• Journal of Microbiology and Biotechnology
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• v.15 no.4
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• pp.866-872
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• 2005

H. pylori is known to cause severe gastric diseases, including peptic ulcers and gastric cancers, and a link has also been suggested with iron-deficiency anemia (IDA). However, little is known about the pathogenesis of H. pylori-associated IDA. In the present study, to determine whether H. pylori strains are correlated with the prevalence of IDA, we analyzed and compared the sequences of the napA genes encoding a bacterioferritin-like protein in H. pylori strains. A total of 20 H. pylori strains were isolated from antral biopsies of patients with and without IDA, and the napA genes amplified from the genomic DNA were sequenced. A comparison of the deduced amino acid sequences for NapA revealed two sites with major variations. At residue 70, five out of the 12 non-IDA strains ($41.7\%$) contained serine, while only one of the 8 IDA strains ($12.5\%$) contained serine, indicating a significantly higher frequency of serine in the non-IDA strains. In addition, the NapA proteins from all 17 Western strains available on Web sites were found to contain serine residues at this position. Meanwhile, the other major variation was located at residue 73, where all eight IDA strains ($100\%$) contained leucine, while this was only true for eight of the 12 non-IDA strains ($66.7\%$). Therefore, these results indicated that the strains within each group were more genetically related to each other than to strains in the other group. When the expression level of the napA genes in the H. pylori strains was measured using RT-PCR, no significant difference was observed between the two groups, suggesting a similar intensity for the inflammatory responses induced by the NapA protein among the strains. Consequently, when taken together, the present data suggest that the occurrence of H. pylori-associated IDA may be partly determined by the infecting H. pylori strain, and the non-IDA strains are more closely related to Western strains than the IDA strains.

• Journal of Microbiology and Biotechnology
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• v.15 no.6
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• pp.1240-1249
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• 2005

Saccharomyces cerevisiae KNU5377 has potential as an industrial strain that can ferment wasted paper for fuel ethanol at $40^{\circ}C$ [15, 16]. To understand the characteristics of the strain, genome-wide expression was performed using DNA microarray technology. We compared the homology of the DNA microarray between genomic DNAs of S. cerevisiae KNU5377 and a control strain, S. cerevisiae S288C. Approximately $97\%$ of the genes in S. cerevisiae KNU5377 were identified with those of the reference strain. YHR053c (CUP1), YLR155c (ASP3), and YDR038c (ENA5) showed lower homology than those of S. cerevisiae S288C. In particular, the differences in the regions of YHR053c and YLR155c were confirmed by Southern hybridization, but did not with that of the region of YDR038c. The expression level of mRNA in S. cerevisiae KNU5377 and S288C was also compared: the 550 ORFs of S. cerevisiae KNU5377 showed more than two-fold higher intensity than those of S. cerevisiae S288C. Among the 550 ORFs, 59 ORFs belonged to the groups of ribosomal proteins and mitochondrial ribosomal proteins, and 200 ORFs belonged to the group of cellular organization. DIP5 and GAP1 were the most highly expressed genes. These results suggest that upregulated DIP5 and GAP 1 might take the place of ASP3 and, additionally, the sensitivity against copper might be contributable to the lowest expression level of copper-binding metallothioneins encoded by CUP 1a (YHR053c) and CUP1b (YHR055c) in S. cerevisiae KNU5377.

• Journal of Microbiology and Biotechnology
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• v.16 no.3
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• pp.450-456
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• 2006

Pseudomonas fluorescens MC07 is a growth-promoting rhizobacterium that suppresses mycelial growth in fungi such as Rhizoctonia solani, Pythium ultimum, Fusarium oxysporum, and Phytophthora capsici. To determine the role of the bacterium's antifungal activity in disease suppression, we screened 2,500 colonies generated by Tn5lacZ insertions, and isolated a mutant 157 that had lost antifungal activity. The EcoRI fragment carrying Tn5lacZ was cloned into pBluescript II SK(+) and used as a probe to isolate wild-type clones from a genomic library of the parent strain, MC07. Two overlapping cosmid clones, pEH4 and pEH5, that had hybridized with the mutant clone were isolated. pEH4 conferred antifungal activity to the heterologous host P.fluorescens strain 1855.344, whereas pEH5 did not. Through transposon mutagenesis of pEH4 and complementation analyses, we delineated the 14.7-kb DNA region that is responsible for the biosynthesis of an antifungal compound. DNA sequence analysis of the region identified 11 possible open reading frames (ORF), ORF1 through ORF11. A BLAST search of each putative protein implied that the proteins may be involved in an antifungal activity similar to polyketides.

