• Korean Journal of Microbiology
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• v.54 no.4
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• pp.448-452
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• 2018

The full genome sequence of Bacillus safensis KCTC 12796BP which had been isolated from the marine sponge in the seawater of Jeju Island, was determined by Pac-Bio next-generation sequencing system. A circular chromosome in the length of 3,935,874 bp was obtained in addition to a circular form of plasmid having 36,690 bp. The G + C content of chromosome was 41.4%, and that of plasmid was 37.3%. The number of deduced CDSs in the chromosome was 3,980, whereas 36 CDS regions were determined in a plasmid. Among the deduced CDSs in chromosome, 81 tRNA genes and 24 rRNA genes in addition to one tmRNA were allocated. More than 30 CDSs for sporulation, 16 CDSs for spore coat, and 20 CDSs for germination were also assigned in the chromosome. Several genes for capsular polysaccharide biosynthesis and for flagella biosynthesis and chemotaxis in addition to genes for osmotic tolerance through glycine-choline betaine pathway were also identified. Above all, the biosynthetic gene cluster for anti-allergic compounds seongsanamides were found among two non-ribosomal peptide synthetase (NRPS) gene clusters for secondary metabolites.

• Animal Bioscience
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• v.35 no.1
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• pp.115-125
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• 2022

Objective: Intramuscular fat (IMF) is a critical economic indicator of pork quality. Studies on IMF among different pig breeds have been performed via high-throughput sequencing, but comparisons within the same pig breed remain unreported. Methods: This study was performed to explore the gene profile and identify candidate long noncoding RNA (lncRNAs) and mRNAs associated with IMF deposition among Laiwu pigs with different IMF contents. Based on the longissimus dorsi muscle IMF content, eight pigs from the same breed and management were selected and divided into two groups: a high IMF (>12%, H) and low IMF group (<5%, L). Whole-transcriptome sequencing was performed to explore the differentially expressed (DE) genes between these two groups. Results: The IMF content varied greatly among Laiwu pig individuals (2.17% to 13.93%). Seventeen DE lncRNAs (11 upregulated and 6 downregulated) and 180 mRNAs (112 upregulated and 68 downregulated) were found. Gene Ontology analysis indicated that the following biological processes played an important role in IMF deposition: fatty acid and lipid biosynthetic processes; the extracellular signal-regulated kinase cascade; and white fat cell differentiation. In addition, the peroxisome proliferator-activated receptor, phosphatidylinositol-3-kinase-protein kinase B, and mammalian target of rapamycin pathways were enriched in the pathway analysis. Intersection analysis of the target genes of DE lncRNAs and mRNAs revealed seven candidate genes associated with IMF accumulation. Five DE lncRNAs and 20 DE mRNAs based on the pig quantitative trait locus database were identified and shown to be related to fat deposition. The expression of five DE lncRNAs and mRNAs was verified by quantitative real time polymerase chain reaction (qRT-PCR). The results of qRT-PCR and RNA-sequencing were consistent. Conclusion: These results demonstrated that the different IMF contents among pig individuals may be due to the DE lncRNAs and mRNAs associated with lipid droplets and fat deposition.

• Microbiology and Biotechnology Letters
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• v.44 no.3
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• pp.355-362
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• 2016

The phosphomannomutase/phosphoglucomutase gene (pmm/pgm) of Vibrio anguillarum (the causative agent of fish vibriosis) was cloned, and the open reading frame corresponded to a protein with 446 amino acids. The pmm/pgm gene showed a significant degree of sequence homology with the previously reported genes from V. mimicus, V. vulnificus, V. splendidus, and V. harveyi, with 92.3%, 91.4%, 89.9%, and 89.9% amino acid identity, respectively. By reverse transcriptase-polymerase chain reaction, we found that the pmm/pgm gene was upregulated under cold stress condition. The PMM/PGM protein is known to catalyze the interconversion between mannose-1-phosphate and mannose-6-phosphate or glucose-1-phosphate and glucose-6-phosphate, which are important intermediates for lipopolysaccharide (LPS) biosynthesis. To confirm the role of PMM/PGM in the LPS biosynthetic pathway, we constructed a knock out mutant by homologous recombination. The respective LPSs were isolated from the V. anguillarum wild-type and mutant strains, and changes were compared by subjecting them to sodium dodecyl sulfate polyacrylamide gel electrophoresis. Based on the different patterns of the LPSs, we expect the pmm/pgm gene to have an important role in LPS biosynthesis. The pmm/pgm-deficient mutant of V. anguillarum will contribute to further studies about the role of LPS in V. anguillarum pathogenesis.

