Abstract:Elementary mode analysis is the widely applied tool in metabolic pathway analysis. Studies based on elementary mode analysis (EMA) were performed for both metabolic network and signal transduction network. Its analytical objective is from cell to bioreactor, and even ecological system. EMA is available to describe biological behaviors by steady state and dynamic models. Not only microorganism metabolism but also human health could be evaluated by EMA. The algorithms and software for calculating elementary mode (EM) were analyzed. The applications of EMA are reviewed such as special metabolic pathway and robustness of metabolic network, metabolic flux decomposition, metabolic flux analysis at steady state, dynamic model and bioprocess simulation, network structure and regulation, strain design and signal transduction network. Solving combinatorial explosion, exploring the relations between EM and metabolic regulation, and improving the algorithm efficiency of strain design are important issues of EMA in future.

Abstract:Von Hippel-Lindau(VHL) disease is an autosomal dominant disorder and its clinical manifestation including haemangioblastomas of the central nervous system, renal cell carcinoma, haeochromocytomas, and pancreatic cyst. The deletion, mutation and promoter methylation of VHL gene can cause VHL disease. Swine is considered as an ideal model for human disease because of its physiological and anatomical similarity to human. We cloned pig VHL gene that is 2 725 bp in length. VHL highly expressed in adrenal gland, liver, pancreas, heart and testis. We designed 5 shRNAs and screened the most effective interference RNA fragment with a knockdown efficiency of 72%. Porcine embryonic fibroblasts stably transfected with pGenesil-shRNA vector were used as donor cells for nuclear transfer and there was no significant difference of embryo development compared with the control group. Moreover, VHL was efficiently knocked-down with efficiency of 71% in porcine cloned blastocyst, these results lay a solid foundation for constructing the VHL knock-down model of pig.

Abstract:Constructing robust gene circuits is a fundamental work for synthetic biology. Bacteria with suicide gene circuit based on quorum-sensing will kill themselves in a controllable pattern upon certain cell density. In the media of different IPTG inducer concentration, we observed the growth and suicidal behavior of the Escherichia coli. Top10F’ with such gene circuit, screened the mutants and determined their mutated loci. The results show that, with higher IPTG concentration, the more wild type bacteria were killed; as well the mutants emerged earlier and spread over the population more quickly. The sequence of plasmids in those mutants revealed that a transposon inserted into the luxR gene and therefore disrupted Quorum-Sensing of these individuals. Furthermore, the insertion sequence of the plasmid can solely result in the mutants escaping from suicide.

Abstract:In this study, we investigated the mechanism of transformation by Bacillus subtilis strain 168 by proteomic analysis. B. subtilis strain 168 was able to stereoselectively transform cis-propenylphosphonic acid (cPPA) to fosfomycin. The maximal fosfomycin production was 816.6 μg/mL after two days cultivation, with a conversion rate of 36.05%. We separated the whole cellular proteins by two-dimensional gel electrophoresis (2-DE) method, and 562 protein spots were detected in the presence of cPPA in the medium, while 527 protein spots were detected in the absence of cPPA. Of them, 98 differentially expressed protein spots were found. Among them, 52 proteins were up-regulated whereas 20 were down-regulated in the presence of cPPA in the medium, and 26 induced at the presence of cPPA. The differentially expressed proteins were analyzed by combined MS and MS/MS methods. Eighty protein spots, including 45 up-regulated proteins, 17 down-regulated proteins, and 18 induced by cPPA were identified. Based on the results of proteomic analysis, we postulated two steps of transformation: in the first step, cPPA was hydrated to 2-hydroxypropylphosphonic acid; in the second step, 2-hydroxypropylphosphonic acid was transformed to fosfomycin via a dehydrogenation reaction.

