Transcriptomic and metabolomic correlation analysis: effect of initial SO2 addition on higher alcohol synthesis in Saccharomyces cerevisiae and identification of key regulatory genes.

Introduction: Higher alcohols are volatile compounds produced during alcoholic fermentation that affect the quality and safety of the final product. This study used a correlation analysis of transcriptomics and metabolomics to study the impact of the initial addition of SO2 (30, 60, and 90 mg/L) on the synthesis of higher alcohols in Saccharomyces cerevisiae EC1118a and to identify key genes and metabolic pathways involved in their metabolism. Methods: Transcriptomics and metabolomics correlation analyses were performed and differentially expressed genes (DEGs) and differential metabolites were identified. Single-gene knockouts for targeting genes of important pathways were generated to study the roles of key genes involved in the regulation of higher alcohol production. Results: We found that, as the SO2 concentration increased, the production of total higher alcohols showed an overall trend of first increasing and then decreasing. Multi-omics correlation analysis revealed that the addition of SO2 affected carbon metabolism (ko01200), pyruvate metabolism (ko00620), glycolysis/gluconeogenesis (ko00010), the pentose phosphate pathway (ko00030), and other metabolic pathways, thereby changing the precursor substances. The availability of SO2 indirectly affects the formation of higher alcohols. In addition, excessive SO2 affected the growth of the strain, leading to the emergence of a lag phase. We screened the ten most likely genes and constructed recombinant strains to evaluate the impact of each gene on the formation of higher alcohols. The results showed that ADH4, SER33, and GDH2 are important genes of alcohol metabolism in S. cerevisiae. The isoamyl alcohol content of the EC1118a-ADH4 strain decreased by 21.003%; The isobutanol content of the EC1118a-SER33 strain was reduced by 71.346%; and the 2-phenylethanol content of EC1118a-GDH2 strain was reduced by 25.198%. Conclusion: This study lays a theoretical foundation for investigating the mechanism of initial addition of SO2 in the synthesis of higher alcohols in S. cerevisiae, uncovering DEGs and key metabolic pathways related to the synthesis of higher alcohols, and provides guidance for regulating these mechanisms.

Regulator DegU can remarkably influence alkaline protease AprE biosynthesis in Bacillus licheniformis 2709.

Alkaline protease AprE, produced by Bacillus licheniformis 2709 is an important edible hydrolase, which has potential applications in nutrient acquisition and medicine. The expression of AprE is finely regulated by a complex transcriptional regulation system. However, there is little study on transcriptional regulation mechanism of AprE biosynthesis in Bacillus licheniformis, which limits system engineering and further enhancement of AprE. Here, the severely depressed expression of aprE in degU and degS deletion mutants illustrated that the regulator DegU and its phosphorylation played a crucial part in AprE biosynthesis. Further electrophoretic mobility shift assay (EMSA) in vitro indicated that phosphorylated DegU can directly bind to the regulatory region though the DNase I foot-printing experiments failed to observe protected region. The plasmid-mediated overexpression of degU32 (Hy) obviously improved the yield of AprE by 41.6 % compared with the control strain, which demonstrated the importance of phosphorylation state of DegU on the transcription of aprE in vivo. In this study, the putative binding sequence of aprE (5'-TAAAT……AAAAT…….AACAT…TAAAA-3') located upstream -91 to -87 bp, -101 to -97 bp, -195 to -191 bp, -215 to -211 bp of the transcription start site (TSS) in B. licheniformis was computationally identified based on the DNA-binding sites of DegU in Bacillus subtilis. Overall, we systematically investigated the influence of the interplay between phosphorylated DegU and its cognate DNA sequence on expression of aprE, which not only contributes to the further AprE high-production in a genetically modified host in the future, but also significantly increases our understanding of the aprE transcription mechanism.

Multiple Modular Engineering of Bacillus Amyloliquefaciens Cell Factories for Enhanced Production of Alkaline Proteases From B. Clausii.

