• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.231-231
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• 2022

The GASA protein (Gibberellic acid-stimulated Arabidopsis) are family of small cysteine-rich peptides found in plants. These GASA gene family mainly involved in biotic/abiotic stress responses and plant development. Despite being present in a wide plant species, their action and functions still remain unclear. In this study, using the in-silico analysis method we identified 41 GASA genes in peanuts (Arachis hypogaea L.). Based on the phylogenetic analysis 41 GASA genes are classified in the four major clusters and subclades. Mainly, clusters IV and III comprise the majority of GASA genes 15 and 11 genes respectively, followed by cluster I and cluster II with 9 and 6 genes respectively. Additionally, based on in-silico analysis we predicted the post-transcriptional and post-translational changes of GASA proteins under abiotic stresses such as drought and salt stress would aid our understanding of the regulatory mechanisms. Hence, a further study is planned to evaluate the expression of these GASA genes under stress in different plant tissues to elucidate the possible functional role of GASA genes in peanut plants. These findings might offer insightful data for peanut advancement.

• Journal of Animal Science and Technology
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• v.45 no.2
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• pp.169-182
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• 2003

To understand the structure and regulation of bovine ADRP (Adipocyte Differentiation Related Protein) gene, we have isolated the genomic clone of bovine ADRP and determined its sequence. A genomic Southern blot analysis confirmed that ADRP gene is present as a single copy in bovine genome and the ADRP gene spans 12 kb. Bovine ADRP genomic clone, HwADRPg-1, had 8 exons and 7 introns, and all splicing sites conformed to the GT/AG rule with the exon-intron boundaries located exactly. Analysis of the upstream 649 bp of the sequence of HwADRPg-1 showed that it does not contain any canonical TATAA boxes; however Sp1 binding sites and CAAT boxes are found. The promoter contained potential binding sites for AP-1, AP-2 and several putative transcription factor binding sites. The 5'-flanking region of HwADRPg-1 contained muscle specific transcription activator Myo G and C/EBP (CCAAT/ enhancer binding protein) recognizing site. These results suppose that the Myo G transcription activator regulate the transcription of bovine ADRP gene in muscular tissue and its transcriptional activity was triggered by degree of muscular development. Our results provide the necessary analysis for other flanking sequences are needed in addition to the proximal cis elements of this promoter to confer adipocyte differentiation-dependent or growth-dependent transcriptional control.

• Journal of Plant Biotechnology
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• v.34 no.4
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• pp.323-329
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• 2007

Transgene expression was analyzed in tomato plants. Four lines of neomycin phosphotransferase II gene (NPTII) and the trehalose biosynthetic fusion gene (TPSP) transformed $T_0$ plants showed kanamycin resistance on selection medium. However, the analysis of phenotype (kanamycin resistance) and mRNA expression in $T_1$ plants indicated that the expression of the NPTII and TPSP transgenes was down-regulated to an undetectable level in two independent lines 1 and 11. Southern analysis demonstrated that the lines 1 and 11 had multicopies of the transgenes, whereas the typical transgenic lines 2 and 10 had 1 or 2 copies. DNA methylation analysis using methylation sensitive enzyme detected accumulated CpG DNA methylation on TPSP coding region and CaMV35S promoter region in the line 11, but not the typical transgenic line 2. These results suggest that multicopy transgene in plants is attributed to down-regulation of the transgene expression via transcriptional gene silencing.

• Journal of Life Science
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• v.19 no.8
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• pp.1159-1163
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• 2009

It has been postulated that endoplasmic (ER) stress is involved in the development of several diseases. However, the detailed molecular mechanisms have not been fully understood. Therefore, we characterized a genetic network of genes induced by ER stress using cDNA microarray and gene set expression coherence analysis (GSECA), and identified gene function as well as several transcription regulators associated with ER stress. We analyzed time-dependent gene expression profiles in thapsigargin-treated Sk-Hep1 using an oligonucleotide expression chip, and then selected functional gene sets with significantly high expression coherence which was processed into functional clusters according to the expression similarities. The functions related to sugar binding, lysosome, ribosomal protein, ER lumen, and ER to golgi transport increased, whereas the functions with mRNA processing, DNA replication, DNA repair, cell cycle, electron transport chain and helicase activity decreased. Furthermore, functional clusters were investigated for the enrichment of regulatory motifs using GSECA, and several transcriptional regulators associated with regulation of ER-induced gene expression were found.

• International Journal of Industrial Entomology and Biomaterials
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• v.3 no.1
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• pp.57-62
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• 2001

A cDNA encoding the defensin homologue of a novel family member was isolated from the cDNA library of the firefly,Pyrocoelia rufa. Sequence analysis of the cDNA encoding the defensin homologue of P. rufa resulted that the 165 bp cDHA has an open reading frame of 55 amino acid residues. The deduced amino acid sequences of the defensin homologue gene from P. rufa showed identity to known mammalian defensins. Also 6 cystein residues in the P. rufa defensin homologue gene were conserved in the same position as those of known mammalian defensins. The result suggested that P. rufa defensin homologue is a novel member of the insect defensin family. Southern blot analysis suggests that there may be a single copy number of the P.rufa defensin homologue gene and their fat body-specific expression pattern at the transcriptional level was confirmed by Northern blot analysis.