• Journal of Plant Biotechnology
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• v.40 no.4
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• pp.210-216
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• 2013

Efficient regeneration methods and transformation system are a priority for successful application of genetic engineering to vegetative propagated plants such as grape (Vitis labrusca L.). This research is to establish shoot regeneration system from plant explants for 'Campbell Early', 'Tamnara', 'Heukgoosul', 'Heukbosek' using two types of plant growth regulators supplemented to medium. The highest adventitious shoot regeneration rate of 5% was achieved on a medium containing of Murashige and Skoog (MS) inorganic salts and Linsmaier and Skoog (LS) vitamins, 2 mg/L of TDZ and 0.1 mg/L of IBA. Leaf tissue of 'Campbell Early', was co-cultivated with Agrobacterium strains, LBA4404 containing the vector pBI121 carrying with CaMV 35S promoter, gus gene as reporter gene and resistance to kanamycin as selective agent, the other Agrobacterium strains, GV3101 containing the vector pB7 WG2D carrying with mPAP1-D gene. mPAP1-D is a regulatory genes of the anthocyanin biosynthetic pathway. 'Campbell Early' harboring mPAP1-D gene was readily able to be selected by red color due to anthocyanin accumulation in the transformed shoot. These results might be helpful for further studies to enhance the transformation efficiency in grape.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.66 no.3
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• pp.240-247
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• 2021

Anthocyanins are known to be involved in various functions such as antioxidant and antibacterial activities in plants. Although studies on anthocyanins in corn have been conducted recently, basic research related to anthocyanin biosynthesis is insufficient. In this study, we examined the molecular biological and physicochemical properties related to anthocyanin biosynthesis in the tassel and silks of Gwangpyeongok and Dacheongok cultivars. Anthocyanins were not synthesized in either the tassel or silks in Gwangpyeongok, whereas were synthesized in both in Dacheongok. The total anthocyanin content was approximately 30 times higher in the tassel and silks of Dacheongok than in those of Gwangpyeongok. In addition, C-3-G was measured only in the tassel of Dacheongok, and C-3-G, Pg-3-G, and M-3-G were 45.2 times, 27.3 times, and 37.6 times higher, respectively, in the silks of Dacheongok than of Gwangpyeongok. Expression of F3'H, DFR, and GST genes decreased in the tassel, and that of F3'H and DFR genes decreased in the silks of Gwangpyeongok. It was further confirmed that transcription factor P1 and R1 regulate the expression of anthocyanin biosynthetic genes in the tassel and silks, respectively, in Gwangpyeongok. Linoleic acid (C18:2) decreased by 6.6% and 10.9%, and linolenic acid (C18:3) increased by 8.5% and 8.5%, in the tassel and silks, respectively, of Gwangpyeongok compared to those of Dacheongok. Palmitic acid (C16:0) increased by 4.1% and oleic acid (C18:1) decreased by 2.1% in the silks of Gwangpyeongok compared to that in Dacheongok. In addition, the total fatty acid content in the tassel and silks increased by 10.3% and 30.4%, respectively, in Gwangpyeongok compared to that in Dacheongok. However, no significant results were observed in the analysis of phytosterol components. These results may be utilized as useful resources for the development of functional corn containing a large amount of anthocyanins.

• Journal of Life Science
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• v.21 no.10
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• pp.1370-1376
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• 2011

To study the functional genomic analysis of a crenachaeon Sulfolobus acidocaldarius, we have constructed an auxotrophic mutant based on pyrEF, which encodes the pyrimidine biosynthetic enzymes orotate phosphoribosyltransferase and orotidine-5'-monophosphate decarboxylase. S. acidocaldarius was shown to be sensitive to 5-fluoroorotic acid (5-FOA), which can be selected for mutations in pyrEF genes within a pyrimidine biosynthesis cluster. Spontaneous 5-FOA-resistant mutants by ultraviolet, KH1U and KH2U, were found to contain two point mutations and a frame shift mutation in pyrE, respectively. Mutations at these sites from KH1U and KH2U decreased the activity of orotate phosphoribosyltransferase encoded by the pyrE gene and blocked the degradation of 5-FOA into toxic 5-FOMP and 5-FUMP that kill the cells. Therefore, KH1U and KH2U were uracil auxotrophs. Transformation of Sulfolobus-Escherichia coli shuttle vector pC bearing pyrEF genes from S. solfataricus P2 into S. acidocaldarius mutant KH2U restored 5-FOA sensitivity and overcame the uracil auxotrophy. This study establishes an efficient genetic strategy towards the systematic knockout of genes in S. acidocaldarius.

