Metabolic and genetic factors affecting the productivity of pyrimidine nucleoside in Bacillus subtilis

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.

The flavour of wheat gluten hydrolysate after Corynebacterium Glutamicum fermentation: Effect of degrees of hydrolysis and fermentation time

Corynebacterium glutamicum was used to ferment wheat gluten hydrolysates (WGHs) to prepare flavour base. This study investigated the effect of hydrolysis degrees (DHs) and fermentation time on flavour of WGHs. During fermentation, the contents of amino nitrogen, total acid and small peptides increased, while the protein and pH value decreased. Succinic acid, GMP, and Glu were the prominent umami substances in fermented WGHs. The aromas of WGHs with different DHs could be distinguished by electronic nose and GC-IMS. Based on OAV of GC-MS, hexanal was the main compound in WGHs, while phenylethyl alcohol and acetoin were dominant after fermentation. WGHs with high DHs accumulated more flavour metabolites. Correlation analysis showed that small peptides (<1 kDa) could promote the formation of flavour substances, and Asp was potentially relevant flavour precursor. This study indicated that fermented WGHs with different DHs can potentially be used in different food applications based on flavour profiles.

Improving the level of the cytidine biosynthesis in E. coli through atmospheric room temperature plasma mutagenesis and metabolic engineering

AIMS

Cytidine, as an important commercial precursor in the chemical synthesis of antiviral and antitumor drugs, is in great demand in the market. Therefore, the purpose of this study is to build a microbial cell factory with high cytidine production.

METHODS AND RESULTS

A mutant E. coli NXBG-11-F34 with high tolerance to uridine monophosphate structural analogs and good genetic stability was obtained by atmospheric room temperature plasma (ARTP) mutagenesis combined with high-throughput screening. Then, the udk and rihA genes involved in cytidine catabolism were knocked out by CRISPR/Cas9 gene editing technology, and the recombinant strain E. coli NXBG-13 was constructed. The titer, yield, and productivity of cytidine fermented in a 5 l bioreactor were 15.7 g l-1, 0.164 g g-1, and 0.327 g l-1 h-1, respectively. Transcriptome analysis of the original strain and the recombinant strain E. coli NXBG-13 showed that the gene expression profiles of the two strains changed significantly, and the cytidine de novo pathway gene of the recombinant strain was up-regulated significantly.

CONCLUSIONS

ARTP mutagenesis combined with metabolic engineering is an effective method to construct cytidine-producing strains.

Improving Surfactin Production in Bacillus subtilis 168 by Metabolic Engineering

Surfactin is widely used in the petroleum extraction, cosmetics, biopharmaceuticals and agriculture industries. It possesses antibacterial and antiviral activities and can reduce interfacial tension. Bacillus are commonly used as production chassis, but wild-type Bacillus subtilis 168 cannot synthesise surfactin. In this study, the phosphopantetheinyl transferase (PPTase) gene sfp* (with a T base removed) was overexpressed and enzyme activity was restored, enabling B. subtilis 168 to synthesise surfactin with a yield of 747.5 ± 6.5 mg/L. Knocking out ppsD and yvkC did not enhance surfactin synthesis. Overexpression of predicted surfactin transporter gene yfiS increased its titre to 1060.7 ± 89.4 mg/L, while overexpression of yerP, ycxA and ycxA-efp had little or negative effects on surfactin synthesis, suggesting YfiS is involved in surfactin efflux. By replacing the native promoter of the srfA operon encoding surfactin synthase with three promoters, surfactin synthesis was significantly reduced. However, knockout of the global transcriptional regulator gene codY enhanced the surfactin titre to 1601.8 ± 91.9 mg/L. The highest surfactin titre reached 3.89 ± 0.07 g/L, with the yield of 0.63 ± 0.02 g/g DCW, after 36 h of fed-batch fermentation in 5 L fermenter. This study provides a reference for further understanding surfactin synthesis and constructing microbial cell factories.

