• Journal of Microbiology and Biotechnology
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• v.31 no.7
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• pp.912-920
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• 2021

SOS response is a conserved response to DNA damage in prokaryotes and is negatively regulated by LexA protein, which recognizes specifically an "SOS-box" motif present in the promoter region of SOS genes. Myxococcus xanthus DK1622 possesses a lexA gene, and while the deletion of lexA had no significant effect on either bacterial morphology, UV-C resistance, or sporulation, it did delay growth. UV-C radiation resulted in 651 upregulated genes in M. xanthus, including the typical SOS genes lexA, recA, uvrA, recN and so on, mostly enriched in the pathways of DNA replication and repair, secondary metabolism, and signal transduction. The UV-irradiated lexA mutant also showed the induced expression of SOS genes and these SOS genes enriched into a similar pathway profile to that of wild-type strain. Without irradiation treatment, the absence of LexA enhanced the expression of 122 genes that were not enriched in any pathway. Further analysis of the promoter sequence revealed that in the 122 genes, only the promoters of recA2, lexA and an operon composed of three genes (pafB, pafC and cyaA) had SOS box sequence to which the LexA protein is bound directly. These results update our current understanding of SOS response in M. xanthus and show that UV induces more genes involved in secondary metabolism and signal transduction in addition to DNA replication and repair; and while the canonical LexA-dependent regulation on SOS response has shrunk, only 5 SOS genes are directly repressed by LexA.

• Journal of Radiation Industry
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• v.7 no.2_3
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• pp.109-113
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• 2013

In a previous study, a relatively high dose of gamma radiation (1 kGy) did not fully induce typical SOS genes such as sulA, recA, recN, and din in Salmonella Typhimurium (S. Typhimurium) (Lim et al. 2008, Gene expression profiles following high-dose exposure to gamma radiation in Salmonella enterica serovar Typhimuium. J. Radiat. Ind. 3:111-119). In this study, we examined changes in the transcriptional repertoire of S. Typhimurium after a dose of 10 Gy using DNA microarrays. It was found that more than half (~65%) of the 26 up-regulated genes belong to the SOS regulon: ten genes are typical SOS genes, and seven genes are Salmonella prophage genes, which are known to be activated by LexA cleavage. Among 29 down-regulated genes, the function of five genes with the most decreased expression is associated with carbohydrate transport and energy production. This suggests that upon exposure to gamma radiation cells may cease growing by reducing the metabolic activity, and repair DNA damage using a DNA repair system such as the SOS response system. The difference in expression of the SOS genes between a high (1 kGy) and low (10 Gy) dose of radiation shows the possibility that cells may opt for one of multiple regulatory circuits in response to the specific gamma radiation dose.

• Journal of Plant Biotechnology
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• v.42 no.3
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• pp.154-160
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• 2015

The plant breeding technology was developed with genetic engineering. Many researchers and breeders have turned from traditional breeding to molecular breeding. Genetically modified organisms (GMO) were developed via molecular breeding technology. Currently, molecular breeding technologies facilitate efficient plant breeding without introducing foreign genes, in virtue by of gene editing technology. Gene targeting (GT) via homologous recombination (HR) is one of the best gene editing methods available to modify specific DNA sequences in genomes. GT utilizes DNA repair pathways. Thus, DNA repair systems are controlled to enhance HR processing. Engineered sequence specific endonucleases were applied to improve GT efficiency. Engineered sequence specific endonucleases like the zinc finger nuclease (ZFN), TAL effector nuclease (TALEN), and CRISPR-Cas9 create DNA double-strand breaks (DSB) that can stimulate HR at a target site. RecQl4, Exo1 and Rad51 are effectors that enhance DSB repair via the HR pathway. This review focuses on recent developments in engineered sequence specific endonucleases and ways to improve the efficiency of GT via HR effectors in plants.

• The Plant Pathology Journal
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• v.30 no.2
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• pp.117-124
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• 2014

The plant pathogenic bacterial genus Pectobacteirum consists of heterogeneous strains. The P. carotovorum species is a complex strain showing divergent characteristics, and a new subspecies named P. carotovorum subsp. brasiliensis has been identified recently. In this paper, we re-identified the P. carotovorum subsp. brasiliensis isolates from those classified under the subspecies carotovorum and newly isolated P. carotovorum subsp. brasiliensis strains. All isolates were able to produce plant cell-wall degrading enzymes such as pectate lyase, polygalacturonase, cellulase and protease. We used genetic and biochemical methods to examine the diversity of P. carotovorum subsp. brasiliensis isolates, and found genetic diversity within the brasiliensis subsp. isolates in Korea. The restriction fragment length polymorphism analysis based on the recA gene revealed a unique pattern for the brasiliensis subspecies. The Korean brasiliensis subsp. isolates were divided into four clades based on pulsed-field gel electrophoresis. However, correlations between clades and isolated hosts or year could not be found, suggesting that diverse brasiliensis subsp. isolates existed.

• Korean Journal of Microbiology
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• v.51 no.2
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• pp.169-176
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• 2015

The malolactic fermentation (MLF), which is widely used in winemaking, is the conversion of malic acid to lactic acid conducted by the malolactic enzyme (Mle) of lactic acid bacteria. In order to select the strains with MLF among 54 lactic acid bacteria isolated from the traditionally fermented foods, we designed a primer set that specifically targets the conserved regions of the mle gene and then selected four strains that harbor the mle gene of Lactobacillus plantarum. All strains were identified as L. plantarum by analyzing the 16S rRNA sequences, biochemical properties, and the PCR products of the recA gene. From comparison of the mle gene sequences consisting of 1,644 bp, the nucleotide and amino acid sequence of strain JBE60 correspond to 96.7% and 99.5% with those of other three strains, respectively. The strain JBE60 showed the highest resistant against 10% (v/v) ethanol among the strains. The strains lowered the concentration of malic acid to average 43%. Considering the ethanol resistance and conversion of malic acid, the strain JBE60 is considered as a potential starter for the malolactic fermentation.