Bacillus amyloliquefaciens is a generally recognized as safe (GRAS) microorganism that presents great potential for the production of heterologous proteins. In this study, we performed genomic and comparative transcriptome to investigate the critical modular in B. amyloliquefaciens on the production of heterologous alkaline proteases (AprE). After investigation, it was concluded that the key modules affecting the production of alkaline protease were the sporulation germination module (Module I), extracellular protease synthesis module (Module II), and extracellular polysaccharide synthesis module (Module III) in B. amyloliquefaciens. In Module I, AprE yield for mutant BA ΔsigF was 25.3% greater than that of BA Δupp. Combining Module I synergistically with mutation of extracellular proteases in Module II significantly increased AprE production by 36.1% compared with production by BA Δupp. In Module III, the mutation of genes controlling extracellular polysaccharides reduced the viscosity and the accumulation of sediment, and increased the rate of dissolved oxygen in fermentation. Moreover, AprE production was 39.6% higher than in BA Δupp when Modules I, II and III were engineered in combination. This study provides modular engineering strategies for the modification of B. amyloliquefaciens for the production of alkaline proteases.

Construction of an alkaline protease overproducer strain based on Bacillus licheniformis 2709 using an integrative approach.

Bacillus licheniformis 2709 is a potential cell factory for the production of alkaline protease AprE, which has important value in industrial application but still lacks sufficient production capacity. To address this problem, we investigated the effects of the secretory viscous materials on the synthesis of AprE, which might seriously affect the industrial fermentation. Furthermore, an iterative chromosomal integration strategy at various chromosomal loci was implemented to achieve stable high-level expression of AprE in B. licheniformis 2709. The host was genetically modified by disrupting the native pgs cluster controlling the biosynthesis of viscous poly-glutamic acid identified in the study by GC/MS, generating a mutant with significantly higher biomass and better bioreactor performance. We further enhanced the expression of alkaline protease by integrating two additional aprE expression cassettes into the genome, generating the integration mutant BL ∆UEP-3 with three aprE expression cassettes, whose AprE enzyme activity in shake flasks reached 25,736 ± 997 U/mL, which was 136% higher than that of the original strain, while the aprE transcription level increased 4.05 times. Thus, an AprE high-yielding strain with excellent fermentation traits was engineered, which was more suitable for bulk-production. Finally, the AprE titer was further increased in a 5-L fermenter, reaching 57,763 ± 1039 U/mL. In summary, genetic modification is an enabling technology for enhancing enzyme production by eliminating the unfavorable characteristics of the host and optimizing the expression of aprE through iterative chromosomal integration. We believe that the protocol developed in this study provides a valuable reference for chromosomal overexpression of proteins or bioactive molecules in other Bacillus species.

Reducing the cell lysis to enhance yield of acid-stable alpha amylase by deletion of multiple peptidoglycan hydrolase-related genes in Bacillus amyloliquefaciens.

Bacillus amyloliquefaciens is a major industrial host for extracellular protein production, with great potential in the enzyme industry. However, the strain has accelerated the autolysis drawback in the process of secreting extracellular enzymes, which can significantly lower the density of cells and decrease the product yield. To identify target genes, we employed comparative transcriptome sequencing and KEGG analysis to indicate the increased expression of peptidoglycan hydrolase-regulated genes from the exponential phase to the apoptotic phase of growth; this was further confirmed by quantitative RT-PCR. By deleting lytD, lytE, and sigD genes, cell lysis was reduced and the production of acid-stable Bacillus licheniformis alpha-amylase was enhanced. After 36 h of culture, multiple deletion mutant BA ΔSDE had significantly more viable cells compared to the control strain BA Δupp, and flow cytometry analysis indicated that 48.43% and 64.03% of the cells were lysed in cultures of BA ΔSDE and BA Δupp, respectively. In a 2-L fed-batch fermenter, viable cell number of the triple deletion mutant BA ΔSDE increased by 2.79 Log/cfu/mL, and the activity of acid-stable alpha-amylase increased by 48.4%, compared to BA Δupp. Systematic multiple peptidoglycan hydrolases deletion relieved the autolysis and increased the production of industrial enzymes, and provided a useful strategy for guiding efforts to manipulate the genomes of other B. amyloliquefaciens used for chassis host.

Transcriptome based functional identification and application of regulator AbrB on alkaline protease synthesis in Bacillus licheniformis 2709.