Transcriptomic and biochemical analysis of metabolic remodeling in Bacillus subtilis MSC4 under Benzo[a]pyrene stress

Polyaromatic benzo[a]pyrene (B[a]P) is a toxic carcinogenic environmental pollutant, and the use of microorganisms to remediate B[a]P contamination is considered to be one of the most effective strategies. However, there is still a gap in studying the metabolic remodeling of microorganisms under B[a]P stress. In this study, our systematically investigated the effects of B[a]P on the metabolism of Bacillus subtilis MSC4 based on transcriptomic, molecular and biochemical analyses. The results showed that in response to B[a]P stress, MSC4 formed more biofilm matrix and endospores, the structure of the endospores also was changed, which led to a reduction in their resistance and made them more difficult to germinate. In addition to an increase in glycolysis activity, the activities of tricarboxylic acid cycle, pentose phosphate pathway and the electron transport chain were decreased. B[a]P stress forced MSC4 to strengthen arginine synthesis, urea cycle, and urea decomposition, meanwhile, synthesize more ribonucleotides. The activity of DNA replication, transcription activities and the expression of multiple ribosomal protein genes were reduced. Moreover, all of the reported enzymes involved in B[a]P degradation showed decreased transcript abundance, and the degradation of B[a]P caused significant up-regulation of the gene expression of the acid inducible enzyme OxdC and the synthesis of acetoin. In addition, the cytotoxicity of B[a]P to bacteria was directly displayed in four aspects: increased intracellular level of reactive oxygen species (ROS), elevated cell membrane permeability, up-regulation of the cell envelope stress-sensing two-component system LiaRS, and downregulation of siderophores biosynthesis. Finally, B[a]P also caused morphological changes in the cells, with some cells exhibiting significant deformation and concavity. These findings provide effective research directions for targeted improvement the cellular activity of B[a]P-degrading strains, and is beneficial for further application of microorganisms to remediate B[a]P -contaminated soils.

Regulatory mechanisms of submerged macrophyte on bacterial community recovery in decabromodiphenyl ether contaminated sediment: Microbiological and metabolomic perspectives

Polybrominated diphenyl ether contamination in sediments poses serious threats to human health and ecological safety. Despite the broad application of submerged macrophytes for remediating pollutants, their regulatory influence on bacterial communities in contaminated sediments remains unclear. Herein, we analyzed the effects of decabromodiphenyl ether (BDE-209) and Hydrilla verticillata on sediment bacterial community and function using 16S rRNA gene sequencing and sediment metabolomics. Results showed that BDE-209 significantly inhibited sediment bacterial diversity and metabolic functions. It also enhanced bacterial interactions and altered both the bacterial community and metabolite composition. Uridine and inosine were critical metabolites that positively co-occurred with bacterial taxa inhibited by BDE-209. Notably, planting H. verticillata effectively alleviated the adverse impacts of BDE-209 by reducing its residuals, increasing the total organic carbon, and modifying metabolic profiles. Such mitigation was evidenced by enhancing bacterial diversity, restoring metabolic functions, and attenuating bacterial interactions. However, mitigation effectiveness depended on treatment time. Additionally, propionic acid, palmitic acid, and palmitoleic acid may facilitate the restoration of phylum Proteobacteria and class Planctomycetacia in H. verticillata planted sediment. Together, these findings improve understanding of BDE-209's impacts on aquatic ecosystems and provide valuable insights for ecological restoration using submerged macrophytes.

A model industrial workhorse: Bacillus subtilis strain 168 and its genome after a quarter of a century

The vast majority of genomic sequences are automatically annotated using various software programs. The accuracy of these annotations depends heavily on the very few manual annotation efforts that combine verified experimental data with genomic sequences from model organisms. Here, we summarize the updated functional annotation of Bacillus subtilis strain 168, a quarter century after its genome sequence was first made public. Since the last such effort 5 years ago, 1168 genetic functions have been updated, allowing the construction of a new metabolic model of this organism of environmental and industrial interest. The emphasis in this review is on new metabolic insights, the role of metals in metabolism and macromolecule biosynthesis, functions involved in biofilm formation, features controlling cell growth, and finally, protein agents that allow class discrimination, thus allowing maintenance management, and accuracy of all cell processes. New 'genomic objects' and an extensive updated literature review have been included for the sequence, now available at the International Nucleotide Sequence Database Collaboration (INSDC: AccNum AL009126.4).