Abstract:Linalool is an important monoterpene, and widely used in food, pharmaceutical and cosmetic industry. The low concentration in plants and the difficulties in extraction restrict its large scale production. Saccharomyces cerevisiae can provide the monoterpene precursor, geranyl diphosphate (GPP) through its endogenous isoprenoid pathway. Therefore, it could be used as the host for monoterpene production. However, the weak metabolic flux through the isoprenoid pathway leads to the insufficient supply of GPP, and results in low monoterpene productivity. In order to increase the metabolic flux, we constructed the integrated expression plasmid pRS305-tHMG1 and free expression plasmid pYLIS-IDI1 to enhance the expression levels of isopentenyl diphosphate isomerase (IDI1) and a truncated 3-hydroxyl-3-methylglutaryl-CoA reductase gene (tHMG1). The two plasmids were separately transformed into S. cerevisiae CEN.PK2-1C, resulting in strains LS01 and LS02. The plasmid pYLIS-IDI1 was further transformed into strain LS01, resulting in strain LS03. GC-MS analysis showed that the linalool concentration was increased by 1.3 times and reached (127.71±7.68) mg/L. In conclusion, enhancement of the supply of GPP precursors through the regulation of isoprenoid pathway could increase the linalool production in S. cerevisiae.

Abstract:Promoter is one of important elements for gene expression and regulation. In the construction of recombinants for metabolic engineering and synthetic biology, it is necessary to have the promoters with varying strengths for fine-tuning metabolic pathway to reach the metabolic balance, decrease the accumulation of intermediate and increase the production of target metabolite. However, the natural promoters available are not completely suitable for fine-tuning metabolic pathway due to discrete strength, lack of versatility and standardization. To deal with this problem, in this study, a new 88 bp synthetic promoter, which contains the typical ?35 box, ?10 box as well as ribosome bind site, was designed. Then, the promoter library was constructed by introducing some degenerate base pairs in the sequence of 6 bp in the upstream of the initial transcription site and 14 bp in spacer region between ?35 and ?10 box. 720 promoters with varying strengths were screened out from a library of more than 5 000 clones via the expression of red fluorescent protein mCherry under the control of the synthetic promoter. The sequence analysis based on 35 promoters with varying strengths showed the promoters with varying strengths are base preference. The purine bases in ?13 site and pyrimidine bases in the transcriptional initiation sequence are of high frequency; the purine and pyrimidine bases are of the similar frequency in the spacer sequence between ?35 and ?10 box in strong promoter. In the end, five characterized promoters with varying strengths were selected to tune the synthetic pathway of cis,cis-muconic acid in Escherichia coli. The results showed that the promoters with varying strengths can regulate the production of cis, cis-muconic acid and the accumulation of the intermediate catechol.

Abstract:Dye-decolorizing peroxidase (DyP-type peroxidase) represents a group of heme-containing peroxidases able to decolour various organic dyes, most of which are xenobiotics. To identify and characterize a new DyP-type peroxidase (ZmDyP) from Zymomonas mobilis ZM4 (ATCC 31821), ZmDyP was amplified from the genomic DNA of Z. mobilis by PCR, and cloned into the Escherichia coli expression vector pET-21b(+). Alignment of the amino acid sequence of ZmDyP with other members of the DyP-type peroxidases revealed the presence of the active site conserved residues D149, R239, T254, F256 as well as the typical GXXDG motif, indicating that ZmDyP is a new member of the Dyp-type peroxidase family. pET-21b(+) containing ZmDyP gene was expressed in E. coli by IPTG induction. The expressed enzyme was purified by Ni-Chelating chromatography. SDS-PAGE analysis of the purified enzyme revealed a molecular weight of 36 kDa, whereas activity staining gave a molecular weight of 108 kDa, suggesting that the enzyme could be a trimer. In addition, ZmDyP is a heme-containing enzyme as shown by a typical heme absorption peak of Soret band. Moreover, ZmDyP showed high catalytic efficiency with 2, 2'-Azinobis-(3-ethylbenzthiazoline-6-sulphonate) as a substrate. These results enrich the pool of DyP-type peroxidases and lay a foundation for further studies.