Bacillus licheniformis 2709 is the major alkaline protease producer, which has great potential value of industrial application, but how the high-producer can be regulated rationally is still not completely understood. It's meaningful to understand the metabolic processes during alkaline protease production in industrial fermentation medium. Here, we collected the transcription database at various enzyme-producing stages (preliminary stage, stable phase and decline phase) to specifically research the synthesized and regulatory mechanism of alkaline protease in B. licheniformis. The RNA-sequencing analysis showed differential expression of numerous genes related to several processes, among which genes correlated with regulators were concerned, especially the major differential gene abrB on enzyme (AprE) synthesis was investigated. It was further verified that AbrB is a repressor of AprE by plasmid-mediated over-expression due to the severely descending enzyme activity (11,300 U/mL to 2695 U/mL), but interestingly it is indispensable for alkaline protease production because the enzyme activity of the null abrB mutant was just about 2279 U/mL. Thus, we investigated the aprE transcription by eliminating the theoretical binding site (TGGAA) of AbrB protein predicated by computational strategy, which significantly improved the enzyme activity by 1.21-fold and gene transcription level by 1.77-fold in the mid-log phase at a cultivation time of 18 h. Taken together, it is of great significance to improve the production strategy, control the metabolic process and oriented engineering by rational molecular modification of regulatory network based on the high throughput sequencing and computational prediction.

Spo0A can efficiently enhance the expression of the alkaline protease gene aprE in Bacillus licheniformis by specifically binding to its regulatory region.

The expression of enzymes in Bacillus licheniformis, such as the valuable extracellular alkaline protease AprE, is highly regulated by a complex transcriptional regulation mechanism. Here, we found that the transcript abundance of aprE varies >343-fold in response to the supply of nutrients or to environmental challenges. To identify the underlying regulatory mechanism, the core promoter of aprE and several important upstream regulatory regions outside the promoter were firstly confirmed by 5'-RACE and mutagenesis experiments. The specific proteins that bind to the identified sequences were subsequently captured by DNA pull-down experiments, which yielded the transcriptional factors (TFs) Spo0A, CggR, FruR, YhcZ, as well as fragments of functionally unassigned proteins. Further electrophoretic mobility shift assay (EMSA) and DNase I foot-printing experiments indicated that Spo0A can directly bind to the region from -92 to -118 nucleotides upstream of the transcription start site, and the deletion of this specific region drastically decreased the production of AprE. Taken together, these results indicated that the expression of aprE was mainly regulated by the interplay between Spo0A and its cognate DNA sequence, which was successfully applied to overproduce AprE in a genetically modified host harboring three aprE expression cassettes. The DNA binding proteins may serve to increase the efficiency of transcription by creating an additional binding site for RNA polymerase. The discovery of this mechanism significantly increases our understanding of the aprE transcription mechanism, which is of great importance for AprE overproduction.

Optimized expression and enhanced production of alkaline protease by genetically modified Bacillus licheniformis 2709.

BACKGROUND: Bacillus licheniformis 2709 is extensively applied as a host for the high-level production of heterologous proteins, but Bacillus cells often possess unfavorable wild-type properties, such as production of viscous materials and foam during fermentation, which seriously influenced the application in industrial fermentation. How to develop it from a soil bacterium to a super-secreting cell factory harboring less undomesticated properties always plays vital role in industrial production. Besides, the optimal expression pattern of the inducible enzymes like alkaline protease has not been optimized by comparing the transcriptional efficiency of different plasmids and genomic integration sites in B. licheniformis. RESULT: Bacillus licheniformis 2709 was genetically modified by disrupting the native lchAC genes related to foaming and the eps cluster encoding the extracellular mucopolysaccharide via a markerless genome-editing method. We further optimized the expression of the alkaline protease gene (aprE) by screening the most efficient expression system among different modular plasmids and genomic loci. The results indicated that genomic expression of aprE was superior to plasmid expression and finally the transcriptional level of aprE greatly increased 1.67-fold through host optimization and chromosomal integration in the vicinity of the origin of replication, while the enzyme activity significantly improved 62.19% compared with the wild-type alkaline protease-producing strain B. licheniformis. CONCLUSION: We successfully engineered an AprE high-yielding strain free of undesirable properties and its fermentation traits could be applied to bulk-production by host genetic modification and expression optimization. In summary, host optimization is an enabling technology for improving enzyme production by eliminating the harmful traits of the host and optimizing expression patterns. We believe that these strategies can be applied to improve heterologous protein expression in other Bacillus species.