Computer-Based Design of a Cell Factory for High-Yield Cytidine Production

Pyrimidine ribonucleotide de novo biosynthesis pathway (PRdnBP) is an important pathway to produce pyrimidine nucleosides. We attempted to systematically investigate PRdnBP in Escherichia coli with genome-scale metabolic models and utilized the models to guide strain design. The balance of central carbon metabolism and PRdnBP affected the production of cytidine from glucose. Using Bayesian metabolic flux analysis, the effect of modified PRdnBP on the metabolic network was analyzed. The acetate overflow became coupled with PRdnBP flux, while they were originally independent under oxygen-sufficient conditions. The coupling between cytidine production and acetate secretion in the modified strain was weakened by arcA deletion, which resulted in further improving the efficient accumulation of cytidine. In total, 1.28 g/L of cytidine with a yield of 0.26 g/g glucose was produced. The yield of cytidine produced by E. coli is higher than previous reports. Our strategy provides an effective attempt to find metabolic bottlenecks in genetically engineered bacteria by using flux coupling analysis.

The Effect of E. coli Uridine-Cytidine Kinase Gene Deletion on Cytidine Synthesis and Transcriptome Analysis

Cytidine is an antiviral and anticancer drug intermediate, its primary method of manufacture being fermentation. Uridine-cytidine kinase (UCK) catalyzes the reverse process of phosphorylation of cytidine to produce cytidylic acid, which influences cytidine accumulation in the Escherichia coli cytidine biosynthesis pathway. The cytidine-producing strain E. coli NXBG-11 was used as the starting strain in this work; the udk gene coding UCK was knocked out of the chromosomal genome using clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology. The mutant strain E. coli NXBG-12 was obtained; its transcriptomics were studied to see how udk gene deletion affected cytidine synthesis and cell-wide transcription. The mutant strain E. coli NXBG-12 generated 1.28 times more cytidine than the original strain E. coli NXBG-11 after 40 h of shake-flask fermentation at 37 °C. The udk gene was knocked out, and transcriptome analysis showed that there were 1168 differentially expressed genes between the mutant and original strains, 559 upregulated genes and 609 downregulated genes. It was primarily shown that udk gene knockout has a positive impact on the cytidine synthesis network because genes involved in cytidine synthesis were significantly upregulated (p < 0.05) and genes related to the cytidine precursor PRPP and cofactor NADPH were upregulated in the PPP and TCA pathways. These results principally demonstrate that udk gene deletion has a favorable impact on the cytidine synthesis network. The continual improvement of cytidine synthesis and metasynthesis is made possible by this information, which is also useful for further converting microorganisms that produce cytidine.

NupR Responding to Multiple Signals Is a Nucleoside Permease Regulator in Bacillus thuringiensis BMB171

Nucleoside transport is essential for maintaining intracellular nucleoside and nucleobase homeostasis for living cells. Here, we identified an uncharacterized GntR/HutC family transcriptional regulator, NagR2, renamed NupR (nucleoside permease regulator), that mainly controls nucleoside transport in the Bacillus thuringiensis BMB171 strain. The deletion or overexpression of nupR affected the bacteria's utilization of guanosine, adenosine, uridine, and cytidine rather than thymidine. We further demonstrated that zinc ion is an effector for the NupR, dissociating NupR from its target DNA. Moreover, the expression of nupR is inhibited by NupR, ComK, and PurR, while it is promoted by CcpA. Also, a purine riboswitch located in its 5′ noncoding region influences the expression of nupR. Guanine is the ligand of the riboswitch, reducing the expression of nupR by terminating the transcription of nupR in advance. Hence, our results reveal an exquisite regulation mechanism enabling NupR to respond to multiple signals, control genes involved in nucleoside transport, and contribute to nucleoside substance utilization. Overall, this study provides essential clues for future studies exploring the function of the NupR homolog in other bacteria, such as Bacillus cereus, Bacillus anthracis, Klebsiella pneumoniae, and Streptococcus pneumoniae.

