• Journal of Microbiology and Biotechnology
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• v.17 no.3
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• pp.496-510
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• 2007

This paper describes the use of a discrete mathematical model to represent the basic mechanisms of regulation of the bacteria E. coli in batch fermentation. The specific phenomena studied were the changes in metabolism and genetic regulation when the bacteria use three different carbon substrates (glucose, glycerol, and acetate). The model correctly predicts the behavior of E. coli vis-a-vis substrate mixtures. In a mixture of glucose, glycerol, and acetate, it prefers glucose, then glycerol, and finally acetate. The model included 67 nodes; 28 were genes, 20 enzymes, and 19 regulators/biochemical compounds. The model represents both the genetic regulation and metabolic networks in an integrated form, which is how they function biologically. This is one of the first attempts to include both of these networks in one model. Previously, discrete mathematical models were used only to describe genetic regulation networks. The study of the network dynamics generated 8 $(2^3)$ fixed points, one for each nutrient configuration (substrate mixture) in the medium. The fixed points of the discrete model reflect the phenotypes described. Gene expression and the patterns of the metabolic fluxes generated are described accurately. The activation of the gene regulation network depends basically on the presence of glucose and glycerol. The model predicts the behavior when mixed carbon sources are utilized as well as when there is no carbon source present. Fictitious jokers (Joker1, Joker2, and Repressor SdhC) had to be created to control 12 genes whose regulation mechanism is unknown, since glycerol and glucose do not act directly on the genes. The approach presented in this paper is particularly useful to investigate potential unknown gene regulation mechanisms; such a novel approach can also be used to describe other gene regulation situations such as the comparison between non-recombinant and recombinant yeast strain, producing recombinant proteins, presently under investigation in our group.

• Biotechnology and Bioprocess Engineering:BBE
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• v.3 no.1
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• pp.11-14
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• 1998

A toluene-oxidizing strain of Pseudomanas mendocina KR1 containing toluene-4-mono-oxygenase (TMO) completely degrades TCE with the addition of toluene as a co-substrate in aerobic condition. In order to construct in situ bioremediation system for TCE degradation without any growth-stimulating nutrients or toxic inducer such as toluene, we used the carbon-starvation promoter of Pseudomonas putida MK1 (Kim, Y. et al., J. bacteriol., 1995). Upon entry into the stationary phase due to the deprivation of nutrients, this promoter is strongly induced without further cell growth. The TMO gene cluster (4.5 kb) was spliced downstream of the carbon starvation promoter of Pseudomonas putida MK1, already cloned in pUC19. TMO under the carbon starvation promoter was not expressed in E. coli cells either in stationary phase or exponential phase. For TMO expression in Pseudomonas strains, tmo and carbon starvation promoter region were recloned into a modified broad-host range vector pMMB67HES which was made from pMMB67HE(8.9 kb) by deletion of tac promoter and lacIq (about 1.5 kb). Indigo was produced by TMO under the carbon starvation promoter in a Pseudomonas strain of post-exponential phase on M9 (0.2% glucose and 1mM indole) or LB. 18% of TCE was degraded in 14 hours after entering the stationary phase at the initial concentration of 6.6 ${\mu}$M in liquid phase.

• International Journal of Industrial Entomology and Biomaterials
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• v.21 no.1
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• pp.127-132
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• 2010

We have characterized full-length cDNA encoding Gall-6-tox protein, which was cloned from the fat body of the immunized Galleria mellonella larvae. The cloned cDNA of Gall-6-tox consists of 1301 nucleotides and contained an open reading frame of 891 nucleotides corresponding to a protein of 296 residues that includes a putative 16-residue signal sequence and a 280-residue mature peptide with a calculated mass of 30,707.73 Da. The deduced mature peptide contains conserved tandem repeats of six cysteine-stabilized alpha beta ($Cs{\alpha}{\beta}$) motifs, which was detected in scorpion toxins and insect defensins. In the sequence homology search, mature Gall-6-tox showed 34% and 28% amino acid sequence homology with Bomb-6-tox from Bombyx mori and Spod-11-tox from Spodoptera frugiperda, respectively. Gall-6-tox orthologs were only found in Lepidopteran species, indicating that this new immune-related gene family is specific to this insect order. RT-PCR analysis revealed that Gall-6-tox was expressed primarily in the larval fat bodies, hemocytes, and midgut against invading bacteria into hemocoel. Moreover, the expression time course of Gall-6-tox was examined up to 24 h in the fat bodies and midgut after injection of E. coli. Altogether, these results suggest that Gall-6-tox is derived from defensins and Gall-6-tox may play a critical role in Lepidoptera immune system.