• The Korean Journal of Pesticide Science
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• v.20 no.3
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• pp.189-196
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• 2016

Several microorganisms in particular Bacillus subtilis group have been isolated from diverse places such as soils and the gastrointestinal tract of ruminants etc., and used as biocontrol agent against various plant pathogens and utilized as plant growth promoting agents. Among them, Bacillus is well known as one of the most useful bacteria for biocontrol and plant growth promotion. Bacterium GH1-13 was isolated from a reclaimed paddy field in Wando Island and identified as Bacillus velezensis using phylogenetic analysis on the basis of 16S rRNA and gyrB gene. It was confirmed that GH1-13 produced indole acetic acid (IAA) associated with promoted growth of rice root. GH1-13 showed characteristics of antagonization against the main pathogen of rice as well as diverse pathogenic fungi. GH1-13 had biosynthetic genes, bacillomycin, bacilycin, fengycin, iturin, and surfactin which are considered to be associated closely with inhibition of growth of pathogenic fungi and bacteria. This study showed that GH1-13 could be used as a multifunctional agent for biocontrol and growth promotion of crop.

• Microbiology and Biotechnology Letters
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• v.39 no.2
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• pp.104-110
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• 2011

Actinomycetes, Gram positive soil bacteria, are valuable microorganisms which produce useful secondary metabolites including antibiotics, antiparasitic substances, anti-cancer drugs, and immunosuppressants. Although a major family of actinomycetes, known as streptomycetes, has been intensively investigated at the molecular level for several decades, a potentially valuable and only recently isolated non-streptomycetes rare actinomycetes (NSRA) family has been poorly characterized due to lack of proper genetic manipulation systems. Here we report that a PCR-based genome screening strategy was performed with approximately 180 independently isolated actinomycetes strains to isolate potentially valuable NSRA strains. Thanks to this simple PCR-based genome screening strategy we were able to identify only seven NSRA strains, followed by 16S rRNA sequencing for confirmation. Through further bioassays, one potentially valuable NSRA strain (tentatively named Nocardiopsis species MMBL010) was identified which possessed both antifungal and antibacterial activities, along with the presence of polyketide synthase and non-ribosomal peptide synthase genes. Moreover, Nocardiopsis species MMBL010, which was intrinsically recalcitrant to genetic manipulation, was successfully transformed via E. coli-driven conjugation. These results suggest that PCR-based genome screening, followed by the establishment of an E. coli-driven conjugation system, is an efficient strategy to maximize potentially valuable compounds and their biosynthetic genes from NSRA strains isolated from various environments.

• KSBB Journal
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• v.24 no.3
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• pp.259-266
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• 2009

AfsR2 in Streptomyces lividans, a 63-amino acid protein with limited sequence homology to Streptomyces sigma factors, has been known for a global regulatory protein stimulating multiple antibiotic biosynthetic pathways. Although the detailed regulatory mechanism of AfsK-AfsR-AfsR2 system has been well characterized, very little information about the AfsR2-dependent down-stream regulatory genes were characterized. Recently, the null mutant of afsS in S. coelicolor (the identical ortholog of afsR2) has been characterized through DNA microarray system, revealing that afsS deletion regulated several genes involved in antibiotic biosynthesis as well as phosphate-starvation. Through comparative DNA microarray analysis of afsR2-overexpressed S. lividans, here we also identify several afsR2-dependent genes involved in phosphate starvation, morphological differentiation, and antibiotic regulation in S. lividans, confirming that the AfsR2 plays an important pleiotrophic regulatory role in Streptomyces species.

• Journal of Plant Biotechnology
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• v.33 no.2
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• pp.85-91
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• 2006

Flavanone 3$\beta$-hydroxylase (FHT) is an enzyme acting in the central part of the flavonoid biosynthesis pathway. FHT catalyses the hydroxylation of flavanone to dihydroflavonols in the anthocyanin pathway. In this paper we describe the cloning and expression of the genes encoding the flavonoid-biosynthetic enzyme FHT in Gypsophila paniculata L. A heterologous cDHA probe from Dianthus cavophyllus was used to isolate FHT-encoding cDHA clones from Gypsophila paniculata L.. Inspection of the 1471 bp long sequence revealed an open reading frame 1047 bp, including a 190 bp 5' leader region and 288 bp 3' untranslated region. Comparison of the coding region of this FHT cDHA sequence including the sequences of Arabidopsis thaliana, Citrus sinensis, Dianthus caryophyllus, Ipomoea batatas, Matthiola incana, Nierembergia sp, Petunia hybrida, Solanum tuberosum, Vitis vinifera reveals a identity higher than 69% at the nucleotide level. The function of this nucleotide sequences were verified by comparison with amino acid sequences of the amino-terminus and tryptic peptides from purified plant enzyme, by northern blotting with mRHA from wild type and mutant plants, by in vitro expression yielding and enzymatically active hydroxylase, as indicated by the small dihydrokaempferol peak. Genomic southern blot analysis showed the presence of only one gene for FHT in Gypsophila paniculata.