• KOREAN JOURNAL OF CROP SCIENCE
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• v.59 no.3
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• pp.263-281
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• 2014

Transcription factors are essential for the regulation of gene expression in plant. They are binding to either enhancer or promoter region of DNA adjacent to the gene and are related to basal transcription regulation, differential enhancement of transcription, development, response to intercellular signals or environment, and cell cycle control. The mechanism in controlling gene expression of transcription can be understood through the assessment of the complete sequence for the maize genome. It is possible that the maize genome encodes 4,000 or more transcription factors because it has undergone whole duplication in the past. Previously, several transcription factors of maize have been characterized. In this review article, the transcription factors were selected using Pfam database, including many family members in comparison with other family and listed as follows: ABI3/VP1, AP2/EREBP, ARF, ARID, AS2, AUX/IAA, BES1, bHLH, bZIP, C2C2-CO-like, C2C2-Dof, C2C2-GATA, C2C2-YABBY, C2H2, E2F/DP, FHA, GARP-ARR-B, GeBP, GRAS, HMG, HSF, MADS, MYB, MYB-related, NAC, PHD, and WRKY family. For analyzing motifs, each amino acid sequence has been aligned with ClustalW and the conserved sequence was shown by sequence logo. This review article will contribute to further study of molecular biological analysis and breeding using the transcription factor of maize as a strategy for selecting target gene.

• BMB Reports
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• v.39 no.5
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• pp.595-606
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• 2006

Metallothioneins are a group of low molecular mass and cysteine-rich metal-binding proteins, ubiquitously found in most living organisms. They play an important role in maintaining intracellular metal homeostasis, eliminating metal toxification and protecting against intracellular oxidative damages. Analysis of complete rice genome sequences revealed eleven genes encoding putative metallothionein (OsMT), indicating that OsMTs constitute a small gene family in rice. Expression profiling revealed that each member of the OsMT gene family differs not only in sequence but also in their tissue expression patterns, suggesting that these isoforms may have different functions they perform in specific tissues. On the basis of OsMT structural and phylogenetic analysis, the OsMT family was classified as two classes and class I was subdivided into four types. Additionally, in this paper we also present a complete overview of this family, describing the gene structure, genome localization, upstream regulatory element, and exon/intron organization of each member in order to provide valuable insight into this OsMT gene family.

• Korean Journal of Microbiology
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• v.55 no.2
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• pp.164-166
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• 2019

The complete genomic information of Microbacterium aurum KACC $15219^T$ (= IFO $15204^T$ = DSM $8600^T$) is described. The genome of M. aurum KACC $15219^T$ contains 3,096 protein coding genes and an average G+C content of 69.9% in its chromosome (3.42 Mbp). This strain can use various carbon sources for growth, including quinic acid. Quinic acid is used as a substrate for the synthesis of aromatic amino acids via the shikimate pathway which are useful in the industry. M. aurum KACC $15219^T$ will provide basis to improve our understanding of this organism and allow more efficient application of the strain to industry.

• Bulletin of the Korean Chemical Society
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• v.32 no.6
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• pp.1925-1930
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• 2011

Psychrophilic bacteria have acquired cold-resistance in order to protect themselves against freezing temperatures, which would otherwise be lethal. DnaK/DnaJ/GrpE systems are molecular chaperones which facilitate proper folding of newly synthesized proteins. Efficient folding processes are of great importance especially in a cold environment, such as the Arctic. In order to understand the protection mechanisms of psychrophilic bacteria against cold temperatures, we have explored a genome of KOPRI22215, tentatively identified as Psychromonas arctica, whose genome sequence has not yet been discovered. With an aim of searching for a coding gene of DnaK from KOPRI22215, we have applied a series of polymerase chain reactions (PCR) with homologous primers designed from other Psychromonas species and LA PCR in vitro cloning. 1917 bp complete coding sequence of dnaK from KOPRI22215 was identified including upstream promoter sites. Recombinant plasmids to overexpress PaDnaK along with EcDnaK (DnaK of E. coli) were then constructed in pAED4 vector and the pET-based system to induce PaDnaK expression by IPTG. Characterization assays of expressed PaDnaK were carried out by measuring survival rates upon 4 day incubation at 4 $^{\circ}C$: a refolding assay as molecular chaperone, and ATPase assay for functional activity. Taking account of all the data together, we conclude that PaDnaK was identified, successfully expressed, and found to be more efficient in providing cold-resistance for bacterial cells.