• Journal of Microbiology and Biotechnology
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• v.21 no.4
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• pp.333-340
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• 2011

Herbicide-tolerant Zoysia grass has been previously developed through Agrobacterium-mediated transformation. We investigated the effects of genetically modified (GM) Zoysia grass and the associated herbicide application on bacterial community structure by using culture-independent approaches. To assess the possible horizontal gene transfer (HGT) of transgenic DNA to soil microorganisms, total soil DNAs were amplified by PCR with two primer sets for the bar and hpt genes, which were introduced into the GM Zoysia grass by a callus-type transformation. The transgenic genes were not detected from the total genomic DNAs extracted from 1.5 g of each rhizosphere soils of GM and non-GM Zoysia grasses. The structures and diversities of the bacterial communities in rhizosphere soils of GM and non-GM Zoysia grasses were investigated by constructing 16S rDNA clone libraries. Classifier, provided in the RDP II, assigned 100 clones in the 16S rRNA gene sequences library into 11 bacterial phyla. The most abundant phyla in both clone libraries were Acidobacteria and Proteobacteria. The bacterial diversity of the GM clone library was lower than that of the non- GM library. The former contained four phyla, whereas the latter had seven phyla. Phylogenetic trees were constructed to confirm these results. Phylogenetic analyses of the two clone libraries revealed considerable difference from each other. The significance of difference between clone libraries was examined with LIBSHUFF statistics. LIBSHUFF analysis revealed that the two clone libraries differed significantly (P<0.025), suggesting alterations in the composition of the microbial community associated with GM Zoysia grass.

• Journal of Microbiology and Biotechnology
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• v.18 no.6
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• pp.1011-1015
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• 2008

A Gram-negative, strictly aerobic, motile bacterial strain, designated Gsoil $124^T$, was isolated from a soil sample taken from a ginseng field in Pocheon Province (South Korea). The isolate contained Q-10 as the predominant lipoquinone, plus $C_{18:1}\;{\omega}7c$ and summed feature 4 ($C_{16:1}\;{\omega}6c$ and/or iso-$C_{15:0}$ 2-OH) as the major fatty acids. The G+C content of the genomic DNA was 68.1 mol%, and the major polar lipids consisted of sphingoglycolipid, phosphatidylglycerol, phosphatidylcholine, and phosphatidylethanolamine. A comparative 16S rRNA gene sequence analysis showed that strain Gsoil $124^T$ was most closely related to Sphingopyxis chilensis (98.7%), Sphingopyxis alaskensis (98.2%), Sphingopyxis witflariensis (98.2%), Sphingopyxis taejonensis (98.0%), and Sphingopyxis macrogoltabida (97.6%). However, the DNA-DNA relatedness between strain Gsoil $124^T$ and its phylogenetically closest neighbors was less than 22%. Thus, on the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil $124^T$ should be classified as representing a novel species in the genus Sphingopyxis, for which the name Sphingopyxis panaciterrae sp. nov. is proposed. The type strain is Gsoil $124^T$ (=KCTC $12580^T$=LMG $24003^T$).

• Applied Biological Chemistry
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• v.48 no.4
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• pp.331-334
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• 2005

In this study, the effects of five extraction methods for raw and processed corns were compared with respect to the integrity, yields and quality of DNA extracted from them and the results were assessed by PCR analysis. From the comparison of five extraction methods, DNA integrity showed a similar pattern. Amounts of genomic DNA obtained from the five extraction methods varies from $0.25{\mu}g\;to\;234{\mu}g$ per 1 g sample. The DNA yield extracted with CTAB method and DNeasy Plant Maxi kit is greater than that obtained from other extraction methods. These results would be applicable for the selection of an adequate extraction method for specific samples.

• Horticultural Science & Technology
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• v.32 no.2
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• pp.227-234
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• 2014

