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Gene knockout strategies for metabolic pathway regulation in industrial microbes.

Chinese Journal of Biotechnology.2010;26(9):1199-1208.

Gene knockout, an important technology in molecular biology, has been broadly applied in industrial microbial metabolic engineering. From the basic mechanism of DNA recombination, we summarized and compared in this review different gene knockout strategies. Three most hot and important approaches, including the lambda Red recombination system using the linear dsDNA as recombination substrate, the single or double crossover homologous recombination using the circular plasmid DNA as substrate, and the transposase mediated transposition recombination, were summarized in detail. Developing frontiers and application prospects of gene knockout were further discussed.
Biotechnology ; methods ; Gene Knockout Techniques ; methods ; Industrial Microbiology ; methods ; Metabolic Engineering ; methods ; Metabolic Networks and Pathways

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Transcriptome platforms and applications to metabolic engineering.

Shuobo SHI ; Tao CHEN ; Xueming ZHAO

Chinese Journal of Biotechnology.2010;26(9):1187-1198.

Omics technologies have profoundly promoted development and applications of metabolic engineering by analysis of cell metabolism at a system level. Whole genome transcription profiles have provided researchers more rigorous evaluation of cell phenotype and an increased understanding of cellular metabolism. Furthermore, transcriptome analysis can conduce to identification of effective gene targets for strain improvement, and consequently accelerates rational design and construction of microbial cell factories for desired product. In this review, we briefly introduced the principle of three main platforms of transcriptome, and reviewed the recent applications of the transcriptome to metabolic engineering, finally provided conclusions and future prospects.
Biotechnology ; methods ; Genomics ; methods ; Industrial Microbiology ; methods ; Metabolic Engineering ; methods ; Metabolic Networks and Pathways ; Transcriptome

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Reconstruction and application of genome-scale metabolic network model.

Liming LIU ; Jian CHEN

Chinese Journal of Biotechnology.2010;26(9):1176-1186.

The exploitation of microbial manufacture process (MMP) in industrial biotechnology requires a comprehensive understanding and an efficient modification of microorganism physiology. The availability of genome sequences and accumulation of -omics data allow us to understand of microbial physiology at the systems level, and genome-scale metabolic model (GSMM) represents a valuable framework for integrative analysis of metabolism of microorganisms. Genome scale metabolic models are reconstructed based on a combination of genome sequence and the more detailed biochemical knowledge, and these reconstructed models can be used for analyzing and simulating the operation of metabolism in response to different perturbations. Here we describe the reconstruction protocols for GSMM in further detail and provide the perspective of GSMM.
Biotechnology ; methods ; Genetic Engineering ; Genomics ; methods ; Industrial Microbiology ; Metabolic Networks and Pathways ; physiology ; Models, Biological

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Industrial biotechnology in the post-genomic era.

Yanping ZHANG ; Yin LI

Chinese Journal of Biotechnology.2010;26(9):1171-1175.

The background and the importance of developing industrial biotechnology were illustrated, followed by a brief analysis on the driving effect of genomics and functional genomics. Seventeen papers covering metabolic engineering, fermentation engineering, industrial enzymes and biocatalysis are published in this special issue. These papers were briefly introduced to show the most recent developments of industrial biotechnology.
Biocatalysis ; Bioelectric Energy Sources ; Biotechnology ; methods ; trends ; Genetic Engineering ; methods ; Genomics ; methods ; Industrial Microbiology ; methods

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Chromatography-assisted refolding of a fusion protein containing multiple disulfide bonds.

Weiquan XIE ; Guifeng ZHANG ; Ling GAO ; Yongdong LIU ; Rong YU ; Zhiguo SU

Chinese Journal of Biotechnology.2010;26(8):1157-1164.

To establish a refolding process for the protein fused with 12-peptide of hirudin and reteplase (HV12p-rPA), we developed an anion-exchange chromatography assisted method to form correct disulfide bonds. After evaluating various parameters by orthogonal experiments with Q Sepharose XL as refolding medium, we found that urea gradient, sample loading size and L-Arg concentration were three major factors to affect the refolding outcomes, and urea gradient was critical to the recovery yield. Meanwhile, enzymatic activity of the refolded protein was decreased by the increase of sample loading size, and the optimal concentration of L-Arg in the eluting buffer was 1 mol/L. Thus, a dual-gradient of urea and pH on the anion-exchange chromatography resulted in remarkable increase of specific fibrinolytic and anti-coagulative activities of the refolded protein. Compared with the dilution method for refolding HV12p-rPA, the present approach was more effective and advantageous.
Chromatography, Ion Exchange ; methods ; Disulfides ; chemistry ; Fibrinolytic Agents ; analysis ; chemistry ; Hirudins ; analysis ; chemistry ; Protein Refolding ; Recombinant Fusion Proteins ; analysis ; chemistry ; Recombinant Proteins ; analysis ; chemistry ; Tissue Plasminogen Activator ; analysis ; chemistry

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Chemiluminescent immunoassay for high-sensitivity C-reactive protein.