• Korean Journal of Microbiology
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• v.41 no.1
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• pp.8-12
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• 2005

Some genes, which are involved in the biosynthesis of polysaccharides, could be found by the genome project of Sphingomonas chungbukensis DJ77. In this study, we identified the complete nucleotide sequence of a gene, encoding the glucosyl-isoprenyl phosphate-transferase, which catalyzes the first step in the biochemical pathway for the synthesis of the sphingan type polysaccharide. This gene, named spsB, is initiated by the ATG codon and terminated by the TGA, and its open reading frame consists of 1392 bp, encoding 463 amino acids. The predicted amino acid sequence of this enzyme indicates $50\%$ similarity to SpsB of Sphingomonas spp S88, also produces sphingan, and $48\%$ to GelB of Sphingomonas paucimobilis ATCC 31461.

• KSBB Journal
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• v.13 no.2
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• pp.214-219
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• 1998

Polymerase chain reaction(PCR) was conducted to obtain the gene encoding glucose oxidase(GOD) from Aspergillus niger(ATCC 2110) and the DNA sequence determined was coincided with published GOD sequence from A. niger. Recombinant transforming vector containing GOD and hygromycin B(hyg.B) resistant gene(hph) was constructed and used for further transformation of A. niger ATCC 2110. Selectivity of hyg.B against A. niger differed depending on which media were used i.e., nutrient-rich media such as potato dextrose agar(PDA) and complete medium(CM) showed only 50% growth inhibition at 400 $\mu$m ml$^-1$ of hyg.B while the minimal media inhibited mycelial growth completely at 200 $\mu$m ml$^-1$ of hyg.B. Twenty to sixty putative transformants were isolated from the hyg.B-containing minimal top agar, transferred successively onto alternating selective and nonselective media for a mitotic stability of hyg.B resistance and, then, single-spored. Among the stable transformants, the transformant(GOD1-6) grown by flask culture showed the considerable increase of extracellular GOD activity, which was estimated to the degree of 50% - 100% comparing to that of wild type. Transformation of tGOD1-6 was resulted from integration of the vectors into heterologous as well as homologous regions of the A. niger genome. Southern blot analysis revealed that there were two independent integrations of vector into fungal genome and one into the GOD gene due to homologous recombination. In addition, GOD activity and sodium gluconate production when tGOD1-6 was fed-batch fermented were enhanced 11 fold and 2.25 fold, respectively, compared to that of the wild type.

• Genomics & Informatics
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• v.13 no.2
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• pp.53-59
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• 2015

In developing countries threat of cholera is a significant health concern whenever water purification and sewage disposal systems are inadequate. Vibrio cholerae is one of the responsible bacteria involved in cholera disease. The complete genome sequence of V. cholerae deciphers the presence of various genes and hypothetical proteins whose function are not yet understood. Hence analyzing and annotating the structure and function of hypothetical proteins is important for understanding the V. cholerae. V. cholerae O139 is the most common and pathogenic bacterial strain among various V. cholerae strains. In this study sequence of six hypothetical proteins of V. cholerae O139 has been annotated from NCBI. Various computational tools and databases have been used to determine domain family, protein-protein interaction, solubility of protein, ligand binding sites etc. The three dimensional structure of two proteins were modeled and their ligand binding sites were identified. We have found domains and families of only one protein. The analysis revealed that these proteins might have antibiotic resistance activity, DNA breaking-rejoining activity, integrase enzyme activity, restriction endonuclease, etc. Structural prediction of these proteins and detection of binding sites from this study would indicate a potential target aiding docking studies for therapeutic designing against cholera.

