• Molecules and Cells
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• v.42 no.2
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• pp.123-134
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• 2019

Lysophosphatidic acid (LPA) is an endogenous lysophospholipid with signaling properties outside of the cell and it signals through specific G protein-coupled receptors, known as $LPA_{1-6}$. For one of its receptors, $LPA_1$ (gene name Lpar1), details on the cis-acting elements for transcriptional control have not been defined. Using 5'RACE analysis, we report the identification of an alternative transcription start site of mouse Lpar1 and characterize approximately 3,500 bp of non-coding flanking sequence 5' of mouse Lpar1 gene for promoter activity. Transient transfection of cells derived from mouse neocortical neuroblasts with constructs from the 5' regions of mouse Lpar1 gene revealed the region between -248 to +225 serving as the basal promoter for Lpar1. This region also lacks a TATA box. For the region between -761 to -248, a negative regulatory element affected the basal expression of Lpar1. This region has three E-box sequences and mutagenesis of these E-boxes, followed by transient expression, demonstrated that two of the E-boxes act as negative modulators of Lpar1. One of these E-box sequences bound the HeLa E-box binding protein (HEB), and modulation of HEB levels in the transfected cells regulated the transcription of the reporter gene. Based on our data, we propose that HEB may be required for a proper regulation of Lpar1 expression in the embryonic neocortical neuroblast cells and to affect its function in both normal brain development and disease settings.

• Journal of Plant Biotechnology
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• v.46 no.2
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• pp.97-105
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• 2019

Dehydration Responsive Element Binding (DREB) gene is one of the essential transcription factors plants use for responding to stress conditions including salinity, drought, and cold stress. The purpose of this study was to isolate the full length and characterize the DREB gene from three different genotypes of sugarcane, wild, commercial cultivar, and interspecific hybrid sugarcane. The length of the gene, designated ScDREB was 789 bp, and coding for a putative polypeptide of 262 amino acid residues. Sequences of the gene were submitted to the GenBank database with accession numbers of KX280722.1, KX280721.1, and KX280719.1 for wild sugarcane, commercial cultivar (KPS94-13), and interspecific hybrid (Biotec2), respectively. In silico characterization indicated that the deduced polypeptide contains a putative nuclear localization signal (NLS) sequence, and a conserved AP2/ERF domain of the DREB family, at 82-140 amino residues. Based on multiple sequence alignment, sequences of the gene from the three sugarcane genotypes were classified in the DREB2 group. Gene expression analysis indicated, that ScDREB2 expression pattern in tested sugarcane was up-regulated by salt stress. When the plants were under 100 mM NaCl stress, relative expressions of the gene in leaves was higher than those in roots. In contrast, under 200 mM NaCl stress, relative expressions of the gene in roots was higher than those in leaves. This is the first report on cloning the full length and characterization, of ScDREB2 gene of sugarcane. Results indicate that ScDREB2 is highly responsive to salt stress.

• Journal of Plant Biotechnology
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• v.49 no.1
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• pp.46-60
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• 2022

The genetic variability and population structure of apple mosaic virus (ApMV) have been studied; however, synonymous codon usage patterns influencing the survival rates and fitness of ApMV have not been reported. Based on phylogenetic analyses of 52 ApMV coat protein (CP) sequences obtained from apple, pear, and hazelnut, ApMV isolates were clustered into two groups. High molecular diversity in GII may indicate their recent expansion. A constant and conserved genomic composition of the CP sequences was inferred from the low codon usage bias. Nucleotide composition and relative synonymous codon usage (RSCU) analysis indicated that the ApMV CP gene is AU-rich, but G- and U-ending codons are favored while coding amino acids. This unequal use of nucleotides together with parity rule 2 and the effective number of codon (ENC) plots indicate that mutation pressure together with natural selection drives codon usage patterns in the CP gene. However, in this combination, selection pressure plays a more crucial role. Based on principal component analysis plots, ApMV seems to have originated from apple trees in Europe. However, according to the relative codon deoptimization index and codon adaptation index (CAI) analyses, ApMV exhibited the greatest fitness to hazelnut. As inferred from the results of the similarity index analysis, hazelnut has a major role in shaping ApMV RSCU patterns, which is consistent with the CAI analysis results. This study contributes to the understanding of plant virus evolution, reveals novel information about ApMV evolutionary fitness, and helps find better ApMV management strategies.