Identification of two novel highly inducible promoters from Bacillus licheniformis by screening transcriptomic data.

Bacillus licheniformis TCCC11148 is an important industrial strain used to produce alkaline protease. In this study, the transcriptome of B. licheniformis TCCC11148 was analyzed by high throughput RNA sequencing (RNA-Seq) to identify genes that are expressed differentially in the different phases were detected using RNA-Seq. In total, 440 differentially expressed genes between the 12 h and 48 h groups were identified, including 267 up- and 173 downregulated genes. Additionally, 198 differentially expressed genes were identified in the 48 h vs. the 60 h group, including 182 up- and 16 downregulated genes. To screen for novel inducible promoters, an alkaline protease reporter gene was used to test 24 promoters from 66 candidate genes with obviously higher expression levels (RPKM values) than the control group based on the transcriptome data of B. licheniformis in different phases. Gene 707, related to coenzyme transport and metabolism, and gene 1004, related to posttranslational modification were identified as likely having inducible promoters. The expression level of recombinant strains with reporter genes under the control of promoters p707 and p1004 were 8 times higher than that of the control group. This study contributes a method for finding useful inducible promoters for industrial use based on transcriptomic data.

Optimization of alkaline protease production by rational deletion of sporulation related genes in Bacillus licheniformis.

BACKGROUND: Our laboratory has constructed a Bacillus licheniformis strain that secretes alkaline protease (AprE) with excellent enzymatic properties. B. licheniformis is generally regarded as safe and has a high industrial exoenzyme secretion capacity, but the host retains some undomesticated characteristic that increase its competitiveness and survival, such as spore-formation, which increases the requirements and difficulties in industrial operations (e.g. sterilization and enzyme activity control). Furthermore, the influence of sporulation on alkaline protease production in B. licheniformis has not been elucidated in detail. RESULT: A series of asporogenic variants of the parent strain were constructed by individually knocking out the master regulator genes (spo0A, sigF and sigE) involved in sporulation. Most of the variants formed abortively disporic cells characterized by asymmetric septa at the poles and unable to survive incubation at 75 °C for 10 min. Two of them (ΔsigF and ΔsigE) exhibited superior characteristics in protease production, especially improving the expression of the aprE gene. Under the currently used fermentation conditions, the vegetative production phase of ΔsigF can be prolonged to 72 h, and the highest protease production of ΔsigF reached 29,494 ± 1053 U/mL, which was about 19.7% higher than that of the wild-type strain. CONCLUSION: We first constructed three key sporulation-deficient strain to investigate the effect of sporulation on alkaline protease synthesis. The sigF mutant retained important industrial properties such as facilitating the sterilization process, a prolonged stable phase of enzyme production and slower decreasing trend, which will be superior in energy conservation, simpler operations and target product controlling effect. In summary, the work provides a useful industrial host with preferable characteristics and a novel strategy to enhance the production of protease.

Sensitivity Enhancement of Two-Dimensional Materials Based on Genetic Optimization in Surface Plasmon Resonance.

Sensitivity is an important performance index for evaluating surface plasmon resonance (SPR) biosensors. Sensitivity enhancement has always been a hot topic. It is found that the different refractive indices of samples require different combinations of prism and metal film for better sensitivity. Furthermore, the sensitivity can be enhanced by coating two-dimensional (2D) materials with appropriate layers on the metal film. At this time, it is necessary to choose the best film configuration to enhance sensitivity. With the emergence of more and more 2D materials, selecting the best configuration manually is becoming more complicated. Compared with the traditional manual method of selecting materials and layers, this paper proposes an optimization method based on a genetic algorithm to quickly and effectively find the optimal film configuration that enhances sensitivity. By using this method, not only can the optimal number of layers of 2D materials be determined quickly, but also the optimal configuration can be conveniently found when many materials are available. The maximum sensitivity can reach 400°/RIU after optimization. The method provided application value for the relevant researchers seeking to enhance sensitivity.

Engineered variants of a lipase from Yarrowia lipolytica with improved trypsin resistance for enzyme replacement therapy.