• Journal of Microbiology and Biotechnology
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• v.17 no.2
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• pp.359-363
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• 2007

Because of the importance of the type III protein-secretion system in bacteria-plant interaction, its function in bacterial pathogenesis of plants has been intensively studied. To identity bacterial proteins interacting with Xanthomonas hrp gene products that are involved in pathogenicity, we performed the glutathione-bead binding analysis of Xanthomonas lysates containing GST-tagged Hrp proteins. Analysis of glutathione-bead bound proteins by 1-DE and MALDI-TOF has demonstrated that Avr proteins, RecA, and several components of the type III secretion system interact with HrpB protein. This proteomic approach could provide a powerful tool in finding interaction partners of Hrp proteins whose roles in host-pathogen interaction need further studies.

• Journal of Microbiology and Biotechnology
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• v.10 no.2
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• pp.272-274
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• 2000

Temperate bacteriophage P2 has a nonessential gene called old(overcoming lysoginization defection). In the presence of old, the growth of the host (Escherichia coli) with recBC- genotype is ingibited, and another bacteriophage, lambda, cannot superinfect. The Old protein has been shown to possess an exonuclease actibity. Three mutant P2s(old 1, old 17, old 49) which did gene was coned into expression vectors to produce hexahistidine-tagged proteins. The proteins were affinity-purified and shown to lose its exonuclease activity on both double-stranded and single-stranded DNA substrates. Thus, it was concluded that the lambda exclusion was related to Old's exonuclease activity.

• Journal of Microbiology and Biotechnology
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• v.21 no.11
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• pp.1166-1173
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• 2011

Meju is a traditional Korean fermented soy product used as a key element for soy sauce and doenjang. Bacilli with antimicrobial activity were isolated from meju prepared by traditional methods at Sunchang county, Jeollabukdo, Korea. Six isolates were identified as Bacillus amyloliquefaciens by recA gene sequencing and RAPD-PCR. One isolate, B. amyloliquefaciens MJ5-41, showed the strongest fibrinolytic activity. A 27 kDa active fibrinolytic enzyme, AprE5-41, was purified from the culture supernatant of MJ5-41 grown on LB by chromatographic methods. The optimum pH and temperature for purified AprE5-41 were 7.0 and $45^{\circ}C$, respectively. AprE5-41 quickly degraded $A{\alpha}$ and $B{\beta}$ chains but not the ${\gamma}$-chain of fibrinogen. AprE5-41 exhibited the highest specificity for N-succinyl-Ala-Ala-Pro-Phe p-nitroanilide, a known substrate for ${\alpha}$-chymotrypsin, cathepsin G, and subtilisin BPN'. The structural gene, aprE5-41, was cloned by PCR and successfully expressed in B. subtilis.

• The Plant Pathology Journal
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• v.31 no.2
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• pp.108-114
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• 2015

Curvularia lunata is an important maize foliar fungal pathogen that distributes widely in maize growing area in China, and several key pathogenic factors have been isolated. An yeast two-hybrid (Y2H) library is a very useful platform to further unravel novel pathogenic factors in C. lunata. To construct a high-quality full length-expression cDNA library from the C. lunata for application to pathogenesis-related protein-protein interaction screening, total RNA was extracted. The SMART (Switching Mechanism At 5' end of the RNA Transcript) technique was used for cDNA synthesis. Double-stranded cDNA was ligated into the pGADT7-Rec vector with Herring Testes Carrier DNA using homologous recombination method. The ligation mixture was transformed into competent yeast AH109 cells to construct the primary cDNA library. Eventually, a high qualitative library was successfully established according to an evaluation on quality. The transformation efficiency was about $6.39{\times}10^5$ transformants/$3{\mu}g$ pGADT7-Rec. The titer of the primary cDNA library was $2.5{\times}10^8cfu/mL$. The numbers for the cDNA library was $2.46{\times}10^5$. Randomly picked clones show that the recombination rate was 88.24%. Gel electrophoresis results indicated that the fragments ranged from 0.4 kb to 3.0 kb. Melanin synthesis protein Brn1 (1,3,8-hydroxynaphthalene reductase) was used as a "bait" to test the sufficiency of the Y2H library. As a result, a cDNA clone encoding VelB protein that was known to be involved in the regulation of diverse cellular processes, including control of secondary metabolism containing melanin and toxin production in many filamentous fungi was identified. Further study on the exact role of the VelB gene is underway.

• Preventive Nutrition and Food Science
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• v.17 no.1
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• pp.64-70
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• 2012

Bacilli with fibrinolytic activities were isolated from traditionally-prepared Meju and some of these strains showed strong antifungal activities. One isolate, MJ1-4, showed the strongest antifungal activity. MJ1-4 and other isolates were identified as B. amyloliquefaciens strains by recA gene sequencing and RAPD-PCR results. B. amyloliqufaciens MJ1-4 efficiently inhibited an Aspergillus spp.-producing aflatoxin B1 ($AFB_1$) and a Penicillium spp.-producing ochratoxin (OTA) in addition to other fungi. Antifungal activity of B. amyloliquefaciens MJ1-4 culture reached its maximum (40 AU/mg protein) in LB or TSB medium around 48 hr at $37^{\circ}C$. Antifungal activity of the concentrated culture supernatant was not decreased significantly by protease treatments, implying that the antifungal substance might not be a simple peptide or protein. Considering its antifungal and fibrinolytic activities together, B. amyloliquefaciens MJ1-4 can serve as a starter for fermented soyfoods such as Cheonggukjang and Doenjang.