• Journal of Microbiology and Biotechnology
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• v.22 no.7
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• pp.930-938
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• 2012

High levels of xylanase activity (143.98 IU/ml) produced by the newly isolated Paenibacillus campinasensis G1-1 were detected when it was cultivated in a synthetic medium. A thermostable xylanase, designated XynG1-1, from P. campinasensis G1-1 was purified to homogeneity by Octyl-Sepharose hydrophobic-interaction chromatography, Sephadex G75 gel-filter chromatography, and Q-Sepharose ion-exchange chromatography, consecutively. By multistep purification, the specific activity of XynG1-1 was up to 1,865.5 IU/mg with a 9.1-fold purification. The molecular mass of purified XynG1-1 was about 41.3 kDa as estimated by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Sequence analysis revealed that XynG1-1 containing 377 amino acids encoded by 1,134 bp genomic sequences of P. campinasensis G1-1 shared 96% homology with XylX from Paenibacillus campinasensis BL11 and 77%~78% homology with xylanases from Bacillus sp. YA-335 and Bacillus sp. 41M-1, respectively. The activity of XynG1-1 was stimulated by $Ca^{2+}$, $Ba^{2+}$, DTT, and ${\beta}$-mercaptoethanol, but was inhibited by $Ni^{2+}$, $Fe^{2+}$, $Fe^{3+}$, $Zn^{2+}$, SDS, and EDTA. The purified XynG1-1 displayed a greater affinity for birchwood xylan, with an optimal temperature of $60^{\circ}C$ and an optimal pH of 7.5. The fact that XynG1-1 is cellulose-free, thermostable (stability at high temperature of $70^{\circ}C{\sim}80^{\circ}C$), and active over a wide pH range (pH 5.0~9.0) suggests that the enzyme is potentially valuable for various industrial applications, especially for pulp bleaching pretreatment.

• Journal of Applied Biological Chemistry
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• v.43 no.1
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• pp.5-11
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• 2000

Three cDNA clones encoding rice calmodulin (CaM) isoforms (OsCaM-1, OsCaM-2, and OsCaM-3) were isolated from a rice cDNA library constructed from suspension-cultured rice cells treated with fungal elicitor. The coding regions of OsCaM-1 and O.sCaM-2 were 89% homologous at DNA Ievel, whereas the 5' and 3' untranslated regions were highly divergent. The polypeptides encoded by OsCaM-1 and OsCaM-2 was identical except two conservative substitution at position 8 and 75. The coding region of OsCaM-3 was consist of a typical conserved CaM domain and an additional C-terminal extension. The amino acid sequence of conserved CaM domain of OsCaM-3 shared only 86% identity with that OsCaM-1. The OsCaM-3 cDNA is belongs to a novel group of calmodulin gene due to its C-terminal extension of 38 amino acids, a large number of which are positively charged. The extension also contains a C-terminal CaaX-box prenylation site (CVlL). Genomic Southern analysis revealed at least six copies of CaM or CaM-related genes, suggesting that calmodulin may be represented by a small multigene family in the rice geneme. Expression of OsCaM gene was examined through Northern blot analysis. Transcript level of OsCaM-3 was increased by treatment with a fungal elicitor, whereas the OsCaM-1 and OsCaM-2 genes did not respond to the fungal elicitor. The expression of OsCaM-3 gene was remarkable inhibited in the rice cells treated with cyclosporine A, calcinurin inhibitor.

• Journal of Microbiology
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• v.43 no.4
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• pp.325-330
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• 2005

Rhodococcus sp. strain YU6 was isolated from soil for the ability to grow on o-xylene as the sole carbon and energy source. Unlike most other o-xylene-degrading bacteria, YU6 is able to grow on p-xylene. Numerous growth substrate range experiments, in addition to the ring-cleavage enzyme assay data, suggest that YU6 initially metabolizes 0- and p-xylene by direct aromatic ring oxidation. This leads to the formation of dimethylcatechols, which was further degraded largely through meta-cleavage path-way. The gene encoding meta-cleavage dioxygenase enzyme was PCR cloned from genomic YU6 DNA using previously known gene sequence data from the o-xylene-degrading Rhodococcus sp. strain DK17. Subsequent sequencing of the 918-bp PCR product revealed a $98\%$ identity to the gene, encoding meth-ylcatechol 2,3-dioxygenase from DK17. PFGE analysis followed by Southern hybridization with the catechol 2,3-dioxygenase gene demonstrated that the gene is located on an approximately 560-kb megaplasmid, designated pJY J1

• Journal of Microbiology
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• v.43 no.4
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• pp.331-336
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• 2005

The objective of this study was to assess the strain-specificity of a DNA probe, Fu12, for Fusobacterium nucleatum subsp. nucleatum ATCC $25586^T$ (F. nucleatum ATCC $25586^T$), and to develop sets of strain-specific polymerase chain reaction (PCR) primers. Strain-specificity was tested against 16 strains of F. nucleatum and 3 strains of distinct Fusobacterium species. Southern blot hybridization revealed that the Fu12 reacted exclusively with the HindIII-digested genomic DNA of F. nucleatum ATCC $25586^T$. The results of PCR revealed that three pairs of PCR primers, based on the nucleotide sequence of Fu12, generated the strain-specific amplicons from F. nucleatum ATCC $25586^T$. These results suggest that the DNA probe Fu12 and the three pairs of PCR primers could be useful in the identification of F. nucleatum ATCC $25586^T$, especially with regard to the determination of the authenticity of the strain.