The responses to chilling temperature of 12 Korean cucumber varieties was compared to those of two U.S.A. (previously determined cold tolerant NC76 and 'Chipper'), and Chinese and Japanese germplasms. Seedlings of each entry were exposed to $4^{\circ}C$ (Experiment 1) and $1^{\circ}C$ (Experiments 2 and 3) at the first-true leaf stage for eight and nine hours, respectively, under 80% relative humidity (RH) and $149{\mu}moles{\cdot}m^{-2}{\cdot}s^{-1}$ photosynthetic photon flux (PPF). The chilling response [damage rating (DR)] of each accession was based on visual ratings (1 to 5) after treatment, where 1 = no damage, 2 = slight, 3 = moderate, 4 = advanced, and 5 = severe damage. Predictably the cumulative average DR of chilling tolerant line NC76 and 'Chipper' after chilling w as 1 and 1.1, respectively. Korean 'Nacdongchungjang' was most sensitive to chilling temperatures [DR = 2.3] when compared to the other entries examined. The sensitivity to chilling of 'Nacdongchungjang' was followed by Chinese 'Dongguan' [DR = 1.7]. In contrast, 'Saeronchungjang' (DR = 1) and 'Janghyungnachap' (DR = 1) were the most chilling tolerant of the Korean accessions examined and equivalent to the response of line NC76 and 'Chipper'. Nevertheless, chloroplast type genotyping of these accessions with known chilling-linked sdCAPS genomic markers revealed genotypic differences between chilling tolerant lines (NC76 and 'Chipper') and all Korean lines examined.

• Clinical and Experimental Pediatrics
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• v.48 no.5
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• pp.551-556
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• 2005

Wiskott-Aldrich syndrome(WAS) is an X-linked recessive immunodeficiency characterized by thrombocytopenia with small platelet volume, eczema, and recurrent infections, and is also characterized by increased incidence of auto immune diseases and malignancies. The phenotype observed in this syndrome is caused by mutation in the Wiskott-Aldrich syndrome protein(WASP) gene localized to the proximal short arm of the X chromosome and recently isolated through positional cloning. The gene encodes a 502 amino acid protein, which contains 12 exons and spans 9 kb of genomic DNA. The function of the encoded protein is not well understood. The clinical diagnosis of WAS can be difficult and is usually confirmed by the detection of WASP gene mutations and the expression of WSAP in patient blood sample using genetic analysis. We reported a case of a 13-month old boy with WAS who was identified with the novel mutation in exon 2 of WASP gene by direct sequencing and the complete absence of WASP expression by immunoblotting.

• Journal of Microbiology and Biotechnology
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• v.15 no.5
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• pp.1094-1099
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• 2005

Photosynthetic dinoflagellates contain a water-soluble, light-harvesting antenna called the peridinin-chlorophyll-protein (PCP) complex, which has an apoprotein with no sequence similarity to other known proteins. There are two forms of PCP apoproteins; the 15-kDa short form and the 32- to 35­kDa long form. The present study describes the PCP protein and its cDNA from Alexandrium tamarense. A cDNA library was constructed from mRNA isolated from A. tamarense. The complete PCP cDNA was generated by reverse-transcription coupled to polymerase chain reaction (RT-PCR), together with rapid-amplification of cDNA ends (RACE). The A. tamarense PCP cDNA encoded a 55-amino acid signal peptide and a 313-amino acid mature protein with a calculated mass of 32 kDa, which corresponded to that of the long form of PCP. Phylogenetic analysis indicated that the sequence of A. tamarense PCP did not cluster with the short-form PCPs, to which it was only about $55\%$ identical, but which were $79-83\%$ identical to other long-form PCPs. The deduced amino acid sequence of A. tamarense PCP contains an internal duplication, which suggests the possibility that long-form PCPs arose by gene duplication or by the fusion of genes encoding the short form. The abundance of PCP mRNA changed substantially in response to different light conditions, indicating the possible existence of a photo-acclimation response in A. tamarense.

• Microbiology and Biotechnology Letters
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• v.34 no.1
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• pp.1-6
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• 2006

Harmful algal blooms (HABs or red tides), caused by uncontrolled proliferation of marine phytoplankton, impose a severe environmental problem and occasionally threaten even public health. We sequenced the genome of an EPS-producing marine bacterium Hahella chejuensis that produces a red pigment with the lytic activity against red-tide dinoflagellates at parts per billion level. H. chejuensis is the first sequenced species among algicidal bacteria as well as in the order Oceanospirillales. Sequence analysis indicated a distant relationship to the Pseudomonas group. Its 7.2-megabase genome encodes basic metabolic functions and a large number of proteins involved in regulation or transport. One of the prominent features of the H. chejuensis genome is a multitude of genes of functional equivalence or of possible foreign origin. A significant proportion (${\sim}23%$) of the genome appears to be of foreign origin, i.e. genomic islands, which encode genes for biosynthesis of exopolysaccharides, toxins, polyketides or non-ribosomal peptides, iron utilization, motility, type III protein secretion and pigment production. Molecular structure of the algicidal pigment was determined to be prodigiosin by LC-ESI-MS/MS and NMR analyses. The genomics-based research on H. chejuensis opens a new possibility for controlling algal blooms by exploiting biotic interactions in the natural environment and provides a model in marine bioprospecting through genome research.