• Asian-Australasian Journal of Animal Sciences
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• 제28권8호
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• pp.1075-1083
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• 2015

Adipose tissue deposited within muscle fibers, known as intramuscular fat (IMF or marbling), is a major determinant of meat quality and thereby affects its economic value. The biological mechanisms that determine IMF content are therefore of interest. In this study, 48 genes involved in the bovine peroxisome proliferator-activated receptor signaling pathway, which is involved in lipid metabolism, were investigated to identify candidate genes associated with IMF in the longissimus dorsi of Hanwoo (Korean cattle). Ten genes, retinoid X receptor alpha, peroxisome proliferator-activated receptor gamma (PPARG), phospholipid transfer protein, stearoyl-CoA desaturase, nuclear receptor subfamily 1 group H member 3, fatty acid binding protein 3 (FABP3), carnitine palmitoyltransferase II, acyl-Coenzyme A dehydrogenase long chain (ACADL), acyl-Coenzyme A oxidase 2 branched chain, and fatty acid binding protein 4, showed significant effects with regard to IMF and were differentially expressed between the low- and high-marbled groups (p<0.05). Analysis of the gene co-expression network based on Pearson's correlation coefficients identified 10 up-regulated genes in the high-marbled group that formed a major cluster. Among these genes, the PPARG-FABP4 gene pair exhibited the strongest correlation in the network. Glycerol kinase was found to play a role in mediating activation of the differentially expressed genes. We categorized the 10 significantly differentially expressed genes into the corresponding downstream pathways and investigated the direct interactive relationships among these genes. We suggest that fatty acid oxidation is the major downstream pathway affecting IMF content. The PPARG/RXRA complex triggers activation of target genes involved in fatty acid oxidation resulting in increased triglyceride formation by ATP production. Our findings highlight candidate genes associated with the IMF content of the loin muscle of Korean cattle and provide insight into the biological mechanisms that determine adipose deposition within muscle.

• Journal of Microbiology and Biotechnology
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• 제20권11호
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• pp.1484-1490
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• 2010

In the Streptomyces hygroscopicus JCM4427 geldanamycin biosynthetic gene cluster, five putative regulatory genes were identified by protein homology searching. Among those genes, gel14, gel17, and gel19 are located downstream of polyketide synthase genes. Gel14 and Gel17 are members of the LAL family of transcriptional regulators, including an ATP/GTP-binding domain at the N-terminus and a DNA-binding helix-turn-helix domain at the C-terminus. Gel19 is a member of the TetR family of transcriptional regulators, which generally act to repress transcription. To verify the biological significance of the putative regulators in geldanamycin production, they were individually characterized by gene disruption, genetic complementation, and transcriptional analyses. All three genes were confirmed as positive regulators of geldanamycin production. Specifically, Gel17 and Gel19 are required for gel14 as well as gelA gene expression.

• 대한의생명과학회지
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• 제29권3호
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• pp.103-108
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• 2023

Enhancers are cis-elements to regulate transcription of cell/tissue-specific genes in multicellular organisms. These elements locate in upstream or downstream regions of target genes and are found in a long distance up to 100 Kb in some cases. Transcription factors and coactivators bind to enhancers in a chromatin environment. Enhancers appear to facilitate the transcription of target genes by communicating with promoters and activating them. As transcription activation mechanism of enhancers, chromatin looping between enhancers and promoters, tracking of enhancer activity to promoters along the intervening regions, and movement of enhancers and promoters into transcription condensates have been suggested based on various molecular and cellular biology studies. These mechanisms are likely to act together rather than exclusive each other for gene transcription. Understanding of enhancer action mechanism may provide a way to regulate the transcription of cell/tissue-specific genes relating with aging or various diseases.