• Korean Journal of Microbiology
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• v.53 no.2
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• pp.141-143
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• 2017

Caballeronia sordidicola strain PAMC 26577 was isolated from Cladonia sp., a lichen collected from Svalbard Archipelago in the Arctic Ocean. Draft genomic sequences of PAMC 26577 were determined using Illumina and 182 contigs were submitted to GenBank and N50 value was 159,226. The genome of PAMC 26577 was comprised of 8,334,211 base pairs and %G+C content was 59.4. The genome included 8 ribosomal RNA genes and 51 tRNA genes as non-coding sequences. Protein-coding genes were 8,065 in number and they included central metabolism genes as well as butanol/butyrate biosynthesis, polyhydroxybutyrate metabolism, serine cycle methylotrophy genes, and glycogen metabolism. Membrane transporters were more than two-hundreds in number, but sugar phosphotransferase system and TRAP transporters were lacking. PAMC 26577 lacked CRISPR-associated sequences and proteins. No transposable elements were observed and there were only limited number of phage remnant regions with 11 phage-related genes.

• Korean Journal of Plant Tissue Culture
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• v.25 no.4
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• pp.237-243
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• 1998

To understand the tissue specific expression pattern of S RNase genes associated with self-incompatibility in L. peruvianum, two promoter regions of $S_{11}$ and $S_{12}$ RNase genes were compared. Homologous sequences between two S RNase gene promoters were found within 300 bp upstream of transcription start site. Moreover short direct repeat sequences within $S_{11}$ RNase gene promoter existed in the vicinity of 350-500 bp upstream of transcription start site. To identify whether the unique promoter sequences of $S_{11}$ RNase gene confer the tissue specific expression, six deletion fragments for $S_{11}$ genomic gene promoter constructed by PCR were fused to $\beta$-glucuronidase gene, and introduced into various tissues of L. peruvianum by microprojectile bombardment. Transient expression assays indicated that $S_{11}$ RNase gene promoter contained the positive and negative regulatory sequences, which can control the floral tissue-specific expression in L. peruvianum.

• Molecules and Cells
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• v.23 no.3
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• pp.280-286
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• 2007

L-asparaginase (EC 3.5.1.1) catalyzes the hydrolysis of the amide group of L-asparagine, releasing aspartate and $NH_4{^+}$. We isolated a low temperature-inducible cDNA sequence encoding L-asparaginase from soybean leaves. The full-length L-asparaginase cDNA, designated GmASP1, contains an open reading frame of 1,258 bp coding for a protein of 326 amino acids. Genomic DNA blotting and fluorescence in situ hybridization showed that the soybean genome has two copies of GmASP1. GmASP1 mRNA was induced by low temperature, ABA and NaCl, but not by heat shock or drought stress. E. coli cells expressing recombinant GmASP1 had 3-fold increased L-asparaginase activity. A possible function of L-asparaginase in the early response to low temperature stress is discussed.

• Journal of Genetic Medicine
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• v.7 no.2
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• pp.119-124
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• 2010

More than 7,000 rare Mendelian diseases have been reported, but less than half of all rare monogenic disorders has been discovered. In addition, the majority of mutations that are known to cause Mendelian disorders are located in protein-coding regions. Therefore, exome sequencing is an efficient strategy to selectively sequence the coding regions of the human genome to identify novel genes associated with rare genetic disorders. The "exome" represents all of the exons in the human genome, constituting about 1.5% of the human genome. Exome sequencing is carried out by targeted capture and intense parallel sequencing. After the first report of successful exome sequencing for the identification of causal genes and mutations in Freeman Sheldon syndrome, exome sequencing has become a standard approach to identify genes in rare Mendelian disorders. Exome sequencing is also used to search the causal genes and variants in complex diseases. The successful use of exome sequencing in Mendelian disorders and complex diseases will facilitate the development of personalized genomic medicine.

• Korean Journal of Ecology and Environment
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• v.47 no.spc
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• pp.39-47
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• 2014

Sponge in Lake Baikal is an unique organism. Microorganisms in sponges are assumed as precious resources for bioactive materials. For understanding the bacterial community in Baikalian sponges by cultivation, 92 strains of bacteria were isolated from lake water and 2 species of sponges, Baikalospongia sp. and Lubomirskia sp., Thirty five bacterial strains are isolated from ambient water near the sponge, 27 bacterial strains from Baikalospongia sp., 30 bacterial strains from Lubomirskia sp.. As a result, 78.3% and 57.6% of isolated bacterial strains has amylase and protease activity respectively, while strains with cellulose and lipase activities were 38.0% and 34.8%. By 16S rRNA sequence analysis of selected strains, 13 strains which were isolated from Baikalospongia sp. were belong to Pseudomonas spp.. Whereas, 14 strains which were isolated from Lubomirskia sp. were Pseudomonas spp., Buttiauxella agrestis, Pseudomonas fluorescens, Yersinia ruckeri, Bacillus spp., Paenibacillus spp., Bacillus thuringiensis, Bacillus simplex, Brevibacterium spp., Acinetobacter lwoffii. In culture media, Pseudomonas spp. dominance was supposed that according to allelophathy.

• Journal of fish pathology
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• v.25 no.3
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• pp.173-180
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• 2012

Vibriosis is one of the most prevalent fish disease belonging to the genus Vibrio. In present study, Vibrio sp. isolated from Japanese eel was confirmed as Vibrio scophthalmi using analysis of the genomic sequence of 16S rRNA. The major signs were hemorrhage of body surface and inner surface of abdomen, severe enteritis and retention of ascitis. Histopathological examination revealed blood cell degenerations in various organs (gills, liver, spleen, kidney, heart, intestine), exfoliate of intestinal epithelium, and congestion and hemorrhage in intestinal lamina propria. This is the first case report on V. scophthalmi infection in Japanese eel Anguilla japonica.