• Journal of Microbiology and Biotechnology
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• v.18 no.6
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• pp.1005-1010
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• 2008

The genus Burkholderia consists of extremely versatile bacteria that occupy diverse niches and are commonly encountered in the rhizosphere of crop plants. In this study, we characterized three plant growth promoting strains assigned as Burkholderia sp. using biochemical and molecular characterization. The Burkholderia spp. strains CBMB40, CBPB-HIM, and CBPB-HOD were characterized using biochemical tests, BIOLOG carbon substrate utilization, fatty acid methyl ester analysis, analysis of recA gene sequences, and DNA-DNA hybridization. The results from these studies indicated that the strains CBMB40, CBPB-HIM, and CBPB-HOD can be assigned under Burkholderia vietnamiensis, Burkholderia ubonensis, and Burkholderia pyrrocinia, respectively.

• Journal of Microbiology and Biotechnology
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• v.17 no.8
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• pp.1262-1270
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• 2007

Some hot springs located in the west of Turkey were investigated with respect to the presence of thermophilic microorganisms. Based on phenotyping characteristics and 16S rRNA gene sequence analysis, 16 of the isolates belonged to the genus Geobacillus and grew optimally at about $60^{\circ}C$ on nutrient agar. 16S rRNA gene sequence analysis showed that these isolates resembled Geobacillus species by ${\ge}97%$, but SDS-PAGE profiles of these 16 isolates differ from some of the other species of the genus Geobacillus. However, it is also known that analysis of 16S rRNA gene sequences may be insufficient to distinguish between some species. It is proposed that recN sequence comparisons could accurately measure genome similarities for the Geobacillus genus. Based on recN sequence analysis, isolates 11, IT3, and 12 are strains of G stearothermophilus; isolate 14.3 is a strain of G thermodenitrificans; isolates 9.1, IT4.1, and 4.5 are uncertain and it is required to make further analysis. The presence of xylanase and arabinofuranosidase activities, and their optimum temperature and pH were also investigated. These results showed that 7 of the strains have both xylanase and arabinofuranosidase activities, 4 of them has only xylanase, and the remaning 5 strains have neither of these activities. The isolates 9.1, 7.1, and 3.3 have the highest temperature optima ($80^{\circ}C$), and 7.2, 9.1, AO4, 9.2, and AO17 have the highest pH optima (pH 8) of xylanase. Isolates 7.2, AO4, AC15, and 12 have optimum arabinofuranosidase activities at $75^{\circ}C$, and only isolate AC15 has the lowest pH of 5.5.

• Journal of Microbiology and Biotechnology
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• v.27 no.1
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• pp.112-121
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• 2017

Edwardsiella tarda is a gram-negative pathogenic bacterium in aquaculture that can cause hemorrhagic septicemia in fish. Many secreted proteins have already been identified as virulent factors of E. tarda. Moreover, since virulent phenotypes are based on the expression regulation of virulent genes, understanding the expression profile of virulent genes is important. A quantitative RT-PCR is one of the preferred methods for determining different gene expressions. However, this requires the selection of a stable reference gene in E. tarda, which has not yet been systematically studied. Accordingly, this study evaluated nine candidate reference genes (recA, uup, rpoB, rho, topA, gyrA, groEL, rpoD, and 16S rRNA) using the Excel-based programs BestKeeper, GeNorm, and NormFinder under different culture conditions. The results showed that 16S rRNA was more stable than the other genes at different culture growth phases. However, at the same culture time, topA was identified as the reference gene under the conditions of different strains, different culture media, and infection, whereas gyrA was identified under the condition of different temperatures. Thus, in experiments, the expression of gapA and fbaA in E. tarda was analyzed by RT-qPCR using 16S rRNA, recA, and uup as the reference genes. The results showed that 16S rRNA was the most suitable reference gene in this analysis, and that using unsuitable reference genes resulted in inaccurate results.

• Proceedings of the Microbiological Society of Korea Conference
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• 2002.10a
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• pp.140-147
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• 2002

• Journal of Microbiology and Biotechnology
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• v.17 no.8
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• pp.1390-1393
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• 2007

In this study, three of the representative EDCs, $17{\beta}$-estradiol, bisphenol A, and styrene, were employed to find their mode of toxic actions in E. coli. To accomplish this, four different stress response genes, recA, katG, fabA, and grpE genes, were used as a representative for DNA, oxidative, membrane, or protein damage, respectively. The expression levels of these four genes were quantified using a real-time RT-PCR after challenge with three different EDCs individually. Bisphenol A and styrene caused high-level expression of recA and katG genes, respectively, whereas $17{\beta}$-estradiol made no significant changes in expression of any of those genes. These results lead to the classification of the mode of toxic actions of EDCs on E. coli.

• Korean Journal of Microbiology
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• v.28 no.2
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• pp.109-113
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• 1990

The mutagenesis-enhancing plasmid pKM101 and its mutant pSL4 were introduced into Escherichia coli B/r strains possessing different DNA repair capacities ($phr^{-}, recA^{-}, uvrA^{-}, uvrB^{-}$) and determined the protection effect and mutagenecity for UV and MNNG. The mutability and protection effect of plasmid pKM101 and pSL4 were affected by different DNA repair capacity. The mutagenecity and resistance of two plasmids were increased against UV and MNNG, and plasmid pSL4 had a higher effect than pKM101. We suggest that the functional differences between pKM101 and pSL4 is due to the variety of mutator gene.