To improve the proteolytic stability of the lipase LIP2 from Yarrowia lipolytica, the peptide bonds susceptible to trypsin in LIP2 were analyzed by tandem mass spectrometry and redesigned by site-directed mutagenesis. Different variants of the enzyme were expressed in Pichia pastoris GS115 and their biochemical properties were subsequently investigated. Although most of the variants were still cleaved by trypsin, some of them did show an evident increase of resistance against proteolytic degradation. The most stable mutant was LIP2-C5, in which five trypsin-cleavage sites were replaced by non-preferred amino acids. Upon incubation with human trypsin for 80 min at 37°C, the mutant LIP2-C5 was found to retain >70% of its initial activity, compared to only 10% for the wild-type.

Development and application of a CRISPR/Cas9 system for Bacillus licheniformis genome editing.

A highly efficient genome editing system for Bacillus licheniformis was developed based on single-plasmid CRISPR/Cas9. For highly efficient genome editing the shuttle vector pWH1520 was selected to construct the knockout plasmids. A construct harboring a pS promoter driving cas9 endonuclease expression, a strong pLY-2 promoter driving the transcription of a single guide RNA was demonstrated as being the most effective. To verify the feasibility of the method the uprT gene coding uracil phosphoribosyltransferase was selected as the reporter gene. The efficiency of introducing nucleotide point mutations and single gene deletion reached an editing efficiency of up to 99.2% and 97.3%, respectively. After a upp-deficient strain was engineered, the system and strain were applied to introduce genomic deletions of another two genes, amyL and chiA (encoding amylase and chitinase, respectively) with about 90% deletion efficiency. As two native extracellular proteins with relatively high secretion in the host, amylase and chitinase can hamper the secretion and expression of alkaline protease. It was demonstrated that the mutant with deletions of the two genes effectively improved the alkaline protease yield by 24.8%. The results illustrated that the establishment of a CRISPR/Cas9 system for Bacillus licheniformis is of significance, and confirmed the system's high efficiency. The system provides support for effective molecular modification and metabolic regulation of Bacillus licheniformis, and offers promise for applications in genetic modification of other industrially relevant Bacillus species.

[Individualized scalp acupuncture for motor dysfunction in stroke: a randomized controlled trial].

OBJECTIVE: To evaluate the effect of individualized scalp acupuncture base on location of brain function for motor dysfunction in stroke patients. METHODS: A total of 180 patients were randomly assigned into an individualized scalp acupuncture (ISA) group, a conventional scalp acupuncture (CSA) group and a rehabilitation group, 60 cases in each one. In the ISA group, we stimulated Sishencong (EX-HN 1), motor area and balance area, matched with pre-motor area for higher muscle tension, application area and NIE 's three-needle for involuntary motion, application area for poor motor coordination, forehead five-needle for cognitive disorder, sensory area for sensory disturbance. In the CSA group, the affected Dingnieqianxiexian (MS 6), Dingniehouxiexian (MS 7) and Zhenxiapangxian (MS 14) were selected. Rehabilitation was used during needle retained in the two groups. Simple rehabilitation was used in the rehabilitation group. All the treatment was given from Monday to Friday for 4 weeks, once a day for 20 times. Eight-week follow-up was applied. The Fugl-Meyer assessment (FMA) for motor function, modified Barthel Index (MBI) were used to evaluate clinical effect. RESULTS: After treatment and at follow-up, FMA and MBI scores increased compared with those before treatment in the three groups（all P<0.01）, with significant differences among the three groups (all P<0.000 1) and better results in the ISA group compared with those in the other two groups (P<0.05, P<0.01) at the two time points. The FMA and MBI scores in the CSA group were higher than those in the rehabilitation group after treatment and at follow-up (all P<0.05). CONCLUSION: The individualized scalp acupuncture can improve motor dysfunction and self-care ability of daily life for stroke patients.

[Interactive dynamic scalp acupuncture combined with occupational therapy for upper limb motor impairment in stroke: a randomized controlled trial].