IMPORTANCE The transport of nucleosides and their homeostasis within the cell are essential for growth and proliferation. Here, we have identified a novel transcription factor, NupR, which, to our knowledge, is the first GntR family transcription factor primarily involved in the regulation of nucleoside transport. Moreover, responding to diverse intracellular signals, NupR regulates nucleoside transport. It is vital for utilizing extracellular nucleosides and maintaining intracellular nucleoside homeostasis. NupR may also be involved in other pathways such as pH homeostasis, molybdenum cofactor biosynthesis, nitrate metabolism, and transport. In addition, nucleosides have various applications, such as antiviral drugs. Thus, the elucidation of the transport mechanism of nucleosides could be helpful for the construction of engineered strains for nucleoside production.

Construction of a mutant Bacillus subtilis strain for high purity poly-γ-glutamic acid production

OBJECTIVE

To construct a Bacillus subtilis strain for improved purity of poly-γ-glutamic acid.

RESULTS

The construction of strain GH16 was achieved by knocking out five genes encoding extracellular proteins and an operon from Bacillus subtilis G423. We then analyzed the amount of protein impurities in the γ-PGA produced by the resulting strain GH16/pHPG, which decreased from 1.48 to 1.39%. Subsequently the fla-che operon, PBSX, as well as the yrpD, ywoF and yclQ genes were knocked out successively, resulting in the mutant strains GH17, GH18 and GH19. Ultimately, the amount of protein impurities was reduced from 1.48 to 0.83%. In addition, the amount of polysaccharide impurities in the γ-PGA was also decreased from 2.21 to 1.93% after knocking out the epsA-O operon.

CONCLUSIONS

The high purity γ-PGA producer was constructed, and the resulting strain was a promising platform for the manufacture of other highly pure extracellular products and secretory proteins.

Microbial Succession and Interactions During the Manufacture of Fu Brick Tea

Fu Brick tea is a very popular post-fermented tea that is known for its “golden flower fungus,” Aspergillus cristatus, which becomes the dominant microbe during the maturation process. This study used both culture-dependent methods and high-throughput sequencing to track microbial succession and interactions during the development of the golden flower fungus, a crucial component of the manufacturing process of Fu Brick tea. Among the bacterial communities, Klebsiella and Lactobacillus were consistently cultured from both fresh tea leaves and in post-fermentation Fu Brick tea. Methylobacterium, Pelomonas, and Sphingomonas were dominant genera in fresh tea leaves but declined once fermentation started, while Bacillus, Kluyvera, and Paenibacillus became dominant after piling fermentation. The abundance of A. cristatus increased during the manufacturing process, accounting for over 98% of all fungi present after the golden flower bloom in the Fu Brick tea product. Despite their consistent presence during culture work, network analysis showed Lactobacillus and Klebsiella to be negatively correlated with A. cristatus. Bacillus spp., as expected from culture work, positively correlated with the presence of golden flower fungus. This study provides complete insights about the succession of microbial communities and highlights the importance of co-occurrence microbes with A. cristatus during the manufacturing process of Fu Brick tea.