• Journal of Microbiology and Biotechnology
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• v.20 no.2
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• pp.375-382
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• 2010

The available techniques for heterologous protein secretion in Lactobacillus strains are limited. The aim of the present study was to develop an efficient protein-secretion system using recombinant lactobacilli for various applications such as live delivery of biotherapeutics. For the construction of expression vectors, the Lactobacillus brevis slpA promoter, Lactobacillus casei prtP signal sequence, and mouse IL-10 sequences were used as a model system. Interestingly, the slpA promoter exhibited strong activity in L. casei, contrary to previous observations. In order to stabilize replication of the plasmid in E. coli, a removable terminator sequence was built into the promoter region. For the improvement of secretion efficiency, a DTNSD oligopeptide was added to the cleavage site of signal peptidase. The resulting plasmids provided remarkably efficient IL-10 secretion. Accumulation of the protein in the culture supernatant varied widely according to the pH conditions. By analysis of the secreted protein, formation of homodimers, and biological activity, IL-10 was confirmed to be functional. The presently constructed plasmids could be useful tools for heterologous protein secretion in L. casei.

• BMB Reports
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• v.40 no.3
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• pp.333-340
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• 2007

Gene encoding cyclodextrin glycosyltransferase (CGTase), from thermotolerant Paenibacillus sp. T16 isolated from hot spring area in northern Thailand, was cloned and expressed in E. coli (JM109). The nucleotide sequences of both wild type and transformed CGTases consisted of 2139 bp open reading frame, 713 deduced amino acids residues with difference of 4 amino acid residues. The recombinant cells required 24 h culture time and a neutral pH for culture medium to produce compatible amount of CGTase compared to 72 h culture time and pH 10 for wild type. The recombinant and wild-type CGTases were purified by starch adsorption and phenyl sepharose column chromatography and characterized in parallel. Both enzymes showed molecular weight of 77 kDa and similar optimum pHs and temperatures with recombinant enzyme showing broader range. There were some significant difference in pH, temperature stability and kinetic parameters. The presence of high starch concentration resulted in higher thermostability in recombinant enzyme than the wild type. The recombinant enzyme was more stable at higher temperature and lower pH, with lower $K_m$ for coupling reaction using cellobiose and cyclodextrins as substrates.

• Journal of Microbiology and Biotechnology
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• v.16 no.7
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• pp.1163-1168
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• 2006

The recombinant plasmid pLEX2FP complements the mutation in Zoogloea ramigera 115MM1, and the complemented mutant produces an exopolysaccharide that shows higher affinity for the calcofluor dye than the exopolysaccharide from Z. ramigera 115SLR, resulting in higher fluorescence intensity under UV light. A compositional and structural analysis of the exopolysaccharide from Z. ramigera 115MM1 showed that the different fluorescent properties were due to a lower content of acetyl groups when compared with Z. ramigera 115SLR exopolysaccharide. These results were in agreement with a sequence analysis of the gene carried in the plasmid pLEX2FP, which appeared to encode an O-acyltransferase highly homologous to the 3-O-acyltransferase of Streptomyces mycarofaciens. The gene encoding the acyltransferase from Z. ramigera 115SLR was expressed as a GST-fusion protein with 70,000 daltons in E. coli.

• KSBB Journal
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• v.16 no.6
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• pp.562-567
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• 2001

Aspergillus niger LK harboring the enantioselective epoxide hydrolase (EHase) activity was isolated, and enantioselectivity of EHase was tested for various racemic aromatic epoxides. The gene encoding epoxide hydrolase was cloned from cDNA library generated by reverse transcriptase-polymerase chain reaction of the isolated total mRNA. Sequence analysis showed that the cloned gene encodes 398 amino acids with a deduced molecular mass of 44.5 kDa. Database comparison of the amino acid sequence reveals that it is similar to fungal EHase, whereas the sequence identity with bacterial EHase is very low. Recombinant expression of the cloned EHase in Escherichia coli BL21 yielded an active EHases, which can offer a potential biocatalyst for the production of chiral epoxides.

