• BMB Reports
• /
• v.44 no.1
• /
• pp.11-21
• /
• 2011

During the last decade small regulatory RNA (srRNA) emerged as central players in the regulation of gene expression in all kingdoms of life. Multiple pathways for srRNA biogenesis and diverse mechanisms of gene regulation may indicate that srRNA regulation evolved independently multiple times. However, small RNA pathways share numerous properties, including the ability of a single srRNA to regulate multiple targets. Some of the mechanisms of gene regulation by srRNAs have significant effect on the abundance of free srRNAs that are ready to interact with new targets. This results in indirect interactions among seemingly unrelated genes, as well as in a crosstalk between different srRNA pathways. Here we briefly review and compare the major srRNA pathways, and argue that the impact of srRNA is always at the system level. We demonstrate how a simple mathematical model can ease the discussion of governing principles. To demonstrate these points we review a few examples from bacteria and animals.

• Korean Journal of Psychosomatic Medicine
• /
• v.4 no.1
• /
• pp.146-154
• /
• 1996

The impact of stress on immune function is known to be associated with the interactions among the central nervous system(CNS), neuroendocrine system, and immune system. The main pathways between stress and immune system are wiring of lymphoid organs and neuroendocrine system. Immune system also produces neuropeptides, which modulate immune system. Mediators of psychosocial influences on immune function are found to be peptides released by the pituitry, hormones, md autonomic nervous system. Hypothalamus integrates endocrine, neural and immune systems. Particularly, paraventricular nucleus appears to play a central role in this integration. On the other hand, endocrine system receives feedback from the immune system. The major regulatory pathways which pituitary modulates include the hypothalamic-pituitary-adrenal-thymic(HPAT) axis, hypothalamic-pituitary-gonadal-thymic(HPGT) axis, pineal-hypothalamic-pituitary(PHP) axis. Bidirectional pathways such as feedforward and feedback pathways are suggested in the interaction between stress and immune system. It suggests that psychosocial inputs affect immune function, but also that immunological inputs affect psychosocial function. Thus, prospective studies for elucidating the relationship between stress and immune function should incorporate measures of immune function as well as measures of endocrine, autonomic, and brain activities at the same time.

• Genomics & Informatics
• /
• v.20 no.3
• /
• pp.26.1-26.19
• /
• 2022

Diabetes and its related complications are associated with long term damage and failure of various organ systems. The microvascular complications of diabetes considered in this study are diabetic retinopathy, diabetic neuropathy, and diabetic nephropathy. The aim is to identify the weighted co-expressed and differentially expressed genes (DEGs), major pathways, and their miRNA, transcription factors (TFs) and drugs interacting in all the three conditions. The primary goal is to identify vital DEGs in all the three conditions. The overlapped five genes (AKT1, NFKB1, MAPK3, PDPK1, and TNF) from the DEGs and the co-expressed genes were defined as key genes, which differentially expressed in all the three cases. Then the protein-protein interaction network and gene set linkage analysis (GSLA) of key genes was performed. GSLA, gene ontology, and pathway enrichment analysis of the key genes elucidates nine major pathways in diabetes. Subsequently, we constructed the miRNA-gene and transcription factor-gene regulatory network of the five gene of interest in the nine major pathways were studied. hsa-mir-34a-5p, a major miRNA that interacted with all the five genes. RELA, FOXO3, PDX1, and SREBF1 were the TFs interacting with the major five gene of interest. Finally, drug-gene interaction network elucidates five potential drugs to treat the genes of interest. This research reveals biomarker genes, miRNA, TFs, and therapeutic drugs in the key signaling pathways, which may help us, understand the processes of all three secondary microvascular problems and aid in disease detection and management.