Metabolic engineering of Bacillus subtilis for high-level production of uridine from glucose

As an intermediate in drug synthesis, uridine has practical applications in the pharmaceutical field. Bacillus subtilis is used as a host to boost uridine yield by manipulating its uridine biosynthesis pathway. In this study, we engineered a high-uridine-producing strain of B. subtilis by modifying its metabolic pathways in vivo. Overexpression of the aspartate ammonia-lyase (ansB) gene increased the relative transcriptional level of ansB in B. subtilis TD320 by 13.18 times and improved uridine production to 15.13 g L^-1 after 72-h fermentation. Overexpression of the putative 6-phosphogluconolactonase (ykgB) gene increased uridine production by the derivative strain TD325 to 15.43 g L^-1 . Reducing the translation of the amido phosphoribosyl transferase (purF) gene and inducing expression of the subtilisin E (aprE) gene resulted in a 1.99-fold increase in uridine production after 24 h shaking. Finally, uridine production in the optimal strain B. subtilis TD335, which exhibited reduced urease expression, reached 17.9 g L^-1 with a yield of 314 mg of uridine g^-1 glucose. To our knowledge, this is the first study to obtain high-yield uridine-producing B. subtilis in a medium containing only three components (80 g L^-1 glucose, 20 g L^-1 yeast powder, and 20 g L^-1 urea).

Effects of chlorpyrifos on the metabolic profiling of Bacillus megaterium strain RRB

Many microorganisms have been reported to degrade organic pollutants in the environment and plants, however, the specific information about the effect of organic pollutants on the metabolism of microorganisms is poorly investigated. In the present study, the effect of the pesticide chlorpyrifos on the metabolic profiling of Bacillus megaterium strain RRB was investigated using metabolomics. Our data show that chlorpyrifos acting as an energy source was readily concentrated in the strain RRB from the culture medium. During early cultivation, the shift in energy sources from tryptic soy broth to chlorpyrifos may temporarily cause the strain RRB to enter the starvation stage, where some synthesis-related amino acids and intermediates in the pathways of TCA cycle and pyridoxine metabolism were decreased. The increase of nucleotides and lysine may help the strain RRB cope with the starvation stage. During later cultivation, many metabolites including organic acids, nucleosides and sugar phosphates were gradually accumulated, which indicates that chlorpyrifos could be utilized by the stain RRB to generate metabolites bacteria needed. In addition, arginine acting as a nitrogen-storage amino acid was gradually decreased with later cultivation, suggesting that chlorpyrifos could not provide enough nitrogen for bacteria.

Direct Visualization of Chemical Cues and Cellular Phenotypes throughout Bacillus subtilis Biofilms

Bacillus subtilis is a soil bacterium that can form biofilms, which are communities of cells encased by an extracellular matrix. In these complex communities, cells perform numerous metabolic processes and undergo differentiation into functionally distinct phenotypes as a survival strategy. Because biofilms are often studied in bulk, it remains unclear how metabolite production spatially correlates with B. subtilis phenotypes within biofilm structures. In many cases, we still do not know where these biological processes are occurring in the biofilm. Here, we developed a method to analyze the localization of molecules within sagittal thin sections of B. subtilis biofilms using high-resolution mass spectrometry imaging. We correlated the organization of specific molecules to the localization of well-studied B. subtilis phenotypic reporters determined by confocal laser scanning fluorescence microscopy within analogous biofilm thin sections. The correlations between these two data sets suggest the role of surfactin as a signal for extracellular matrix gene expression in the biofilm periphery and the role of bacillibactin as an iron-scavenging molecule. Taken together, this method will help us generate hypotheses to discover relationships between metabolites and phenotypic cell states in B. subtilis and other biofilm-forming bacteria. IMPORTANCE Bacterial biofilms are complex and heterogeneous structures. Cells within biofilms carry out numerous metabolic processes in a nuanced and organized manner, details of which are still being discovered. Here, we used multimodal imaging to analyze B. subtilis biofilm processes at the metabolic and gene expression levels in biofilm sagittal thin sections. Often, imaging techniques analyze only the top of the surface of the biofilm and miss the multifaceted interactions that occur deep within the biofilm. Our analysis of the sagittal planes of B. subtilis biofilms revealed the distributions of metabolic processes throughout the depths of these structures and allowed us to draw correlations between metabolites and phenotypically important subpopulations of B. subtilis cells. This technique provides a platform to generate hypotheses about the role of specific molecules and their relationships to B. subtilis subpopulations of cells.