• Journal of Life Science
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• v.18 no.7
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• pp.912-917
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• 2008

To investigate the biological activity of recombinant human granulocyte colony-stimulating factor (rec-hG-CSF) in mammalian cells, hG-CSF gene was cloned using the eDNA extracted from the human squamous carcinoma cell lines and rec-hG-CSF was produced in CHO cell lines. To analyze the biological activity in vivo, the rec-hG-CSF protein was injected into mice subcutaneously on days 0 and 2. Blood was withdrawn for white blood cell (WBC) determination 5 days after the first injection. WBC values were found to have increased significantly. A pEGFP-mUII-hG-CSF vector was transfected into somatic cell lines isolated from bovine fetal cells. The colony expressing EGFP signals was observed with a confocal microscope. These data suggest that the rec-hG-CSF produced in this study has potent activity in vivo. Thus, the results of this biological activity show that rec-hG-CSF can be enhanced considerably by genetic engineering that affects potential activity, including mutations, which add the oligosaccharide chain and construct double-fusion proteins. A pEGFP-mUII-hG-CSF vector can be utilized for the production of cloned transgenic livestock.

• Animal cells and systems
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• v.3 no.4
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• pp.413-415
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• 1999

Our previous report demonstrated that the rhp51$^＋$, a recA and RAD51 homolog of the fission yeast, encodes three transcripts of 1.9, 1.6 and 1.3 kb which have at least six polyadenylation sites. The 3'-end of the gene alone can direct the formation of multiple, discrete 3'ends of the transcripts. To identify the regulatory element required for the 3'-end formation of -rhp51$^＋$ deletion mapping analysis was performed. Northern blot analysis revealed that the 254-bp DNA fragment including 4 distinct poly (A) sites downstream from the Hindlll site, is crucial for normal 3'-end formation. Deletion of the 3'-terminal AU rich region caused appearance of read-through RNA, leading to enhancement of survival rate of the rhp51 deletion mutant in response to DNA damaging agent, methylmethane sulfonate (MMS). The results imply that the rhp51$^＋$ system may be useful for molecular analysis of the 3'-end formation of RNA in the fission yeast.

• BMB Reports
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• v.56 no.2
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• pp.108-113
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• 2023

Cohesin is a ring-shaped protein complex that comprises the SMC1, SMC3, and α-kleisin proteins, STAG1/2/3 subunits, and auxiliary factors. Cohesin participates in chromatin remodeling, chromosome segregation, DNA replication, and gene expression regulation during the cell cycle. Mitosis-specific α-kleisin factor RAD21 and meiosis-specific α-kleisin factor REC8 are expressed in embryonic stem cells (ESCs) to maintain pluripotency. Here, we demonstrated that RAD21 and REC8 were involved in maintaining genomic stability and modulating chromatin modification in murine ESCs. When the kleisin subunits were depleted, DNA repair genes were downregulated, thereby reducing cell viability and causing replication protein A (RPA) accumulation. This finding suggested that the repair of exposed single-stranded DNA was inefficient. Furthermore, the depletion of kleisin subunits induced DNA hypermethylation by upregulating DNA methylation proteins. Thus, we proposed that the cohesin complex plays two distinct roles in chromatin remodeling and genomic integrity to ensure the maintenance of pluripotency in ESCs.

• The Plant Pathology Journal
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• v.39 no.2
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• pp.191-206
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• 2023

Ground cherry (Physalis pubescens) is the most prominent species in the Solanaceae family due to its nutritional content, and prospective health advantages. It is grown all over the world, but notably in northern China. In 2019 firstly bacterial leaf spot (BLS) disease was identified on P. pubescens in China that caused by both BLS pathogens Xanthomonas euvesicatoria pv. euvesicatoria resulted in substantial monetary losses. Here, we compared whole genome sequences of X. euvesicatoria to other Xanthomonas species that caused BLS diseases for high similarities and dissimilarities in genomic sequences through average nucleotide identity (ANI) and BLAST comparison. Molecular techniques and phylogenetic trees were adopted to detect X. euvesicatoria on P. pubescens using recQ, hrpB1, and hrpB2 genes for efficient and precise identification. For rapid molecular detection of X. euvesicatoria, loop-mediated isothermal amplification, polymerase chain reaction (PCR), and real-time PCR techniques were used. Whole genome comparison results showed that the genome of X. euvesicatoria was more closely relative to X. perforans than X. vesicatoria, and X. gardneri with 98%, 84%, and 86% ANI, respectively. All infected leaves of P. pubescens found positive amplification, and negative controls did not show amplification. The findings of evolutionary history revealed that isolated strains XeC10RQ, XeH9RQ, XeA10RQ, and XeB10RQ that originated from China were closely relative and highly homologous to the X. euvesicatoria. This research provides information to researchers on genomic variation in BLS pathogens, and further molecular evolution and identification of X. euvesicatoria using the unique target recQ gene through advance molecular approaches.