• Journal of Microbiology and Biotechnology
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• v.17 no.3
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• pp.481-489
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• 2007

[ $\alpha$ ]-L-Arabinofuranosidases (AFases; EC 3.2.1.55) are exo-type enzymes, which hydrolyze terminal nonreducing arabinose residues from various polysaccharides such as arabinan and arabinoxylan. Genome-wide BLAST search showed that various bacterial strains possess the putative AFase genes with well-conserved motif sequences at the nucleotide and amino acid sequence levels. In this study, two sets of degenerate PCR primers were designed and tested to detect putative AFase genes, based on their three highly conserved amino acid blocks (PGGNFV, GNEMDG; and DEWNVW). Among 20 Bacillus-associated species, 13 species were revealed to have putative AFase genes in their genome and they share over 67% of amino acid identities with each other. Based on the partial sequence obtained from an isolate, an AFase from Geobacillus sp. was cloned and expressed in E. coli. Enzymatic characterization has verified that the resulting enzyme corresponds to a typical AFase. Accordingly, degenerate PCR primers developed in this work can be used for fast, easy, and specific detection and isolation of putative AFase genes from bacterial cells.

• Journal of Species Research
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• v.6 no.1
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• pp.25-41
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• 2017

As a subset study for the collection of Korean indigenous prokaryotic species, 62 bacterial strains belonging to the phylum Actinobacteria were isolated from various sources. Each strain showed higher 16S rRNA gene sequence similarity (>98.75%) and formed a robust phylogenetic clade with closest species of the phylum Actinobacteria which were defined with valid names, already. There is no official description on these 62 actinobacterial species in Korea. Consequently, unrecorded 62 species of 25 genera in the 14 families belonging to the order Actinomycetales of the phylum Actinobacteria were found in Korea. Morphological properties, basic biochemical characteristics, isolation source and strain IDs are described in the species descriptions.

• Korean Journal of Microbiology
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• v.52 no.4
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• pp.500-502
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• 2016

Several bacterial species have been reported to be surviving after the ionizing radiation treatment due to the presence of sophisticated enzymes systems and some endospores producing bacterial strains can also resist, due to the presence of thick spore coat. In this study, we report the complete genome sequence of a bacterium Paenibacillus swuensis $DY6^T$, isolated from an irradiated soil sample. The genome comprised of 5,012,599 bp with the G+C content of 49.93%, the genome included 4,463 protein coding genes and 133 RNA genes.

• Journal of Microbiology and Biotechnology
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• v.22 no.12
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• pp.1605-1612
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• 2012

The present study concerned the identification and characterization of a novel bacterial strain isolated from entomopathogenic nematodes collected from different regions in Korea. The bacterial isolate M1021 was Gramnegative, bioluminescent, and produced red colonies on MacConkey agar medium. A rod-shaped structure was confirmed by the electron micrograph. Fatty acid composition was analyzed by using the Sherlock MIDI system. The identification was further supported by 16S rDNA sequence analysis, which revealed 96-99% sequence homology with strains of Photorhabdus temperata. The location of the isolated strain of P. temperata in the phylogenetic tree was confirmed and it was named P. temperata M1021. P. temperata M1021 exhibited catalase, protease, and lipase activities when grown on appropriate media supplemented with respective substrates. The culture of P. temperata M1021 exhibited insecticidal activity against the larvae of Galleria mellonella and the activity was the highest after 3-4 days of cultivation with agitating at $28^{\circ}C$ under 220 rpm. Antibacterial activity was also observed against Salmonella Typhimurium KCTC 1926 and Micrococcus luteus KACC 10488.

• Journal of Species Research
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• v.10 no.1
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• pp.23-45
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• 2021

For the collection of indigenous prokaryotic species in Korea, 77 strains within the phylum Actinobacteria were isolated from various environmental samples, fermented foods, animals and clinical specimens in 2019. Each strain showed high 16S rRNA gene sequence similarity (>98.8%) and formed a robust phylogenetic clade with actinobacterial species that were already defined and validated with nomenclature. There is no official description of these 77 bacterial species in Korea. The isolates were assigned to 77 species, 31 genera, 18 families, 14 orders and 2 classes of the phylum Actinobacteria. All the strains except one Coriobacteriia strain were affiliated within the class Actinomycetia. Among them, the orders Streptomycetales and Microbacteriales were predominant. A number of strains were isolated from forest soils, riverside soils, and ginseng cultivated soils. Twenty-nine strains were isolated from 'Protected Ecosystem and Scenery Areas'. Morphological properties, basic biochemical characteristics, isolation source and strain IDs are described in the species descriptions.