Overexpression of uracil permease and nucleoside transporter from Bacillus amyloliquefaciens improves cytidine production in Escherichia coli

Cytidine is an important raw material for nucleic acid health food and genetic engineering research. In recent years, it has shown irreplaceable effects in anti-virus, anti-tumor, and AIDS drugs. Its biosynthetic pathway is complex and highly regulated. In this study, overexpression of uracil permease and a nucleoside transporter from Bacillus amyloliquefaciens related to cell membrane transport in Escherichia coli strain BG-08 was found to increase cytidine production in shake flask cultivation by 1.3-fold (0.91 ± 0.03 g/L) and 1.8-fold (1.26 ± 0.03 g/L) relative to that of the original strain (0.70 ± 0.03 g/L), respectively. Co-overexpression of uracil permease and a nucleoside transporter further increased cytidine yield by 2.7-fold (1.59 ± 0.05 g/L) compared with that of the original strain. These results indicate that the overexpressed uracil permease and nucleoside transporter can promote the accumulation of cytidine, and the two proteins play a synergistic role in the secretion of cytidine in Escherichia coli.

Improve uridine production by modifying related metabolic pathways in Bacillus subtilis

OBJECTIVES

The metabolic pathway related to uridine production was modified in Bacillus subtilis in order to increase the production of uridine.

RESULTS

Decreasing the relative transcriptional level of pur operon in Bacillus subtilis TD300 to 80%, and the production of the derived strain TD312 was increased to 11.81 g uridine/l and the yield was increased to 270 mg uridine/g glucose. The expression of pucR gene in situ by P_ccpA resulting in a 194.01-fold increase in the relative transcriptional level of pucR gene and 349.71-fold increase in the relative transcriptional level of ure operon, respectively. Furthermore, the production of TD314 reached 13.06 g uridine/l, while the yield reached 250 mg uridine/g glucose.

CONCLUSION

This is the first report that more than 13 g uridine/l with a yield of 250 mg uridine/g glucose is produced in shake flask fermentation of genetically engineered Bacillus subtilis.

Modular Pathway Engineering of Bacillus subtilis To Promote De Novo Biosynthesis of Menaquinone-7

Menaquinone-7 (MK-7), a valuable vitamin K₂, plays an important role in the prevention of osteoporosis and cardiovascular calcification. We chose B. subtilis 168 as the chassis for the modular metabolic engineering design to promote the biosynthesis of MK-7. The biosynthetic pathway of MK-7 was categorized into four modules, namely, the MK-7 pathway (Module I), the shikimate (SA) pathway (Module II), the methylerythritol phosphate (MEP) pathway (Module III), and the glycerol metabolism pathway (Module IV). Overexpression of menA (Module I) resulted in 6.6 ± 0.1 mg/L of MK-7 after 120 h fermentation, which was 2.1-fold that of the starting strain BS168NU (3.1 ± 0.2 mg/L). Overexpression of aroA, aroD, and aroE (Module II) had a negative effect on the synthesis of MK-7. Simultaneous overexpression of dxs, dxr, yacM, and yacN (Module III) enabled the yield of MK-7 to 12.0 ± 0.1 mg/L. Moreover, overexpression of glpD (Module IV) resulted in an increase of the yield of MK-7 to 13.7 ± 0.2 mg/L. Furthermore, deletion of dhbB reduced the consumption of the intermediate metabolite isochorismate, thus promoting the yield of MK-7 to 15.4 ± 0.6 mg/L. Taken together, the final resulting strain MK3-MEP123-Gly2-Δ dhbB with simultaneous overexpression of menA, dxs, dxr, yacM-yacN, glpD and deletion of dhbB enabled the yield of MK-7 to 69.5 ± 2.8 mg/L upon 144 h fermentation in a 2 L baffled flask.