• Journal of fish pathology
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• v.8 no.1
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• pp.37-46
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• 1995

The amino acid analysis of polyhedrin protein and nucleotide sequence of polyhedrin gene in H. cunea nuclear polyhedrosis virus (HcNPV) genome have been studied. Polyhedrin had three polypeptide bands in SDS - polyactylamide gel electrophoresis. The major polypeptide had a molecular weight of 25 kd. The polyhedrin was composed of 17 different amino acids. HcNPV DNA was digested with EcoRI restriction enzyme and hybridized with ($\alpha^{32}P$) -labelled AcNPV polyhedrin gene cDNA. The polyhedrin gene was located on the fragment of EcoRI-H. The EcoRI - H fragment containing polyhedrin gene was cloned into the EcoRI site of pUC8 vector which was confirmed with southern blotting, and the recombinant plasmid containg polyhedrin gene was designated as hPE-H. The promoter region of polyhedrin genomic DNA was sequenced. The sequences identified as the TATA box was found at the 5' flanking region of the polyhedrin genomic DNA approximately -79 bp upstream from the transcriptional start site. But CAAT-like box was not shown near the TATA-like box in the polyhedrin gene. Four tandem repeats with the sequence 5' -CTAATAT-3' and 5'-TAAATAA-3' were found between -141 and -108 or -83 upstream and -52 bp downstream from the translation start site. About -141 bp region upstream from the translational start site was highly AT (78%) rich. The coding region for the polyhedrin starts and ends with ATG and TAA, respectively.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.21-22
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• 2000

Expressed sequence tags (EFTs) are the partial segments of cDNA produced from 5 or 3 single-pass sequencing of cDNA clones, error-prone and generated in highly redundant sets. Advancement and expansion of Genomics made biologists to generate huge amount of ESTs from variety of organisms-human, microorganisms as well as plants, and the cumulated number of ESTs is over 5.3 million, As the EST data being accumulate more rapidly, it becomes bigger that the needs of the EST analysis tools for extraction of biological meaning from EST data. Among the several needs of EST analyses, the extraction of protein sequence or functional motifs from ESTs are important for the identification of their function in vivo. To accomplish that purpose the precise and accurate identification of the region where the coding sequences (CDSs) is a crucial problem to solve primarily, and it will be helpful to extract and detect of genuine CD5s and protein motifs from EST collections. Although several public tools are available for EST analysis, there is not any one to accomplish the object. Furthermore, they are not targeted to the plant ESTs but human or microorganism. Thus, to correspond the urgent needs of collaborators deals with plant ESTs and to establish the analysis system to be used as general-purpose public software we constructed the pipelined-EST analysis system by integration of public software components. The software we used are as follows - Phred/Cross-match for the quality control and vector screening, NCBI Blast for the similarity searching, ICATools for the EST clustering, Phrap for EST contig assembly, and BLOCKS/Prosite for protein motif searching. The sample data set used for the construction and verification of this system was 1,386 ESTs from human intrathymic T-cells that verified using UniGene and Nr database of NCBI. The approach for the extraction of CDSs from sample data set was carried out by comparison between sample data and protein sequences/motif database, determining matched protein sequences/motifs that agree with our defined parameters, and extracting the regions that shows similarities. In recent future, in addition to these components, it is supposed to be also integrated into our system and served that the software for the peptide mass spectrometry fingerprint analysis, one of the proteomics fields. This pipelined-EST analysis system will extend our knowledge on the plant ESTs and proteins by identification of unknown-genes.

• Korean Journal of Plant Resources
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• v.19 no.5
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• pp.628-633
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• 2006

ITS DNA sequences from five individuals, representative of five groups designated according to the degree of leaf teeth and lobes from simple to palmate compound leaf in the Viola albida complex, established and further analysed in order to solve the taxonomic difficulty. A total 702 bp was sequenced at the 5.8S ribosomal DNA and internal transcribed spacer 1 and 2. The 5.8S coding region is 163 bp, and has no sequence variations. The ITS1 and ITS2 noncoding regions have a little bit sequence variations, and those were further analysed by the methods of the analysis of variance (ANOVA), the analysis of sequence divergence and the phylogenetic analysis. The result of ANOVA showed no significant differences among individuals investigated. The analysis of sequence divergence with Kimura 2-parameter distance revealed that in-groups showed much less than 0.05 in absolute value among individuals, while two out groups more than 0.05, V. grypoceras and V. orientalis. This result appeared that the sequence divergence among in-groups was not yet occurred in the species level but situated at somewhere below the species level. In the phylogenetic analysis, two outgroups formed the basal clades in order. Five individuals in-groups formed a clade. The clade was, however, not very robust as around 50% in bootstrap value, suggesting that this result was not meaningful in the phylogenetic point of views.

• Korean Journal of Agricultural Science
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• v.46 no.3
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• pp.507-517
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• 2019

To follow up on a 2017 survey of tomato virus diseases, samples with virus-like symptoms were collected from the same areas (Buyeo-gun, Chungchungnam-Do and Daejeon, Korea) in 2018. While in 2017 mixed infections of Tomato mosaic virus with either Tomato yellow leaf curl virus (TYLCV) or Tomato chlorosis virus were detected, only TYLCV was detected in symptomatic samples in 2018. TYLCV amplicons of c.777 bp representing the coat protein (CP) coding region were cloned from the TYLCV positive samples, and the sequence data showed a 97.17% to 98.84% nucleotide and 98.45% to 99.22% amino acid identity with the 2017 Buyeo-gun isolate (MG787542), which had the highest amino acid (aa) sequence identity of up to 99.2% with four 2018 Buyeo-gun sequences (MK521830, MK521833, MK521834, and MK521835). The lowest aa sequence identity of 98.45% was found in a 2018 Daejeon isolate (MK521836); the distance between Buyeo-gun and Daejeon is about 45 km. Phylogenetic analysis indicated that the currently reported CP sequences are most closely related to Korean sequences from Masan (HM130912), Goseong (JN680149), Busan (GQ141873), Boseong (GU325634), and the 2017 isolate TYLCV-N (MG787543) in the 'Japan' cluster of TYLCV isolates and distinct from the 'China' cluster isolates from Nonsan (GU325632), Jeonju (HM130913) and Jeju (GU325633, HM130914). Our survey data from 2017 and 2018 suggest that TYLCV has become established in Korea and may be spread by whitefly vectors from weed reservoirs within the farm environment.

