• Microbiology and Biotechnology Letters
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• v.17 no.4
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• pp.295-300
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• 1989

Screening of Pseudomonas strains that can be used as hosts for expression of crystal protein gene of Bacillus thuringiensis subsp. kurstaki HD-73 was carried out. From rhizosphere soil of 7 kinds or crops as fluorescent Pseudomonas strains were isolated. A hybrie plasmid, pKTC1, composed of the broad host range vector pKT230 and the crystal protein gene was constructed and used for transformation of the 35 Pseudomonas strains. As the result, the crystal protein gene could be introduced into 4 isolates. Several methods including bioassay and immunochemical detection indicated that the crystall protein gene was expressed in the Pseudomonus isolates.

• Journal of Microbiology and Biotechnology
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• v.12 no.5
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• pp.826-828
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• 2002

In our previous studies, we have cloned and characterized a gene region from Bradyrhizobium japonicum ,which is involved in the synthesis of lipopolysaccharide (LPS). In this study, we have expanded the sequence analysis of the region and found an additional open reading frame (orf), which appeared to be divergently transcribed from the rfaF gene. Sequence alignment of the orf revealed a significant similarity with rfaD genes of Salmonella typhimurium , Escherichia coli, and Neisseria gonorrhoeae. These genes encode a heptose-6-epimerase, which catalyzes the interconversion of ADP -D -glycerol-D-manno-heptose to ADP-L-glycero-D-manno-heptose. This divergent organization of the rfaF and rfaD genes is different from that of other Gram-negative bacteria where two genes form an operon. A rfaD- mutant of E. coli was successfully transformed with plasmid constructs containing the rfaD gene of B. japonicum. Novobiocin sensitivity test showed that the rfaD gene from B. japonicum could complement the rfaD mutation in E. coli, which confirms the functionality of the cloned B. japonicum gene.

• Journal of Microbiology and Biotechnology
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• v.3 no.4
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• pp.224-231
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• 1993

The nucleotide sequence of the xylanase gene (xynY) from alkalophilic Bacillus sp. YC-335 was determined and analyzed. An open reading frame of 1, 062 base pairs for xynY gene was observed and encoded for a protein of 354 amino acids with a molecular weight of 38, 915. S1 nuclease mapping showed that the transcription initiation sites of the xynY gene were different in Bacillus sp. YC-335 and Escherichia coli HB101 (pYS55). S1 mapping also showed that -10 region of the xynY gene recognized by RNA polymerases of E. coli and Bacillus sp. YC-335 were TACAGT and TATGAT , respectively. A ribosome binding site sequence with the free energy of -17.0 Kcal/mol was observed 9 base pairs upstream from the unusual initiation codon, TTG. The proposed signal sequence consisted of 27 amino acids, 2 of which were basic amino acid residues and 21 were hydrophobic amino acid residues. When the amino acid sequences of xylanases were compared, Bacillus sp. YC-335 xylanase showed more than 50% homology with xylanases from B. pumilus, B. subtilis, and B. circulans.

• Journal of Microbiology and Biotechnology
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• v.22 no.6
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• pp.793-799
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• 2012

A gene related to high pristinamycin yield in Streptomyces pristinaespiralis was selected by amplified fragment length polymorphism (AFLP) and its functions were investigated by gene disruption. First, a 561 bp polymorphic sequence was acquired by AFLP from high-yield recombinants compared with the S. pristinaespiralis ancestor ATCC25486, indicating that this approach is an effective means of screening for valuable genes responsible for antibiotic yield. Then, a 2,127 bp open reading frame of a gene designated spy1 that overlaps with the above fragment was identified and its structure and biological functions were investigated. In silico analysis of spy1 encoding a deduced 708-amino-acid-long serine/threonine protein kinase showed that it only contains a catalytic domain in the N-terminal region, which is different from some known homologs. Gene inactivation of chromosomal spy1 indicated that it plays a pleiotropic regulatory function in pristinamycin production, with a positive correlation to pristinamycin I biosynthesis and a negative correlation to pristinamycin II biosynthesis.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.63-68
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• 2005

Transcription factors regulate gene expression by binding to gene upstream region. Each transcription factor has the specific binding site in promoter region. So the analysis of gene upstream sequence is necessary for understanding regulatory mechanism of genes, under a plausible idea that assumption that DNA sequence motif profiles are closely related to gene expression behaviors of the corresponding genes. Here, we present an effective approach to the analysis of the relation between gene expression profiles and gene upstream sequences on the basis of kernel canonical correlation analysis (kernel CCA). Kernel CCA is a useful method for finding relationships underlying between two different data sets. In the application to a yeast cell cycle data set, it is shown that gene upstream sequence profile is closely related to gene expression patterns in terms of canonical correlation scores. By the further analysis of the contributing values or weights of sequence motifs in the construction of a pair of sequence motif profiles and expression profiles, we show that the proposed method can identify significant DNA sequence motifs involved with some specific gene expression patterns, including some well known motifs and those putative, in the process of the yeast cell cycle.

