesses a distinct set of LXG toxin–antitoxin genes, the number and variation of which is sufficient to distinguish each strain. The B. subtilis strain NCIB3610 possesses six LXG toxin–antitoxin operons on its chromosome, and five of the toxins functioned as DNase. In competition assays, deletion mutants of any of the six LXG toxin–antitoxin operons were outcompeted by the wild-type strain. This phenotype was suppressed when the antitoxins were ectopically expressed in the deletion mutants. The fitness defect of the mutants was only observed in solid media that supported biofilm formation. Biofilm matrix polymers, exopolysaccharides and TasA protein polymers were required for LXG toxin function. These results indicate that LXG toxin-antitoxin systems specifically mediate intercellular competition between B. subtilis strains in biofilms. Mutual antagonism between some LXG toxin producers drove the spatial segregation of two strains in a biofilm, indicating that LXG toxins not only mediate competition in biofilms, but may also help to avoid warfare between strains in biofilms. LXG toxins from strain NCIB3610 were effective against some natural isolates, and thus LXG toxin–antitoxin systems have ecological impact. B. subtilis possesses another polymorphic toxin, WapA. WapA had toxic effects under planktonic growth conditions but not under biofilm conditions because exopolysaccharides and TasA protein polymers inhibited WapA function. These results indicate that B. subtilis uses two types of polymorphic toxins for competition, depending on the growth mode.     

Enhanced extracellular production of α-amylase in <Emphasis Type="Italic">Bacillus subtilis</Emphasis> by optimization of regulatory elements and over-expression of PrsA lipoprotein

α-Amylase was used as a heterologous model protein to investigate the effects of promoters, signal peptides and over-expression of an extra-cytoplasmic molecular chaperone, PrsA lipoprotein, on enhancing the secretion of α-amylase in Bacillus subtilis. Four promoters and six signal peptides were compared, successively, and the highest yield of α-amylase was achieved under the promotion mediated by P_AprE, a strong constitutive promoter, and secretion by SP_nprE, a signal peptide from B. subtilis. Moreover, under conditions of overexpressed PrsA lipoprotein, the secretion production and activity of α-amylase increased to 2.5-fold. The performance of the recombinant B. subtilis 1A751PL31 was evaluated with a fed-batch fermentation in a 7.5 l fermentor. Optimization of regulatory elements and over-expression of PrsA lipoprotein had a significant effect on enhancing the production of α-amylase in B. subtilis.     

Expression and secretion of a single-chain sweet protein monellin in <Emphasis Type="Italic">Bacillus subtilis</Emphasis> by <Emphasis Type="Italic">sacB</Emphasis> promoter and signal peptide

The sweet protein monellin gene was expressed in Bacillus subtilis under the control of the Bacillus subtilis sacB promoter and signal peptide sequence. A 294-bp DNA fragment, coding for sweet protein monellin, was ligated into the Escherichia coli/B. subtilis shuttle vector pHPC, producing pHPMS, which was subsequently transformed into B. subtilis QB1098, DB104, and DB403. The peptide efficiently directed the secretion of monellin from the recombinant B. subtilis cells. A maximum yield of monellin of 0.29 g protein l⁻¹ was obtained from the supernatant of B. subtilis DB403 harboring pHPMS. SDS-PAGE confirmed the purity of the recombinant product.     

Comparative proteomics profiling revealed the involvement of GRB2‐ROCK2 axis in Lyme neuroborreliosis caused by Borrelia Burgdorferi

The zoonotic Lyme neuroborreliosis (LNB) disease is caused by Borrelia burgdorferi, with wide distribution, rapid dissemination and high disability rate. However, the molecular mechanism underlying B. burgdorferi mediated neuroborreliosis remains largely unknown. Here, the frontal cortex from rhesus brains was incubated with B. burgdorferi, and proteomics profiling was evaluated by isobaric tag for relative and absolute quantitation. Proteins were identified and quantified, and differentially expressed proteins (DEPs) were isolated by comparing co‐cultured samples and control samples. A total of 43, 164 and 368 DEPs were significantly altered after 6, 12 and 24 h treatment with B. burgdorferi respectively. Gene ontology and KEGG pathway analyses revealed that chemokine biological process was significantly enriched. Two genes in chemokine pathway including GRB2 and ROCK2 were significantly up‐regulated after B. burgdorferi co‐culturing. By in vitro assay, we confirmed that the expression of GRB2 and ROCK2 was increased after B. burgdorferi infection. In conclusion, our study revealed the involvement of chemokine pathway in the pathogenesis of LNB. GRB2 and ROCK2 may be novel biomarkers and therapeutic targets for LNB.     