• The Plant Pathology Journal
• /
• v.26 no.1
• /
• pp.1-7
• /
• 2010

Phosphorylation is a major post-translational modification of proteins that regulate diverse signal transduction pathways in eukaryotic cells. 14-3-3 proteins are regulatory proteins that bind to target proteins in a phosphorylation-dependent manner and have been shown to play an important role in plant growth and development, primary metabolism, and signal transduction. Because phosphorylation plays a critical role in signal transduction pathways to trigger plant immunity, involvement of 14-3-3 proteins in plant immunity has been suggested for a long time. Recent studies have provided new evidence to support a role for 14-3-3 proteins in plant immunity. This review will briefly discuss general characteristics of 14-3-3 proteins and their involvement in plant immunity.

• BMB Reports
• /
• v.53 no.1
• /
• pp.56-63
• /
• 2020

The ubiquitin-proteasome system (UPS) and autophagy are two major degradative pathways of proteins in eukaryotic cells. As about 30% of newly synthesized proteins are known to be misfolded under normal cell conditions, the precise and timely operation of the UPS and autophagy to remove them as well as their tightly controlled regulation, is so important for proper cell function and survival. In the UPS, target proteins are labeled by small proteins called ubiquitin, which are then transported to the proteasome complex for degradation. Alternatively, many greatly damaged proteins are believed to be delivered to the lysosome for autophagic degradation. Although these autophagy and UPS pathways have not been considered to be directly related, many recent studies proposed their close link and dynamic interconversion. In this review, we'll focus on the several regulatory molecules that function in both UPS and autophagy and their crosstalk. Among the proposed multiple modulators, we will take a closer look at the so-called main connector of UPS-autophagy regulation, p62. Last, the functional role of p62 in the mitophagy and its implication for the pathogenesis of Parkinson's disease, one of the major neurodegenerative diseases, will be briefly reviewed.

• Molecules and Cells
• /
• v.44 no.5
• /
• pp.335-341
• /
• 2021

Zinc is an essential micronutrient with crucial roles in multiple facets of biological processes. Dysregulated zinc homeostasis impairs overall immune function and resultantly increases susceptibility to infection. Clinically, zinc supplementation is practiced for treatment of several infectious diseases, such as diarrhea and malaria. Recent focus on zinc as a beneficial element for immune system support has resulted in investigation of the immunomodulatory roles of zinc in a variety of immune cells. Besides its classical role as a cofactor that regulates the structural function of thousands of proteins, accumulating evidence suggests that zinc also acts, in a manner similar to calcium, as an ionic regulator of immune responses via participation as an intracellular messenger in signaling pathways. In this review, we focus on the role of zinc as a signaling molecule in major pathways such as those downstream of Toll-like receptors-, T cell receptor-, and cytokine-mediated signal transduction that regulate the activity and function of monocytes/macrophages and T cells, principal players in the innate and adaptive immune systems.

• Proceedings of the Korean Society of Crop Science Conference
• /
• 2022.10a
• /
• pp.254-254
• /
• 2022

Astragalus membranaceus (A. membranaceus) has traditionally been used as a medicinal plant in East Asia for the treatment ofvarious diseases. A. membranaceus belongs to the legume family and is known to be rich in substances such as flavonoids and saponins. Recent pharmacological studies of A. membranaceus have shown that the plant has immunomodulatory, anti-oxidant, anti-cancer, and anti-inflammatory effects. However, knowledge of major biosynthetic pathways in A. membranaceu is still lacking. Recently developed sequencing techniques enable high-quality transcriptome analysis in plants, which is recognized as an important part in elucidating the regulatory mechanisms of many plant secondary metabolic pathways. However, it is difficult to predict the number of transcripts because plant transcripts contain a large number of isoforms due to alternative splicing events, which can vary depending on the assembly platform used. In this study, we constructed three unigene sets using Pac-Bio isoform sequencing, Trinity and rnaSPAdes assembly for detailed transcriptome analysis mA. membranaceus. Furthermore, all genes involved in the flavonoid biosynthetic pathway were searched from three unigene sets, and structural comparisons and expression profiles between these genes were analyzed. The isoflavone synthesis was active in most tissues. Flavonol synthesis was mainly active in leaves and flowers, and anthocyanin synthesis was specific in flowers. Gene structural analysis revealed structural differences in the flavonoid-related genes derived from the three unigene sets. This study suggests the need for the application of multiple unigene sets for the analysis of key biosynthetic pathways in plants.