Pingguo LIU ; Guoqiang LI ; Yixin CHEN ; Haifeng LUO ; Dedang HUANG ; Yingbin WANG ; Shengxiang GE ; Jun ZHANG ; Ningshao XIA

Chinese Journal of Biotechnology.2010;26(8):1150-1156.

We developed a high-sensitivity C-reactive protein quantifiable chemiluminescent immunoassay (hs-CRP CLIA). The high-purity native CRP was purified from hepatic cirrhosis patient ascetic fluid by affinity and ion exchange chromatography and used as an immunogen to develop the monoclonal antibodies (mAbs) against CRP. Twenty-two mAbs were identified reactive with CRP in ELISA and 13 of them were reactive in the phosphorycholine ligand capture ELISA. The mAbs 10C5 and 10C11 were selected to develop the hs-CRP CLIA. The linearity and performance of the hs-CRP CLIA was characterized. It was showed not reactive when testing against other serum materials (IgG, hemoglobin and triglyceride). The reliable correlation (R2 > 0.993) was obtained between testing value (RLU/S) and the concentration of human serum CRP calibrator. The linearity fell in the range of 0.04-20.38 mg/L. The assay has good accuracy and reproducibility, the mean recovery was 99% and the precision of the intra- and inter assay was CVs (4.2%-5.8%) and (9.0%-11.5%), respectively. In testing of 90 human sera, this assay performed well and correlated comparably with a commercial hs-CRP ELISA kit. Thus, hs-CRP CLIA is an accurate, reliable, quantifiable assay for detection of high-sensitive C-reactive protein in serum, it may be useful to improve the risk assessment of cardiovascular disease and the prognosis of inflammatory bowel disease.
C-Reactive Protein ; analysis ; chemistry ; Humans ; Immunoassay ; methods ; Luminescent Measurements ; methods ; Sensitivity and Specificity

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Effect of trehalose on the freeze-dried boar spermatozoa.

Xiangqian MENG ; Xiaolong GU ; Caifeng WU ; Jianjun DAI ; Tingyu ZHANG ; Yini XIE ; Zhiqiang WU ; Liang LIU ; Hengdong MA ; Defu ZHANG

Chinese Journal of Biotechnology.2010;26(8):1143-1149.

After freeze-drying, the ultrastructure of boar sperms was observed by optical and electron microscopy. The in vitro development ability of the sperm was also examined with intracytoplasmic sperm injection (ICSI). The rate of male pronuclear formation was (68.52%), for cleavage (59.17%) and for blastocyst formation (19.16%) of the trehalose group (0.2 mol/L), significantly higher than those of the 50 mmol/L EDTA group (64.59%, 56.26% and 15.62%) and the control group (35.36%, 52.33% and 8.60%) (P < 0.05). After storage for 60, 120 and 180 d at 4 degrees C, no significant difference in the in vitro development was observed (P > 0.05). The male pronuclear, cleavage and blastocyst formation after ICSI with freeze-dried spermatozoa incubated for 1 h was superior than those incubated for 2 h (P < 0.05). No significant differences in the structures after stored at 4 degrees C or -20 degrees C (P > 0.05) were observed between the trehalose group and EDTA group. The percent of B grade freeze-dried boar spermatozoa in the trehalose group was higher than that of the EDTA group (P < 0.05). Based on the ultrastructure observation, main cryogenic damage in freeze-dried boar spermatozoa was swelling, damage or rupture in the sperm acrosome, neck and tail.
Animals ; Freeze Drying ; Male ; Semen Preservation ; methods ; veterinary ; Sperm Injections, Intracytoplasmic ; veterinary ; Spermatozoa ; Swine ; Trehalose ; pharmacology

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Membrane transfer-based colorimetric DNA detection using enzyme modified gold nanoparticles.

Haiyan LI ; Fengxiang JING ; Qiuyue GAO ; Chunping JIA ; Jiwu CHEN ; Qinghui JIN ; Jianlong ZHAO

Chinese Journal of Biotechnology.2010;26(8):1135-1142.