• The Plant Pathology Journal
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• v.33 no.4
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• pp.382-392
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• 2017

This study reports the findings of a distinct Potato virus Y (PVY) isolate found in Northeast China. One hundred and ten samples (leaves and tubers) were collected from potato plants showing mosaic symptoms around the city of Harbin in Heilongjiang province of China. The collected tubers were planted and let to grow in a greenhouse. New potato plants generated from these tubers showed similar symptoms, except for one plant. Subsequent serological analyses revealed PVY as the causing agent of the disease. A novel PVY isolate (referred to as HLJ-C-44 in this study) was isolated from this sample showing unique mild mosaic and crisped leaf margin symptoms. The complete genome of this isolate was analyzed and determined. The results showed that HLJ-C-44 is a typical PVY isolate. Phylogenetic analysis indicated that this isolate belongs to the N-Wi strain group of PVY recombinants ($PVY^{N-Wi}$) and also shared the highest overall sequence identity (nucleotide and amino acid) with other members of this strain group. However, recombination analysis of isolate HLJ-C-44 revealed a recombination pattern that differed from that of other $PVY^{N-Wi}$ isolates. Moreover, biological assays in four different potato cultivars and in Nicotiana tabacum also revealed a different phenotypic response than that of a typical $PVY^{N-Wi}$ isolate. This data, combined, suggest that HLJ-C-44 is a novel PVY recombinant with distinct biological properties.

• The Plant Pathology Journal
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• v.33 no.5
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• pp.508-513
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• 2017

The complete genome sequence of a Slovak SL-1 isolate of Tomato mosaic virus (ToMV) was determined from the next generation sequencing (NGS) data, further confirming a limited sequence divergence in this tobamovirus species. Tomato genotypes Monalbo, Mobaci and Moperou, respectively carrying the susceptible tm-2 allele or the Tm-1 and Tm-2 resistant alleles, were tested for their susceptibility to ToMV SL-1. Although the three tomato genotypes accumulated ToMV SL-1 to similar amounts as judged by semiquantitative DAS-ELISA, they showed variations in the rate of infection and symptomatology. Possible differences in the intra-isolate variability and polymorphism between viral populations propagating in these tomato genotypes were evaluated by analysis of the capsid protein (CP) encoding region. Irrespective of genotype infected, the intra-isolate haplotype structure showed the presence of the same highly dominant CP sequence and the low level of population diversity (0.08-0.19%). Our results suggest that ToMV CP encoding sequence is relatively stable in the viral population during its replication in vivo and provides further demonstration that RNA viruses may show high sequence stability, probably as a result of purifying selection.

• The Plant Pathology Journal
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• v.39 no.3
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• pp.303-308
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• 2023

The global climate change and international trade have facilitated the movement of plants across borders, increasing the risk of introducing novel plant viruses in new territories. Ixora coccinea exhibited virus-like foliar symptoms, including mosaic and mild mottle. An Oxford Nanopore Technologies-based compact and portable MinION platform was used to identify the causal viral pathogen. The complete genome sequence of jasmine virus H (JaVH; 3867 nt, JaVH-CNU) was determined and found to share 88.4-90.3% nucleotide identity with that of Jasminum sambac JaVH isolate in China. Phylogenetic analysis based on the complete amino acid sequences of RNA-dependent RNA polymerase and coat protein revealed that JaVH-CNU was grouped separately with other JaVH isolates. This is the first report of a natural JaVH infection of I. coccinea. The application of rapid nanopore sequencing for plant virus identification was demonstrated and is expected to provide accurate and rapid diagnosis for virus surveillance.