Abstract:WRKY transcription factors, one of the largest families of transcriptional regulators in plants, involve in multiple life activities including plant growth and development as well as stress responses. However, little is known about the types and functions of WRKY transcription factors in Catharanthus roseus, an important medicinal plant. In this study, we identified 47 CrWRKY transcriptional factors from 26 009 proteins in Catharanthus roseus, and classified them into three distinct groups (G1, G2 and G3) according to the structure of WRKY domain and evolution of the protein family. The expression profiling showed that these CrWRKY genes expressed in a tissue /organ specific manner. The 47 CrWRKY genes were clustered into three types of expression patterns. The first type includes the CrWRKYs highly expressed in flowers and the protoplast treated with methy jasmonate (MeJA) or yeast extraction (YE). The second type contains the CrWRKYs highly expressed in stem and hairy root. The third type represents the CrWRKYs highly expressed in root, stem, leaf, seedling and the hairy root treated by MeJA. Real time quantitative PCR was employed to further identify the expression patterns of the 16 selected CrWRKY genes in various organs, the MeJA-treated protoplasts and hairy roots of Catharanthus roseus, and similar results were obtained. Notably, the expresion of more than 1/3 CrWRKY genes were regulated by MeJA or YE, indicating that these CrWRKYs are likely involed in the signalling webs which modulate the biosynthesis of terpenoid indole alkaloid and plant responses to various stresses. The present results provide a framework for functional identification of the CrWRKYs and understanding of the regulation network of terpenoid indole alkaloid biosynthesis in Catharanthus roseus.

Abstract:As a superantigen protein, Staphylococcal enterotoxin C2 (SEC2) activates the immune system effectively even in extremely low concentrations, and this property could be applied in adjuvant therapy against tumors and infectious diseases. In order to enhance the superantigen activity of SEC2, the residues at position 102?106 of native SEC2 were substituted for WWH, WWT and WWP by over-lap PCR, and three mutants named ST-1, ST-2 and ST-3 were obtained. Stimulating activity to murine lymphocytes proliferation and inhibiting activity to tumor cell growth of the three mutants were significantly improved compared with the native SEC2. Febrile activities of ST-1 and ST-3 were comparable with the native SEC2, but ST-2 showed markedly increased febrile activity than native SEC2. Moreover, the levels of IL-2, IFN-γ and TNF-α secreted by T cells stimulated with the three mutants were significantly improved, which might be the possible reason for enhanced tumor cell growth inhibition activities. Furthermore, mVβ8.2 gene transcription levels of murine splenocytes stimulated by the three mutants were dramatically increased compared with native SEC2, suggesting their increased affinities to TCR mVβ8.2 molecular, which might be the main reason for their enhanced superantigen activities.

Abstract:Schistosomiasis japonica is an endemic, zoonotic disease of major public health importance in China. Vaccination is needed as a complementary approach to the ongoing control programs. In the present study, we determined if the efficacies of DNA vaccine encoding the SjGST and Sj32 asparaginyl endopeptidase protein could be enhanced by boosting with SjGST-32 protein vaccines. Mice were inoculated with a VR1012-SjGST-32 DNA vaccine followed by boosting with rSjGST-32 at 0, 14 and 28 d. Two weeks after the final boost, mice were challenged percutaneously with cercariae. On day 45 following the challenge, all mice were sacrificed and the numbers of recovered worms and hepatic eggs were counted. Moreover, we analyzed the immune response among various vaccination groups. The results showed that DNA vaccine efficacy was enhanced when mice were boosted with protein vaccine. Adult worm and liver egg burdens were reduced 42.3% and 59.6%, respectively. We further found that DNA vaccine followed by boosting with protein significantly increased the IgG titer and T cell proliferation over those seen in mice vaccinated solely with DNA vaccines. Furthermore, the higher level of IFN-γ expression in the splenetic CD4+ T cell showed that DNA prime-Protein boosting vaccine induced CD4+ Th1-type responses. Thus, DNA vaccine efficacy was significantly enhanced via boosting protein vaccine which might provide a basis for rational application of the Schistosoma vaccine.

Abstract:Nine mutants (P2M1–9) were obtained using PCR with 5-BU based on DNA template (P2Y) encoding the active region of Parasporin-2. Mutant proteins were purified after expressing in E. coli BL21 cells, followed by assayed against hepatoma cells and normal liver cells by MTT. They showed diverse anti-hepatoma activities, in which two mutant proteins, P2M1 and P2M8, exhibited high cytotoxicity against hepatoma cell lines SMMC7721 and Bel7402, meanwhile leaving normal liver cells Chang-liver unaffected. Structural comparison among P2Y, P2M1 and P2M8 showed that the length of β-sheet or β-fold, and the amount of α helix greatly affected the anti-hepatoma activity of Parasporin-2. Results based on amino acid alignment, molecular docking between P2Y, P2M1 or P2M8 and receptor, and mimic mutation demonstrated that amino acid residues at the sites of 52, 56, 58 and 208 on P2Y, especially the aromatic amino acids such as Trp, Phe, and Tyr were involved in the interactions.