We report here a novel membrane transfer-based DNA detection method, in which alkaline phosphatase labeled gold nanoparticle (AuNP) probes were used as a means to amplify the detection signal. In this method, the capture probe P1, complimentary to the 3' end of target DNA, was immobilized on the chip. The multi-component AuNP probes were prepared by co-coating AuNPs with the detecting probe P2, complimentary to the 5' end of target DNA, and two biotin-labeled signal probes (T10 and T40) with different lengths. In the presence of target DNA, DNA hybridization led to the attachment of AuNPs on the chip surface where specific DNA sequences were located in a "sandwich" format. Alkaline phosphatase was then introduced to the surface via biotine-streptavidin interaction. By using BCIP/NBT alkaline phosphatase color development kit, a colorimetric DNA detection was achieved through membrane transfer. The signal on the membrane was then detected by the naked eye or an ordinary optical scanner. The method provided a detection of limit of 1 pmol/L for synthesized target DNA and 0.23 pmol/L for PCR products of Mycobacterium tuberculosis 16S rDNA when the ratio of probes used was 9:1:1 (T10:T40:P2). The method described here has many desirable advantages including high sensitivity, simple operation, and no need of sophisticated equipment. The method can be potentially used for reliable biosensings.
Colorimetry ; methods ; DNA Probes ; chemistry ; genetics ; DNA, Bacterial ; genetics ; Gold ; chemistry ; Humans ; Metal Nanoparticles ; chemistry ; Mycobacterium tuberculosis ; isolation & purification ; Nucleic Acid Hybridization ; methods ; Oligonucleotide Array Sequence Analysis ; methods

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Fusion expression of fibrinolytic enzyme gene PPFE-I from endophytic Paenibacillus polymyxa in Escherichia coli and activity analysis.

Fengxia LÜ ; Zhaoxin LU ; Xiaomei BIE ; Qian LIN ; Chong ZHANG ; Lin CAO ; Yao GUO ; Yanchong TANG

Chinese Journal of Biotechnology.2010;26(8):1128-1134.

With the genomic DNA of strain EJS-3 as the template, we amplified the gene of fibrinolytic enzyme from Paenibacillus polymyxa (PPFE-I) by PCR. We purified the PCR product and ligated it into pMD19-T. After DNA sequencing, we cloned the PPFE-I gene into expression vector pET-DsbA and transformed it into Escherichia coli BL21(DE3). Upon induction of IPTG, we found that the activity of recombinant fibrinolytic enzyme fused with DsbA expressed in Escherichia coli was 228 IU/mL. SDS-PAGE analysis showed that the recombinant enzyme was soluble and accounted for about 18.4% of total cell protein. Western blotting demonstrated that the recombinant protein was DsbA-PPFE-I. We purified the recombinant enzyme by Ni affinity chromatography, thrombin digestion and sephadex G-100 gel-filtration, and identified the molecular weight of purified product to be 66.3 kDa with MALDI-TOF mass spectrometry. The purified enzyme exhibited distinct fibrinolytic activity on fibrin plate.
Antifibrinolytic Agents ; pharmacology ; Cloning, Molecular ; Escherichia coli ; genetics ; metabolism ; Fibrinolytic Agents ; metabolism ; Genetic Vectors ; genetics ; Paenibacillus ; chemistry ; enzymology ; Recombinant Fusion Proteins ; biosynthesis ; genetics ; pharmacology

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Characterization and culture of isolated primary dairy goat mammary gland epithelial cells.

Zhen WANG ; Jun LUO ; Wei WANG ; Wangsheng ZHAO ; Xianzi LIN

Chinese Journal of Biotechnology.2010;26(8):1123-1127.

Based on the in vitro culturing system developed for epithelial cells in mammary gland of Xinong Saanen dairy goats using tissue explant culture, high density cultivation, and continuous passaging, the cultured epithelial cells were evaluated by growth curve fitting, karyotype analysis, immunofluorescence staining (keratin, epithelial membrane antigen (EMA), vimentin, beta-casein), oil red staining and RT-PCR of beta-casein gene. The results showed that the growth of epithelial cells with the model number of chromosome of 60 demonstrated a typical 'S' shape curve, the positive gene expression of keratin, EMA, vimentin and beta-casein was detected, the cytoplasmic lipid droplets were observed following the oil red staining, the cultured cells expressed the mRNA of beta-casein. In conclusion, the current in vitro culturing system can obtain the normal mammary gland epithelial cells with the function of secretion.
Animals ; Cell Separation ; methods ; Cells, Cultured ; Epithelial Cells ; cytology ; Female ; Goats ; Mammary Glands, Animal ; cytology ; Primary Cell Culture ; methods

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