• Asian-Australasian Journal of Animal Sciences
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• v.12 no.1
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• pp.77-83
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• 1999

Molecular biological techniques that recently developed, have made it possible to realize some of new attempts in the research field of rumen microbiology. Those are 1) cloning of genes from rumen microorganisms mainly in E. coli, 2) transformation of rumen bacteria and 3) ecological analysis with nonculturing methods. Most of the cloned genes are for polysaccharidase enzymes such as endoglucanase, xylanase, amylase, chitinase and others, and the cloning rendered gene structural analyses by sequencing and also characterization of the translated products through easier purification. Electrotransformation of Butyrivibrio fibrisolvens and Prevotella ruminicola have been made toward the direction for obtaining more fibrolytic, acid-tolerant, depoisoning or essential amino acids-producing rumen bacterium. These primarily required stable and efficient gene transfer systems. Some vectors, constructed from native plasmids of rumen bacteria, are now available for successful gene introduction and expression in those rumen bacterial species. Probing and PCR-based methodologies have also been developed for detecting specific bacterial species and even strains. These are much due to accumulation of rRNA gene sequences of rumen microbes in databases. Although optimized analytical conditions are essential to reliable and reproducible estimation of the targeted microbes, the methods permit long term storage of frozen samples, providing us ease in analytical work as compared with a traditional method based on culturing. Moreover, the methods seem to be promissing for obtaining taxonomic and evolutionary information on all the rumen microbes, whether they are culturable or not.

• 한국생물공학회:학술대회논문집
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• 2003.04a
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• pp.545-549
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• 2003

After irradiation of a cloned dextransucrase gene (dsrB742) with ultrasoft X-ray, an E. coli transformant (pDSRB742CK) was first developed for the expression of an extracellular dextransucrase, having increased activity and the synthesis of a highly branched dextran. Seven nucleotides of the parent gene (dsrB742) were changed in the nucleotide sequences of dsrB742ck. Among them, four nucleotides were changed at the ORF of dsrB742, resulting in a 30 amino acids deletion in the N-terminal of DSRB742 dextransucrase. The activity of DSRB742CK dextransucrase in culture supernatant was approximately 2.6 times higher (0.035 IU/ml) than that of the DSRB742 clone. The pDSRB742CK clone produced DSRB742CK dextransucrase when grown both on a sucrose medium (inducibly) and on a glucose medium (constitutively). The DSRB742 clone did not produce dextran constitutively on a glucose medium. DSRB742CK dextran had 15.6% branching and 2.7-times higher resistance to dextranase hydrolysis compared to DSRB742 dextran. $^{13}C-NMR$ showed that DSRB742CK dextran contained ${\alpha}-(1{\rightarrow}3)$ branch linkages that were not present in DSRB742 dextran.

• Korean Journal of Veterinary Research
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• v.37 no.3
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• pp.547-554
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• 1997

Galectin-3 is known as an animal ${\beta}$-galactoside-binding lectin charicterized with S-type carbohydrate recognition domain. It plays a role in growth, adherence and movement of cells. It is, also, related to the cell transformation and metastasis of tumor cells. In this study, we have expressed and purified recombinant human galectin-3 (rHgalectin-3) using E coli system and asialofetuin affinity chromatography for the future development of monoclonal antibody to Hgalectin-3, which is suggested as the tumor marker for the gastric and thyroid gland cancers. Expressed protein was confirmed as the Hgalectin-3 by immunoblot with cross-reactive murine monoclonal antibody. Lectin activity and specificity of purified protein were, also, confirmed by the competitive inhibition with galectin-3 specific carbohydrate, lactose. Like physiological galectin-3, lectin activity of the molecule was not changed in nonreduced condition. Dimer formation, furthermore, was observed at high concentration of the protein even in the reduced condition, which is well known in physiological galectin-3. These results showed purified rHgalectin-3 has the same activity and molecular nature compared to the physiological galectin-3.