• 한국미생물학회:학술대회논문집
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• 한국미생물학회 2002년도 추계학술대회
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• pp.27-30
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• 2002

Ralstonia eutrupha JMP134 is a well-known soil bacterium which can metabolite diverse aromatic compounds and xenobiotics, such as phenol, 2,4-dichlorophenoxy acetic acid (2, 4-D), and trichloroethylene (TCE), etc. Phenol is degraded through chromosomally encoded phenol degradation pathway. Phenol is first metabolized into catechol by a multicomponent phenol hydroxylase, which is further metabolized to TCA cycle intermediates via a meta-cleavage pathway. The nucleotide sequences of the genes for the phenol hydroxylase have previously been determined, and found to composed of eight genes phlKLMNOPRX in an operon structure. The phlR, whose gene product is a NtrC-like transcriptional activator, was found to be located at the internal region of the structural genes, which is not the case in most bacteria where the regulatory genes lie near the structural genes. In addition to this regulatory gene, we found other regulatory genes, the phlA and phlR2, downstream of the phlX. These genes were found to be overlapped and hence likely to be co-transcribed. The protein similarity analysis has revealed that the PhlA belongs to the GntR family, which are known to be negative regulators, whereas the PhlR2 shares high homology with the NtrC-type family of transcriptional activators like the PhlR. Disruption of the phlA by insertional mutation has led to the constitutive expression of the activity of phenol hydroxylase in JMP134, indicating that PhlA is a negative regulator. Possible regulatory mechanisms of phenol metabolism in R. eutropha JMP134 has been discussed.

• Journal of Plant Biotechnology
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• 제50권
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• pp.225-231
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• 2023

Cold stress is one of the most vulnerable environmental stresses that affect plant growth and crop yields. With the recent advancements in genetic approaches using Arabidopsis and other model systems, genes involved in cold-stress response have been identified and the key cold signaling factors have been characterized. Exposure to low-temperature stress triggers the activation of a set of genes known as cold regulatory (COR) genes. This activation process plays a crucial role in enhancing the resistance of plants to cold and freezing stress. The inducer of the C-repeatbinding factor (CBF) expression 1-CBF module (ICE1-CBF module) is a key cold signaling pathway regulator that enhances the expression of downstream COR genes; however, this signaling module in Panax ginseng remains elusive. Here, we identified cold-signaling-related genes, PgCBF1, PgCBF3, and PgICE1 and conducted functional genomic analysis with a heterologous system. We confirmed that the overexpression of cold- PgCBF3 in the cbf1/2/3 triple Arabidopsis mutant compensated for the cold stress-induced deficiency of COR15A and salt-stress tolerance. In addition, nuclearlocalized PgICE1 has evolutionarily conserved phosphorylation sites that are modulated by brassinsteroid insensitive 2 (PgBIN2) and sucrose non-fermenting 1 (SNF1)-related protein kinase 3 (PgSnRK3), with which it physically interacted in a yeast two-hybrid assay. Overall, our data reveal that the regulators identified in our study, PgICE1 and PgCBFs, are evolutionarily conserved in the P. ginseng genome and are functionally involved in cold and abiotic stress responses.

• Asian-Australasian Journal of Animal Sciences
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• 제32권8호
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• pp.1095-1103
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• 2019

Objective: Among stress responses, the unfolded protein response (UPR) is a well-known mechanism related to endoplasmic reticulum (ER) stress. ER stress is induced by a variety of external and environmental factors such as starvation, ischemia, hypoxia, oxidative stress, and heat stress. Inositol requiring enzyme $1{\alpha}$ ($IRE1{\alpha}$)-X-box protein 1 (XBP1) is the most conserved pathway involved in the UPR and is the main component that mediates $IRE1{\alpha}$ signalling to downstream ER-associated degradation (ERAD)- or UPR-related genes. XBP1 is a transcription factor synthesised via a novel mechanism called 'frame switch splicing', and this process has not yet been studied in the horse XBP1 gene. Therefore, the aim of this study was to confirm the frame switch splicing of horse XBP1 and characterise its dynamics using Thoroughbred muscle cells exposed to heat stress. Methods: Primary horse muscle cells were used to investigate heat stress-induced frame switch splicing of horse XBP1. Frame switch splicing was confirmed by sequencing analysis. XBP1 amino acid sequences and promoter sequences of various species were aligned to confirm the sequence homology and to find conserved cis-acting elements, respectively. The expression of the potential XBP1 downstream genes were analysed by quantitative real-time polymerase chain reaction. Results: We confirmed that splicing of horse XBP1 mRNA was affected by the duration of thermal stress. Twenty-six nucleotides in the mRNA of XBP1 were deleted after heat stress. The protein sequence and the cis-regulatory elements on the promoter of horse XBP1 are highly conserved among the mammals. Induction of putative downstream genes of horse XBP1 was dependent on the duration of heat stress. We confirmed that both the mechanisms of XBP1 frame switch splicing and various binding elements found in downstream gene promoters are highly evolutionarily conserved. Conclusion: The frame switch splicing of horse XBP1 and its dynamics were highly conserved among species. These results facilitate studies of ER-stress in horse.