OBJECTIVE: To compare the clinical efficacy on upper limb motor impairment in stroke between the interactive dynamic scalp acupuncture therapy and the traditional scalp acupuncture therapy. METHODS: The randomized controlled trial and MINIMIZE layering randomization software were adopted. Seventy patients of upper limb with III to V grade in Brunnstrom scale after stroke were randomized into an interactive dynamic scalp acupuncture group and a traditional scalp acupuncture group, 35 cases in each one. In the interactive dynamic scalp acupuncture group, the middle 2/5 of Dingnieqianxiexian (anterior oblique line of vertex-temporal), the middle 2/5 of Dingniehouxiexian (posterior oblique line of vertex-temporal) and Dingpangerxian (lateral line 2 of vertex) on the affected side were selected as the stimulation areas. Additionally, the rehabilitation training was applied during scalp acupuncture treatment. In the traditional scalp acupuncture group, the scalp stimulation areas were same as the interactive dynamic scalp acupuncture group. But the rehabilitation training was applied separately. The rehabilitation training was applied in the morning and the scalp acupuncture was done in the afternoon. The results in Fugl-Meyer for the upper limb motor function (U-FMA), the Wolf motor function measure scale (WM- FT) and the modified Barthel index in the two groups were compared between the two groups before treatment and in 1 and 2 months of treatment, respectively. RESULTS: After treatment, the U-FMA score, WMFT score and the score of the modified Barthel index were all apparently improved as compared with those before treatment (all P < 0.01). The improvement in the U-FMA score after treatment in the interactive dynamic scalp acupuncture group was better than that in the traditional scalp acupuncture group (P < 0.05). For the patients of IV to V grade in Brunnstrom scale, WMFT score in 2 months of treatment and the score of Barthel index after treatment in the interactive dynamic scalp acupuncture group were improved apparently as compared with those in the traditional scalp acupuncture group (P < 0.05, P < 0.01). But, for the patients of III grade in Brunnstrom scale, WMFT score and the score of Barthel index after treatment in the interactive dynamic scalp acupuncture group were not different significantly as compared with those in the traditional scalp acupuncture group (both P > 0.05). CONCLUSION: For the patients of IV to V grade in Brunnstrom scale in stroke, the interactive dynamic scalp acupuncture therapy achieves the superior improvements of the upper limb motor function and the activity of daily life as compared with the traditional scalp acupuncture therapy, and the longer the treatment lasts, the more apparent the improvements are. For the patients of III grade in Brunnstrom scale, the interactive dynamic scalp acupuncture therapy achieves the similar improvement in the upper limb motor impairment as compared with the traditional scalp acupuncture therapy.

[Observation on the clinical efficacy of shoulder pain in post-stroke shoulder-hand syndrome treated with floating acupuncture and rehabilitation training].

OBJECTIVE: To compare the efficacy difference in the treatment of shoulder pain in post-stroke shoulder-hand syndrome among floating acupuncture, oral administration of western medicine and local fumigation of Chinese herbs. METHODS: Ninety cases of post-stroke shoulder-hand syndrome (stage I) were randomized into a floating acupuncture group, a western medicine group and a local Chinese herbs fumigation group, 30 cases in each one. In the floating acupuncture group, two obvious tender points were detected on the shoulder and the site 80-100 mm inferior to each tender point was taken as the inserting point and stimulated with floating needling technique. In the western medicine group, mobic 7.5 mg was prescribed for oral administration. In the local Chinese herbs fumigation group, the formula for activating blood circulation and relaxing tendon was used for local fumigation. All the patients in three groups received rehabilitation training. The floating acupuncture, oral administration of western medicine, local Chinese herbs fumigation and rehabilitation training were given once a day respectively in corresponding group and the cases were observed for 1 month. The visual analogue scale (VAS) and Takagishi shoulder joint function assessment were adopted to evaluate the dynamic change of the patients with shoulder pain before and after treatment in three groups. The modified Barthel index was used to evaluate the dynamic change of daily life activity of the patients in three groups. RESULTS: With floating acupuncture, shoulder pain was relieved and the daily life activity was improved in the patients with post-stroke shoulder-hand syndrome, which was superior to the oral administration of western medicine and local Chinese herbs fumigation (P < 0.01). With local Chinese herbs fumigation, the improvement of shoulder pain was superior to the oral administration of western medicine. The difference in the improvement of daily life activity was not significant statistically between the local Chinese herbs fumigation and oral administration of western medicine, the efficacy was similar between these two therapies (P > 0.05). CONCLUSION: The floating acupuncture relieves shoulder pain of the patients with post-stroke shoulder-hand syndrome promptly and effectively, and the effects on shoulder pain and the improvements of daily life activity are superior to that of the oral administration of western medicine and local Chinese herbs fumigation.