• Korean Journal of Food Science and Technology
• /
• v.41 no.5
• /
• pp.477-482
• /
• 2009

Toll-like receptors (TLRs) play a critical role in the induction of innate immune responses that are essential for host defense against invading microbial pathogens. In general, TLRs have two major downstream signaling pathways, namely MyD88- and TRIF-dependent pathways, leading to the activation of nuclear factor-${\kappa}B$ (NF-${\kappa}B$) and interferon regulatory factor 3 (IRF3) and the expression of inflammatory mediators. TLR4 dimerization is required for the activation of downstream signaling pathways and may be one of the first lines of regulation in activating TLR-mediated signaling pathways. In this paper, the molecular targets of curcumin, 6-shogaol, and cinnamaldehyde in TLR signaling pathways will be discussed. Curcumin, 6-shogaol, and cinnamaldehyde with ${\alpha},{\beta}$-unsaturated carbonyl groups inhibit the dimerization of TLR4 induced by lipopolysaccharide, resulting in the downregulation of NF-${\kappa}B$ and IRF3. These results suggest that phytochemicals with the structural motif conferring Michael addition inhibit TLR4 dimerization, suggesting a novel mechanism for the anti-inflammatory activity of phytochemicals.

• Journal of Ginseng Research
• /
• v.46 no.6
• /
• pp.722-730
• /
• 2022

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the pathogenic virus that causes coronavirus disease 2019 (COVID-19), with major symptoms including hyper-inflammation and cytokine storm, which consequently impairs the respiratory system and multiple organs, or even cause death. SARS-CoV-2 activates inflammasomes and inflammasome-mediated inflammatory signaling pathways, which are key determinants of hyperinflammation and cytokine storm in COVID-19 patients. Additionally, SARS-CoV-2 inhibits inflammasome activation to evade the host's antiviral immunity. Therefore, regulating inflammasome initiation has received increasing attention as a preventive measure in COVID-19 patients. Ginseng and its major active constituents, ginsenosides and saponins, improve the immune system and exert anti-inflammatory effects by targeting inflammasome stimulation. Therefore, this review discussed the potential preventive and therapeutic roles of ginseng in COVID-19 based on its regulatory role in inflammasome initiation and the host's antiviral immunity.

• Proceedings of the Korean Society for Bioinformatics Conference
• /
• 2006.02a
• /
• pp.83-89
• /
• 2006

Cellular functions are carried out by a concerted action of biochemical pathways whose components have genetic interactions. Abnormalities in the activity of the genes that constitute or modulate these pathways frequently have oncogenic implications. Therefore, identifying the upstream regulatory genes for major biochemical pathways and defining their roles in carcinogenesis can have important consequences in establishing an effective target-oriented antitumor strategy We have analyzed the gene expression profiles of human liver cancer samples using cDNA microarray chips enriched in liver and/or stomach-expressed cDNA elements, and identified groups of genes that can tell tumors from non-tumors or normal liver, or classify tumors according to clinical parameters such as tumor grade, age, and inflammation grade. We also set up a high-throughput cell-based assay system (cell chip) that can monitor the activity of major biochemical pathways through a reporter assay. Then, we applied the cell chip platform for the analysis of the HCC-associated genes discovered from transcriptome profiling, and found a number of cancer marker genes having a potential of modulating the activity of cancer-related biochemical pathways such as E2F, TCF, p53, Stat, Smad, AP-1, c-Myc, HIF and NF-kB. Some of these marker genes were previously blown to modulate these pathways, while most of the others not. Upon a fast-track phenotype analysis, a subset of the genes showed increased colony forming abilities in soft agar and altered cell morphology or adherence characteristics in the presence of purified matrix proteins. We are currently analyzing these selected marker genes in more detail for their effects on various biological Processes and for Possible clinical roles in liver cancer development.