• International Journal of Industrial Entomology and Biomaterials
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• v.3 no.1
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• pp.43-49
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• 2001

We have cloned and characterized an immediate early-1 gene, iel, which is activated immediately upon entrance of the viral genome into the cell nucleus, from Bombyx mori nuclear polyhedrosis virus (BmNPV) K1 strain. This gene encodes a protein 584 amino acids with a predicted molecular weight of 67 kDa. The promoter and coding regions of BmNPV-K1 ie1 showed high homology with Autographa californica nuclear polyhedrosis virus and BmNPV T3 strain. The BmNPV-K1 ie1 was different from amino acid sequence at 4 positions in BmNPV T3. The location of ie1 gene in the BmNPV-K1 genome was confirmed by Southern blot analysis and its expression patterns at the transcriptional level in the infected cells were confirmed by Nerthern hybridization analysis.

• Journal of Life Science
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• v.10 no.1
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• pp.40-44
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• 2000

The SNF2/SW ATPase/helicase family comprises proteins form a variety of species with in vivo functions, such as transcriptional regulation, maintenance of chromosome stability during mitosis, and various types of DNA repair. Here, we reported the characterization of h게2+gene which was iolated by PCR amplification using the conserved domain of SNF2 motifs. Sequence analysis of PCR product showed striking evolutionary conservation among the SNF2 family of proteins. Two transcripts of 6.7 and 3.4 Lb were detected by Northern blot analysis. furthermore, the intensities of these two bands were increased by ultraviolet(UV) irradiation. These results indicate that the hrp2+ is a novel member of the SNF2 family of proteins and is one of the UV-inducible genes in S. pombe. To determine the level of transcripts of hrp2+ gene during cellular growth, Northern blot analysis were performed. This result indicates that the level of hrp2+transcript reached its maximum before cells entered the exponential growth phase. This suggests that hrp2+ gene is experssed mainly at the early stage of cell growth.

• Journal of Microbiology and Biotechnology
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• v.23 no.8
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• pp.1055-1059
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• 2013

The ectomycorrhizal fungus Tricholoma matsutake grows symbiotically with Pinus densiflora. Phenylalanine ammonia-lyase (E.C. 4.3.1.24) catalyzes the conversion of L-phenylalanine to trans-cinnamic acid. The role of fungal phenylalanine ammonia-lyase, however, has not been clear until now. In this study, the gene encoding phenylalanine ammonia-lyase (PAL), which was isolated from T. matsutake, was cloned and characterized. The PAL gene (tmpal) consists of 2,160 nucleotides, coding for a polypeptide containing 719 amino acid residues. The deduced amino acid sequence of tmpal from T. matsutake shows high identity (70%) with that from Laccaria bicolor. Comparative analysis of the PAL genes among T. matsutake and other species of the class Agaricomycetes showed that both active sites and binding sites were significantly conserved among these genes. The transcriptional analysis of the PAL gene revealed a differential gene expression pattern depending on the developmental stages (mycelium, primordium, stipe, pileus, and gills) of T. matsutake. These results suggest that the PAL gene in T. matsutake plays an important role in multiple physiological functions.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.8
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• pp.3681-3685
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• 2012

Background: In breast cancer, estrogen receptors have been demonstrated to interact with transcription factors to regulate target gene expression. However, high-throughput identification of the transcription regulation relationship between transcription factors and their target genes in response to estradiol is still in its infancy. Purpose: Thus, the objective of our study was to interpret the transcription regulation network of MCF7 breast cancer cells exposed to estradiol. Methods: In this work, GSE11352 microarray data were used to identify differentially expressed genes (DEGs). Results: Our results showed that the MYB (v-myb myeloblastosis viral oncogene homolog [avian]), PGR (progesterone receptor), and MYC (v-myc myelocytomatosis viral oncogene homolog [avian]) were hub nodes in our transcriptome network, which may interact with ER and, in turn, regulate target gene expression. MYB can up-regulate MCM3 (minichromosome maintenance 3) and MCM7 expression; PGR can suppress BCL2 (B-cell lymphoma 2) expression; MYC can inhibit TGFB2 (transforming growth factor, beta 2) expression. These genes are associated with breast cancer progression via cell cycling and the $TGF{\beta}$ signaling pathway. Conclusion: Analysis of transcriptional regulation may provide a better understanding of molecular mechanisms and clues to potential therapeutic targets in the treatment of breast cancer.

• Journal of Photoscience
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• v.12 no.3
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• pp.129-133
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• 2005

The psbC gene, encoding the intrinsic chlorophyll-binding protein of CP43, one of the PS core complex polypeptides, was cloned from the Panax ginseng chloroplast, which is composed of 1,422 nucleotides and the overall nucleotide sequence shows more than 84% identity to those of eukaryotic photosynthetic organisms. The predicted topology of CP43, based on hydropathy analysis, includes six membrane-spanning ${\alpha}-helices$ resulting in three lumenal and four stromal loops. The putative translation start codon for the psbC gene is located at 48 nucleotides upstream from the stop codon of the psbD gene whose product is also a component of the PSII reaction center, implying that the promoter of the psbC gene is possibly located in the middle of the structural gene of the psbD gene. Northern blot analysis of the in vivo accumulation of the psbC transcript from the plants grown under the various growth light intensities (5%, 10%, 20%, and 100%) of daylight indicated that the steady-state level of the psbC transcript was not significantly affected by light intensity.