Metabolic engineering of Escherichia coli for high-yield uridine production

Uridine is a kind of pyrimidine nucleoside that has been widely applied in the pharmaceutical industry. Although microbial fermentation is a promising method for industrial production of uridine, an efficient microbial cell factory is still lacking. In this study, we constructed a metabolically engineered Escherichia coli capable of high-yield uridine production. First, we developed a CRISPR/Cas9-mediated chromosomal integration strategy to integrate large DNA into the E. coli chromosome, and a 9.7 kb DNA fragment including eight genes in the pyrimidine operon of Bacillus subtilis F126 was integrated into the yghX locus of E. coli W3110. The resultant strain produced 3.3 g/L uridine and 4.5 g/L uracil in shake flask culture for 32 h. Subsequently, five genes involved in uridine catabolism were knocked out, and the uridine titer increased to 7.8 g/L. As carbamyl phosphate, aspartate, and 5'-phosphoribosyl pyrophosphate are important precursors for uridine synthesis, we further modified several metabolism-related genes and synergistically improved the supply of these precursors, leading to a 76.9% increase in uridine production. Finally, nupC and nupG encoding nucleoside transport proteins were deleted, and the extracellular uridine accumulation increased to 14.5 g/L. After 64 h of fed-batch fermentation, the final engineered strain UR6 produced 70.3 g/L uridine with a yield and productivity of 0.259 g/g glucose and 1.1 g/L/h, respectively. To the best of our knowledge, this is the highest uridine titer and productivity ever reported for the fermentative production of uridine.

Production enhancement of the extracellular lipase LipA in Bacillus subtilis: Effects of expression system and Sec pathway components

Lipases are among the most versatile biocatalysts, and are used in a range of industrially relevant bioconversion reactions. However, the production of LipA in recombinant Bacillus subtilis is still limited, due to unresolved issues surrounding the regulation of the expression and secretion systems. In this study, the gene encoding LipA from B. subtilis 168 was expressed in BNA under the control of the P₄₃ and the P_AE promoter. The extracellular lipase activity of the resulting strains BNACL and BNAAL was 7.8 U ml^-1 and 12.6 U ml^-1, respectively. To further enhance the expression of LipA, pHP13L was constructed by inserting the P_AE-lip into the shuttle vector pHP13, which produced an extracellular lipase activity of 180.5 U ml^-1 of BNA/pHP13L. The strain BNAY8 described in Supplement data which lacks eight extracellular proteins was constructed and the deletion a few of the much weaker secreting proteins had no significant effect on the secretion of LipA. Moreover, the four Sec pathway components, secA-prfB, secDF, secYEG, prsA, were individually overexpressed in BNA. The overexpression of secDF and prsA enhanced the production of LipA by 28% and 49%, respectively. Furthermore, the co-overexpression of secDF with prsA improved the extracellular amount of LipA by 59% over that of BNA/pHP13L, reaching 287.8 U ml^-1. It can therefore be said that both regulatory elements and secretion pathway had an impact on the production of secreted LipA. Their optimization and modification is a useful strategy to improve the homologous overproduction of other extracellular proteins in B. subtilis.

Improvement of uridine production of Bacillus subtilis by atmospheric and room temperature plasma mutagenesis and high-throughput screening

In the present study, a novel breeding strategy of atmospheric and room temperature plasma (ARTP) mutagenesis was used to improve the uridine production of engineered Bacillus subtilis TD12np. A high-throughput screening method was established using both resistant plates and 96-well microplates to select the ideal mutants with diverse phenotypes. Mutant F126 accumulated 5.7 and 30.3 g/L uridine after 30 h in shake-flask and 48 h in fed-batch fermentation, respectively, which represented a 4.4- and 8.7-fold increase over the parent strain. Sequence analysis of the pyrimidine nucleotide biosynthetic operon in the representative mutants showed that proline 1016 and glutamate 949 in the large subunit of B. subtilis carbamoyl phosphate synthetase were of importance for the allosteric regulation caused by uridine 5′-monophosphate. The proposed mutation method with efficient high-throughput screening assay was proved to be an appropriate strategy to obtain uridine-overproducing strain.