• Korean Journal of Plant Taxonomy
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• v.53 no.1
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• pp.32-37
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• 2023

Spiraea prunifolia f. simpliciflora Nakai is a perennial shrub widely used for horticultural and medicinal purposes. We simultaneously obtained the complete plastid genome (plastome) and nuclear ribosomal gene transcription units, 45S nuclear ribosomal DNA (nrDNA) and 5S nrDNA of S. prunifolia f. simpliciflora, using Illumina short-read data. The plastome is 155,984 bp in length with a canonical quadripartite structure consisting of 84,417 bp of a large single-copy region, 18,887 bp of a short single-copy region, and 26,340 bp of two inverted repeat regions. Overall, a total of 113 genes (79 protein-coding genes, 30 tRNAs, and four rRNAs) were annotated in the plastome. The 45S nrDNA transcription unit is 5,848 bp in length: 1,809 bp, 161 bp, and 3,397 bp for 18S, 5.8S, and 26S, respectively, and 261 bp and 220 bp for internal transcribed spacer (ITS) 1 and ITS 2 regions, respectively. The 5S nrDNA unit is 512 bp, including 121 bp of 5S rRNA and 391 bp of intergenic spacer regions. Phylogenetic analyses showed that the genus Spiraea was monophyletic and sister to the clade of Sibiraea angustata, Petrophytum caespitosum and Kelseya uniflora. Within the genus Spiraea, the sections Calospira and Spiraea were monophyletic, but the sect. Glomerati was nested within the sect. Chamaedryon. In the sect. Glomerati, S. prunifolia f. simpliciflora formed a subclade with S. media, and the subclade was sister to S. thunbergii and S. mongolica. The close relationship between S. prunifolia f. simpliciflora and S. media was also supported by the nrDNA phylogeny, indicating that the plastome and nrDNA sequences assembled in this study belong to the genus Spiraea. The newly reported complete plastome and nrDNA transcription unit sequences of S. prunifolia f. simpliciflora provide useful information for further phylogenetic and evolutionary studies of the genus Spiraea, as well as the family Rosaceae.

• Journal of Microbiology
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• v.44 no.6
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• pp.607-616
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• 2006

Molecular characterization of ten marine cyanobacterial isolates belonging to the order Oscillatoriales was carried out using the phycocyanin locus (cpcBA-IGS) and the 16S-23S internally transcribed spacer region. DNA sequences from the phycocyanin operon discriminated ten genotypes, which corresponded to seven morphotypes identified by traditional microscopic analysis. The cpcB coding region revealed 17% nucleotide variation, while cpcA exhibited 29% variation across the studied species. Phylogenetic analyses support the conclusion that the Phormidium and Leptolyngbya genera are not monophyletic. The nucleotide variations were heterogeneously distributed with no or minimal informative nucleotides. Our results suggest that the discriminatory power of the phycocyanin region varies across the cyanobacterial species and strains. The DNA sequence analysis of the 16S-23S internally transcribed spacer region also supports the polyphyletic nature of the studied oscillatorian cyanobacteria. This study demonstrated that morphologically very similar strains might differ genotypically. Thus, molecular approaches comprising different gene regions in combination with morphological criteria may provide better taxonomical resolution of the order Oscillatoriales.

• Journal of Microbiology and Biotechnology
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• v.11 no.4
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• pp.693-699
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• 2001

An intracellular levansucrase gene, lscR from Rahnella aquatilis ATCC 15552, was cloned and its nucleotide sequence was determined. Nucleotide sequence analysis of this gene revealed a 1,238 bp open reading frame coding for a protein of 415 amino acids. The levansucrase was expressed by using a T7 promoter in Escherichia coli BL21 (DE3) and the enzyme activity was detected in the cytoplasmic fraction. The optimum pH and temperature of this enzyme for levan formation was pH 6 and $30^{\circ}C$, respectively. The deduced amino acid sequence of the lscR gene showed a high sequence similarity (59-89%) with Gram-negative levansucrses, while the level of similarity with Gram-positive enzymes was less than 42%. Multiple alignments of levansucrase sequences reported from Gram-negative and Gram-positive bacteria revealed seven conserved regions. A comparison of the catalytic properties and deduced amino acid sequence of lscR with those of other bacterial levansucrases strongly suggest that Gram-negative and Gram-positive levansucrases have an overall different structure, but they have a similar structure at the active site.