• Journal of Microbiology and Biotechnology
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• v.11 no.1
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• pp.106-111
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• 2001

A ${\beta}-galactosidase$ gene of Bifidobacterium adolescentis Int57 (INT57) was cloned using the shotgun method. The sequence of the ${\beta}-galactosidase$ gene existing in the sequenced 3,260-bp fragment showed higher than 40% homology with other bacterial ${\beta}-galactosidase$ genes. The expression in Escherichia coli suggested that the ${\beta}-galactosidase$ might have a monomeric, dimeric, or tetrameric protein structure. This is probably the first peer-reviewed sequence analysis of the ${\beta}-galactosidase$ gene of the genus Bifidobacterium.

• Journal of Microbiology and Biotechnology
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• v.8 no.1
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• pp.67-73
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• 1998

A bacterial strain that excretes hemolysins and proteases into the growth medium was isolated from sea water and designated as KYJ 961. A nearly complete nucleotide sequence of a 16S ribosomal RNA gene from the isolate was determined following the isolation and cloning of amplified genes. On the basis of the 16S ribosomal DNA sequence data, and morphological, chemotaxonomic, and physiological characteristics, strain KYJ 961 was classified as a strain of Bacillus cereus.

• Journal of Microbiology
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• v.39 no.4
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• pp.334-337
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• 2001

The degradative pathway of homoprotocatechuate (HPC) is the bacterial routhe wherby 3,4-dihydrox-yphenylactic acid is catabolized to pyruvate and succinate by a series of sequential reactions . The HPC is catalzed by homoprotocatechuate 2, 3-dioxygenase(HPC-2,3O) to from 5-carboxymethy1-2-hydroxy-muco semialdehyde. In this study, the hha D gene encoding. HPC, 2, 3O was Cloned from the chromo-somal DNA of Pseudomonas sp. DJ-12 and its nucleotide sequence was analyzed. The open reding frame of hpaD gene was found to be composed of 864 nucleotide pairs and to encode a poypetide with 287 amino acide residues. The deduced amino acid sequence of the HPC-2,3O from Pseudomonas. sp. DJ-12 exhibited 60~64% homology with those of the corresponding enzymes from E. coli. Salmonella enterica, and Klebsiella pneumoniae.

• Journal of Microbiology and Biotechnology
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• v.24 no.4
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• pp.563-567
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• 2014

Pseudomonas syringae pv. syringae (Psy) is a major bacterial pathogen of many economically important plant species. Despite the severity of its impact, the genome sequence of the type strain has not been reported. Here, we present the draft genome sequence of Psy ATCC 19310. Comparative genomic analysis revealed that Psy ATCC 19310 is closely related to Psy B728a. However, only a few type III effectors, which are key virulence factors, are shared by the two strains, indicating the possibility of host-pathogen specificity and genome dynamics, even under the pathovar level.

• Genomics & Informatics
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• v.20 no.1
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• pp.3.1-3.10
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• 2022

The recent development of whole-genome sequencing technologies paved the way for understanding the genomes of microorganisms. Every whole-genome sequencing (WGS) project requires a considerable cost and a massive effort to address the questions at hand. The final step of WGS is data analysis. The analysis of whole-genome sequence is dependent on highly sophisticated bioinformatics tools that the research personal have to buy. However, many laboratories and research institutions do not have the bioinformatics capabilities to analyze the genomic data and therefore, are unable to take maximum advantage of whole-genome sequencing. In this aspect, this study provides a guide for research personals on a set of bioinformatics tools available online that can be used to analyze whole-genome sequence data of bacterial genomes. The web interfaces described here have many advantages and, in most cases exempting the need for costly analysis tools and intensive computing resources.