Abstract:To improve the expression level of tmAMP1m gene from Tenebrio molitor in Escherichia coli, we studied the effects of expression level and activity of the fusion protein HIS-TmAMP1m by conditions, such as culture temperature, inducing time and the final concentration of inductor Isopropyl beta-D-thiogalactopyranoside( IPTG). We analyzed the optimum expression conditions by Tricine-SDS-PAGE electrophoresis, meanwhile, detected its antibacterial activity by using agarose cavity diffusion method. The results suggest that when inducing the recombinant plasmid with a final IPTG concentration of 0.1 mmol/L at 37 ℃ for 4 h, there was the highest expression level of fusion protein HIS-TmAMP1m in Escherichia coli. Under these conditions, the expression of fusion protein accounted for 40% of the total cell lysate with the best antibacterial activity. We purified the fusion protein HIS-TmAMP1m with nickel-nitrilotriacetic acid (Ni-NTA) metal-affinity chromatography matrices. Western blotting analysis indicates that the His monoclonal antibody could be specifically bound to fusion protein HIS-TmAMP1m. After expression by inducing, the fusion protein could inhibit the growth of host cell transformed by pET30a-tmAMP1m. The fusion protein HIS-TmAMP1m had better stability and remained higher antibacterial activities when incubated at 100 ℃ for 10 h, repeated freeze thawing at ?20 ℃, dissolved in strong acid and alkali, or treated by organic solvents and protease. Moreover, the minimum inhibitory concentration results demonstrated that the fusion protein HIS-TmAMP1m has a good antibacterial activity against Staphylococcus aureus, Staphylococcus sp., Corynebacterium glutamicum, Bacillus thuringiensis, Corynebacterium sp. This study laid the foundation to promote the application of insect antimicrobial peptides and further research.

Abstract:Diosgenin is an important raw material in steroid hormone and widely used in pharmaceutical industry. The traditional method for diosgenin production is acidolysis, which causes serious pollution. In order to obtain a cleaner and more efficient approach of diosgenin production, a strain of Gibberella intermedia WX12 (the sexual stage of Fusarium proliferatum) was screened from the strains deposited in our laboratory. This strain converted saponins in Dioscorea zingiberensis C.H. Wright (DZW) into diosgenin. The conversion medium was optimized by statistical experimental design. The optimized conversion medium was as follows (g/L): glucose 20.6, yeast extract 5.0, NaCl 1, K2PO4 3 , ZnSO4·7H2O 1.5 and saponins 3. Under the optimal conditions, the yield of diosgenin achieved to (31±0.3) mg/g DZW, which was 3 times higher than that of the original medium.

Abstract:To produce recombinant phospholipase A1 (PLA1) by Escherichian coli, the pla gene encoding PLA1 was amplified from Serratia liquefaciens by PCR and cloned into two vectors pET20-b(+) and pET28-a(+). The two recombinant plasmids were then transformed into E. coli BL21 (DE3) individually to express PLA1. E. coli BL21(DE3)/pET28a-pla yielded extracellular PLA1 with an activity of 40.8 U/mL in batch cultivations of shaken flasks by auto-induction, which was accounted for 91% of total enzyme activity. On the basis of primal auto-induction medium, the optimized fermentation medium of PLA1 contained tryptone 10 g/L, yeast extract 5 g/L, glucose 0.8 g/L, lactose 5 g/L, Na2HPO4 25 mmol/L, KH2PO4 25 mmol/L and 1 mmol/L MgSO4 (final concentration). Glycine (7.5 g/L) was added 6 h after inoculated. After incubated at 37 °C for 24 h, extracellular enzyme activity reached 128.7 U/mL.

Abstract:Response surface methodology was applied to optimize the fermentation conditions of FGFC1 (Fungi fibrinolytic compound 1). On the basis of single factor tests, response surface analysis was designed by Design-Expert, and the effects of culture time, ornithine hydrochloride addition and culture temperature on the yield of FGFC1 were studied, the predicted value and measured value were also contrasted. The results show the optimal culture conditions as follows: the culture time is 7 d, ornithine hydrochloride addition is 0.5% (M/V), culture temperature is 28 °C. Under these conditions, the yield of FGFC1 is 1 978.33mg/L, which is consistent with the predicted value. It shows that the experiment is effective.