• Journal of the Korean Institute of Intelligent Systems
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• v.17 no.5
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• pp.707-711
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• 2007

Microarray gene expression data is believed to show the functions of living organism through the gene expression values. We have studied a method to get the informative genes from the microarray gene expression data. There are several ways for this. In recent researches to get more sophisticated and detailed results, it has used the intelligence information theory like fuzzy theory. Some methods are to add fudge factors to the significance test for more refined results. In this paper, we suggest a method to get informative genes from microarray gene expression data. We combined the difference of means between two groups and the fuzzy membership degree which reflects the variance of the gene expression data. We have called our significance test the Fuzzy Information method for Gene Expression data(FIGER). The FIGER calculates FIGER variation ratio and FIGER membership degree to show how strongly each object belongs to the each group and then it results in the significance degree of each gene. The FIGER is focused on the variation and distribution of the data set to adjust the significance level. Out simulation shows that the FIGER-test is an effective and useful significance test.

• Journal of Microbiology and Biotechnology
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• v.18 no.2
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• pp.334-337
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• 2008

A tightly regulated gene expression system composed of a single-copy target gene under the control of a lac promoter derivative and lacI gene in a multicopy plasmid is proposed, and its ability to control the flux of a metabolic pathway is demonstrated. A model system to control the flux of acetyl-CoA to acetyl phosphate was constructed by integrating pta, a gene encoding phosphotransacetylase, under a tac promoter into the chromosome of E. coli with a pta-negative background and transforming a multicopy plasmid containing the $lacI^Q$ gene into the strain. The production rate of acetate was shown to be tightly controlled when varying the concentration of the inducer (IPTG) in he model system.

• BMB Reports
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• v.32 no.1
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• pp.72-75
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• 1999

In an effort to understand the function of the eryBVII gene in the erythromycin biosynthetic gene cluster, we overexpressed the eryBVII gene in E. coli and TDP-6-deoxy-L-threo-D-glycero-4-hexulose was used as a substrate of the overexpressed EryBVII enzyme. The enzymatic reaction product was chemically modified by reduction and peracetylation. Structural analysis of the derivatized enzymatic products by GC-Mass Spectrophotometry indicated that TDP-6-deoxy-L-threo-D-glycero-4-hexulose could be converted into its epimer by EryBVII enzyme. Based on this result, TDP-6-deoxy-L-threo-D-glycero-4-hexulose was indeed the substrate of EryBVII enzyme and the function of the eryBVII gene was confirmed.

• Korean Chemical Engineering Research
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• v.47 no.5
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• pp.538-545
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• 2009

The principle and application of a scanning probe microscopy(SPM) are reviewed briefly, and a low-invasive single cell manipulation and a gene delivery technique using an etched atomic force microscopy(AFM) probe tip, which we call a nanoneedle, are explained in detail. The nanoneedle insertion into a cell can be judged by a sudden drop of force in a force-distance curve. The probabilities of nanoneedle insertion into cells were 80~90%, which were higher than those of typical microinjection capillaries. When the diameter of the nanoneedle was smaller than 400 nm, the nanoneedle insertion into a cell over 1 hour had almost no influence on the cell viability. A highly efficient gene delivery and a high ratio of expressed gene per delivered DNA compared the conventional major nonviral gene delivery methods could be achieved using the gene modified nanoneedle.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.9
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• pp.1349-1353
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• 2007

Calcineurin is a calmodulin dependent protein that functions as a regulator of muscle cell growth and function. Agents capable of interacting with calcineurin could have important applications in muscle disease treatment as well as in the improvement of livestock production. Calsarcins comprise a family of muscle-specific calcineurin binding proteins which play an important role in modulating the function of calcineurin in muscle cells. Recently, we described the first two members of the calsarcin family (calsarcin-1 and calsarcin-2) in the pig. Here, we characterized the third member of the calsarcin family, calsarcin-3, which is also expressed specifically in skeletal muscle. However, unlike calsarcin-1 and calsarcin-2, the calsarcin-3 mRNA expression in skeletal muscle kept rising throughout the prenatal and postnatal development periods. In addition, radiation hybrid mapping indicated that porcine calsarcin-3 mapped to the distal end of the q arm of pig chromosome 2 (SSC2). A C/T single nucleotide polymorphism site in exon 5 was genotyped using the denaturing high performance liquid chromatography (DHPLC) method and the allele frequencies at this locus were significantly different among breeds.