• 한국생물공학회:학술대회논문집
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• 한국생물공학회 2000년도 춘계학술발표대회
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• pp.584-587
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• 2000

The invasion genes from Salmonella typhimurium were identified by the construction of a cosmid library and subcloning genes into a plasmid vector, pGEM-7Z. The 4.65 kb fragment of the invasion-conferring genomic region of the subclone, pSV6235 was sequenced in both direction. The three open reading frames, which were located at downstream of a promoter region, were designated as sir (Salmonella invasion region)A coding for the 36 amino acids, sirB coding for the 132 amino acids and sirC for the 82 amino acids, respectively. Interesingly, the genomic region of pSV6235 was highly homologous to Yersinia enterocolitica genomic DNA for a high pathogenicity island and Salmonella enteritidis insertion element IS1351 and IS200 DNA. These results show that there could be a significant relationship between S. typhimurium, Y. enterocolitica and S. enteritidis with respect to horizontal evolution process and acquisition of virulence determinants by means of transposon, plasmid or bacteriophage.

• 환경생물
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• 제26권4호
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• pp.377-384
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• 2008

A cell is the product of a long period of evolution and can be represented as an optimized system (homeostasis). Stimuli from the outside environment are received by sensory apparatus on the surface of the cell and transferred through complicated pathways and eventually regulate gene expression. These signals affect cell physiology, growth, and development, and the interaction among genes in the signal transduction pathway is a critical part of the regulation. In this study, the interactions of deletion mutants and overexpression of the extracopies of the genes were used to understand their relationships to each other. Also, green fluorescent protein (GFP reporter gene) was fused to the regulatory genes to elucidate their interactions. Cooverexpression of the two genes in extracopy plasmids suggested that patS acts at the downstream of hetR in the regulatory network. The experiments using gfp fusion in different genetic background cells also indicated the epistasis relationships between the two genes. A model describing the regulatory network that controls cell development is presented.

• BMB Reports
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• 제49권4호
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• pp.199-200
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• 2016

Gene regulation in the brain is essential for long-term plasticity and memory formation. Despite this established notion, the quantitative translational map in the brain during memory formation has not been reported. To systematically probe the changes in protein synthesis during memory formation, our recent study exploited ribosome profiling using the mouse hippocampal tissues at multiple time points after a learning event. Analysis of the resulting database revealed novel types of gene regulation after learning. First, the translation of a group of genes was rapidly suppressed without change in mRNA levels. At later time points, the expression of another group of genes was downregulated through reduction in mRNA levels. This reduction was predicted to be downstream of inhibition of ESR1 (Estrogen Receptor 1) signaling. Overexpressing Nrsn1, one of the genes whose translation was suppressed, or activating ESR1 by injecting an agonist interfered with memory formation, suggesting the functional importance of these findings. Moreover, the translation of genes encoding the translational machineries was found to be suppressed, among other genes in the mouse hippocampus. Together, this unbiased approach has revealed previously unidentified characteristics of gene regulation in the brain and highlighted the importance of repressive controls.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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• pp.164-164
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• 2017

High throughput transcriptome investigations of immunity in plants highlight the complexity of gene networks leading to incompatible interaction. To identify genes crucial to resistance against Xanthomonas oryzae pv oryzae, functional genetic analysis of selected differentially expressed genes from our microarray data set was carried out. A total of 13 overexpression vector constructs were made using 35S CaMV promoter which drive constitutive expression in rice. Most of the genes are developmentally expressed especially during maximum tillering stage and are commonly highly expressed in the leaves. When screened against Xoo strain K2, the transgenic plants displayed shorter lesion length compared with wild type Dongjin which indicates partial resistance. The levels of ROS continuously magnified after inoculation which indicates robust cellular sensing necessary to initiate cell death. Elevated transcripts levels of several defense-related genes at the downstream of defense signal network also corroborate the phenotype reaction of the transgenic plants. Moreover, expression assays revealed regulation of these genes by cross-communicating signal-transductions pathways mediated by salicylic and jasmonic acid. These collective findings revealed the key immune signaling conduits critical to mount full defense against Xoo.