Cytokinin-producing, plant growth-promoting rhizobacteria that confer resistance to drought stress in Platycladus orientalis container seedlings

One of the proposed mechanisms through which plant growth-promoting rhizobacteria (PGPR) enhance plant growth is the production of plant growth regulators, especially cytokinin. However, little information is available regarding cytokinin-producing PGPR inoculation on growth and water stress consistence of forest container seedlings under drought condition. This study determined the effects of Bacillus subtilis on hormone concentration, drought resistance, and plant growth under water-stressed conditions. Although no significant difference was observed under well-watered conditions, leaves of inoculated Platycladus orientalis (oriental thuja) seedlings under drought stress had higher relative water content and leaf water potential compared with those of noninoculated ones. Regardless of water supply levels, the root exudates, namely sugars, amino acids and organic acids, significantly increased because of B. subtilis inoculation. Water stress reduced shoot cytokinins by 39.14 %. However, inoculation decreased this deficit to only 10.22 %. The elevated levels of cytokinins in P. orientalis shoot were associated with higher concentration of abscisic acid (ABA). Stomatal conductance was significantly increased by B. subtilis inoculation in well-watered seedlings. However, the promoting effect of cytokinins on stomatal conductance was hampered, possibly by the combined action of elevated cytokinins and ABA. B. subtilis inoculation increased the shoot dry weight of well-watered and drought seedlings by 34.85 and 19.23 %, as well as the root by 15.445 and 13.99 %, respectively. Consequently, the root/shoot ratio significantly decreased, indicative of the greater benefits of PGPR on shoot growth than root. Thus, inoculation of cytokinin-producing PGPR in container seedlings can alleviate the drought stress and interfere with the suppression of shoot growth, showing a real potential to perform as a drought stress inhibitor in arid environments.     

Dynamic flux balance modeling of S. cerevisiae and E. coli co-cultures for efficient consumption of glucose/xylose mixtures

Current researches into the production of biochemicals from lignocellulosic feedstocks are focused on the identification and engineering of individual microbes that utilize complex sugar mixtures. Microbial consortia represent an alternative approach that has the potential to better exploit individual species capabilities for substrate uptake and biochemical production. In this work, we construct and experimentally validate a dynamic flux balance model of a Saccharomyces cerevisiae and Escherichia coli co-culture designed for efficient aerobic consumption of glucose/xylose mixtures. Each microbe is a substrate specialist, with wild-type S. cerevisiae consuming only glucose and engineered E. coli strain ZSC113 consuming only xylose, to avoid diauxic growth commonly observed in individual microbes. Following experimental identification of a common pH and temperature for optimal co-culture batch growth, we demonstrate that pure culture models developed for optimal growth conditions can be adapted to the suboptimal, common growth condition by adjustment of the non-growth associated ATP maintenance of each microbe. By comparing pure culture model predictions to co-culture experimental data, the inhibitory effect of ethanol produced by S. cerevisiae on E. coli growth was found to be the only interaction necessary to include in the co-culture model to generate accurate batch profile predictions. Co-culture model utility was demonstrated by predicting initial cell concentrations that yield simultaneous glucose and xylose exhaustion for different sugar mixtures. Successful experimental validation of the model predictions demonstrated that steady-state metabolic reconstructions developed for individual microbes can be adapted to develop dynamic flux balance models of microbial consortia for the production of renewable chemicals.     

Engineered Bacillus subtilis 168 produces l-malate by heterologous biosynthesis pathway construction and lactate dehydrogenase deletion

In the present work, Bacillus subtilis was engineered to produce l-malate. Initially, the study revealed that the slight fumarase activity under anaerobic conditions is extremely favourable for l-malate one-step fermentation accumulation. Subsequently, an efficient heterologous biosynthesis pathway formed by Escherichia coli phosphoenolpyruvate carboxylase and Saccharomyces cerevisiae malate dehydrogenase was introduced into B. subtilis, which led to 6.04?±?0.19?mM l-malate production. Finally, the l-malate production was increased 1.5-fold to 9.18?±?0.22?mM by the deletion of lactate dehydrogenase. Under two-stage fermentation conditions, the engineered B. subtilis produced up to 15.65?±?0.13?mM l-malate, which was 86.3?% higher than that under anaerobic fermentation conditions. Though the l-malate production by the recombinant was low, this is the first attempt to produce l-malate in engineered B. subtilis and paves the way for further improving l-malate production in B. subtilis.     