Characterization of genome-reduced Bacillus subtilis strains and their application for the production of guanosine and thymidine

Background

Genome streamlining has emerged as an effective strategy to boost the production efficiency of bio-based products. Many efforts have been made to construct desirable chassis cells by reducing the genome size of microbes. It has been reported that the genome-reduced Bacillus subtilis strain MBG874 showed clear advantages for the production of several heterologous enzymes including alkaline cellulase and protease. In addition to enzymes, B. subtilis is also used for the production of chemicals. To our best knowledge, it is still unknown whether genome reduction could be used to optimize the production of chemicals such as nucleoside products.

Results

In this study, we constructed a series of genome-reduced strains by deleting non-essential regions in the chromosome of B. subtilis 168. These strains with genome reductions ranging in size from 581.9 to 814.4 kb displayed markedly decreased growth rates, sporulation ratios, transformation efficiencies and maintenance coefficients, as well as increased cell yields. We re-engineered the genome-reduced strains to produce guanosine and thymidine, respectively. The strain BSK814G2, in which purA was knocked out, and prs, purF and guaB were co-overexpressed, produced 115.2 mg/L of guanosine, which was 4.4-fold higher compared to the control strain constructed by introducing the same gene modifications into the parental strain. We also constructed a thymidine producer by deleting the tdk gene and overexpressing the prs, ushA, thyA, dut, and ndk genes from Escherichia coli in strain BSK756, and the resulting strain BSK756T3 accumulated 151.2 mg/L thymidine, showing a 5.2-fold increase compared to the corresponding control strain.

Conclusions

Genome-scale genetic manipulation has a variety of effects on the physiological characteristics and cell metabolism of B. subtilis. By introducing specific gene modifications related to guanosine and thymidine accumulation, respectively, we demonstrated that genome-reduced strains had greatly improved properties compared to the wild-type strain as chassis cells for the production of these two products. These strains also have great potential for the production of other nucleosides and similar derived chemicals.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-016-0494-7) contains supplementary material, which is available to authorized users.

Deoxycytidine production by a metabolically engineered Escherichia coli strain

Background

Rational engineering studies for deoxycytidine production were initiated due to low intracellular levels and tight regulation. To achieve high-level production of deoxycytidine, a useful precursor of decitabine, genes related to feed-back inhibition as well as the biosynthetic pathway were engineered. Additionally, we predicted the impact of individual gene expression levels on a complex metabolic network by microarray analysis. Based on these findings, we demonstrated rational metabolic engineering strategies capable of producing deoxycytidine.

Results

To prepare the deoxycytidine producing strain, we first deleted 3 degradation enzymes in the salvage pathway (deoA, udp, and deoD) and 4 enzymes involved in the branching pathway (dcd, cdd, codA and thyA) to completely eliminate degradation of deoxycytidine. Second, purR, pepA and argR were knocked out to prevent feedback inhibition of CarAB. Third, to enhance influx to deoxycytidine, we investigated combinatorial expression of pyrG, T4 nrdCAB and yfbR. The best strain carried pETGY (pyrG-yfbR) from the possible combinatorial plasmids. The resulting strain showed high deoxycytidine yield (650 mg/L) but co-produced byproducts. To further improve deoxycytidine yield and reduce byproduct formation, pgi was disrupted to generate a sufficient supply of NADPH and ribose. Overall, in shake-flask cultures, the resulting strain produced 967 mg/L of dCyd with decreased byproducts.

Conclusions

We demonstrated that deoxycytidine could be readily achieved by recombineering with biosynthetic genes and regulatory genes, which appeared to enhance the supply of precursors for synthesis of carbamoyl phosphate, based on transcriptome analysis. In addition, we showed that carbon flux rerouting, by disrupting pgi, efficiently improved deoxycytidine yield and decreased byproduct content.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-015-0291-8) contains supplementary material, which is available to authorized users.