Essentiality of c-di-AMP in Bacillus subtilis: Bypassing mutations converge in potassium and glutamate homeostasis

In order to adjust to changing environmental conditions, bacteria use nucleotide second messengers to transduce external signals and translate them into a specific cellular response. Cyclic di-adenosine monophosphate (c-di-AMP) is the only known essential nucleotide second messenger. In addition to the well-established role of this second messenger in the control of potassium homeostasis, we observed that glutamate is as toxic as potassium for a c-di-AMP-free strain of the Gram-positive model bacterium Bacillus subtilis. In this work, we isolated suppressor mutants that allow growth of a c-di-AMP-free strain under these toxic conditions. Characterization of glutamate resistant suppressors revealed that they contain pairs of mutations, in most cases affecting glutamate and potassium homeostasis. Among these mutations, several independent mutations affected a novel glutamate transporter, AimA (Amino acid importer A, formerly YbeC). This protein is the major transporter for glutamate and serine in B. subtilis. Unexpectedly, some of the isolated suppressor mutants could suppress glutamate toxicity by a combination of mutations that affect phospholipid biosynthesis and a specific gain-of-function mutation of a mechanosensitive channel of small conductance (YfkC) resulting in the acquisition of a device for glutamate export. Cultivation of the c-di-AMP-free strain on complex medium was an even greater challenge because the amounts of potassium, glutamate, and other osmolytes are substantially higher than in minimal medium. Suppressor mutants viable on complex medium could only be isolated under anaerobic conditions if one of the two c-di-AMP receptor proteins, DarA or DarB, was absent. Also on complex medium, potassium and osmolyte toxicity are the major bottlenecks for the growth of B. subtilis in the absence of c-di-AMP. Our results indicate that the essentiality of c-di-AMP in B. subtilis is caused by the global impact of the second messenger nucleotide on different aspects of cellular physiology.     

A Lysine Cluster in Domain II of Bacillus subtilis PBP4a Plays a Role in the Membrane Attachment of This C1-PBP

In PBP4a, a Bacillus subtilis class-C1 penicillin-binding protein (PBP), four clustered lysine (K) residues, K86, K114, K119, and K265, protrude from domain II. Replacement of these amino acids with glutamine (Q) residues by site-directed mutagenesis yielded Mut4KQ PBP4a. When produced in Escherichia coli without its predicted Sec-signal peptide, wild-type (WT) PBP4a was found mainly associated with the host cytoplasmic membrane, whereas Mut4KQ PBP4a remained largely unbound. After purification, the capacities of the two proteins to bind to B. subtilis membranes were compared. The results were similar to those obtained in E. coli: in vitro, a much higher percentage of WT PBP4a than of Mut4KQ PBP4a was found to interact with B. subtilis membranes. Immunodetection of PBP4a in B. subtilis membrane extracts revealed that a processed form of this PBP (as indicated by its size) associates with the B. subtilis cytoplasmic membrane. In the absence of any amphiphilic peptide in PBP4a, the crown of positive charges on the surface of domain II is likely responsible for the cellular localization of this PBP and its attachment to the cytoplasmic membrane.     

Metabolic Engineering of Carotenoid Biosynthesis in Escherichia coli by Ordered Gene Assembly in Bacillus subtilis

We attempted to optimize the production of zeaxanthin in Escherichia coli by reordering five biosynthetic genes in the natural carotenoid cluster of Pantoea ananatis. Newly designed operons for zeaxanthin production were constructed by the ordered gene assembly in Bacillus subtilis (OGAB) method, which can assemble multiple genes in one step using an intrinsic B. subtilis plasmid transformation system. The highest level of production of zeaxanthin in E. coli (820 μg/g [dry weight]) was observed in the transformant with a plasmid in which the gene order corresponds to the order of the zeaxanthin metabolic pathway (crtE-crtB-crtI-crtY-crtZ), among a series of plasmids with circularly permuted gene orders. Although two of five operons using intrinsic zeaxanthin promoters failed to assemble in B. subtilis, the full set of operons was obtained by repressing operon expression during OGAB assembly with a p_R promoter-cI repressor system. This result suggests that repressing the expression of foreign genes in B. subtilis is important for their assembly by the OGAB method. For all tested operons, the abundance of mRNA decreased monotonically with the increasing distance of the gene from the promoter in E. coli, and this may influence the yield of zeaxanthin. Our results suggest that rearrangement of biosynthetic genes in the order of the metabolic pathway by the OGAB method could be a useful approach for metabolic engineering.     

Authentic human basic fibroblast growth factor produced by secretion in Bacillus subtilis

Bacillus subtilis is generally accepted as an inborn host candidate employed for secretory production of heterologous proteins. However, this ideal host system has never been employed for commercial production of medically useful proteins. In this communication, we report for the first time the employment of an engineered B. subtilis system, in conjunction with a facile cell-wall destabilization protocol, to successfully obtain an alluring yield of 40 mg?l^?1 of secreted human basic fibroblast growth factor (hbFGF) in the culture supernatant. The product was not only shown to exhibit potent bioactivity but also revealed to possess a protein sequence identical to that of mature native hbFGF (Mat-hbFGF). Our findings may pave way for the development of a cost-effective process for producing Mat-hbFGF, which is currently sold at an unusually expensive price of over US $1 million?g^?1, for medical and skin care applications.