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

• Proceedings of the Korean Biophysical Society Conference
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• 2002.06b
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• pp.29-29
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• 2002

In response to fungal invasion and other signals, plants accumulate a number of proteins that are involved in defense against pathogens. Osmotin is a 24 kDa protein belonging to the pathogenesis-related (PR) protein, a component of the hypersensitive response in leaves of tobacco plants exposed to tobacco mosaic virus.(omitted)

• The Plant Pathology Journal
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• v.33 no.2
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• pp.148-162
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• 2017

As a step towards discovering novel pathogenesis-related proteins, we performed a genome scale computational identification and characterization of secreted and transmembrane (TM) proteins, which are mainly responsible for bacteria-host interactions and interactions with other bacteria, in the genomes of six representative Burkholderia species. The species comprised plant pathogens (B. glumae BGR1, B. gladioli BSR3), human pathogens (B. pseudomallei K96243, B. cepacia LO6), and plant-growth promoting endophytes (Burkholderia sp. KJ006, B. phytofirmans PsJN). The proportions of putative classically secreted proteins (CSPs) and TM proteins among the species were relatively high, up to approximately 20%. Lower proportions of putative type 3 non-classically secreted proteins (T3NCSPs) (~10%) and unclassified non-classically secreted proteins (NCSPs) (~5%) were observed. The numbers of TM proteins among the three clusters (plant pathogens, human pathogens, and endophytes) were different, while the distribution of these proteins according to the number of TM domains was conserved in which TM proteins possessing 1, 2, 4, or 12 TM domains were the dominant groups in all species. In addition, we observed conservation in the protein size distribution of the secreted protein groups among the species. There were species-specific differences in the functional characteristics of these proteins in the various groups of CSPs, T3NCSPs, and unclassified NCSPs. Furthermore, we assigned the complete sets of the conserved and unique NCSP candidates of the collected Burkholderia species using sequence similarity searching. This study could provide new insights into the relationship among plant-pathogenic, humanpathogenic, and endophytic bacteria.

• CELLMED
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• v.2 no.1
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• pp.2.1-2.11
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• 2012

Tea polyphenols especially catechins have long been studied for their antioxidant and radical scavenging properties. Scientists throughout the world have investigated the usefulness of the regular green tea consumption in several disease conditions. In-vitro and in-vivo experiments on catechins especially epigallocatechingallate have revealed a significant role in many ways. Reactive oxygen species have been increasingly implicated in the pathogenesis of many diseases and important biological processes. Toxic effects of these oxidants, commonly referred to as oxidative stress, can cause cellular damage by oxidizing nucleic acids, proteins, and membrane lipids. Oxidative stress has been related to aging and age related disorders. It is found that in a wide variety of pathological processes, including cancer, atherosclerosis, neurological degeneration, Alzheimer's disease, ageing and autoimmune disorders, oxidative stress has its implications. Catechins have been reported to be useful in combating aging and age related disorders like cancer, cardiovascular disorders and neurodegenerative diseases. In this mini review we will discuss such studies done across the globe.

• The Plant Pathology Journal
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• v.32 no.5
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• pp.377-387
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• 2016

Tomato yellow leaf curl virus (TYLCV), a member of the genus Begomovirus, is one of the most important viruses of cultivated tomatoes worldwide, mainly causing yellowing and curling of leaves with stunting in plants. TYLCV causes severe problems in sub-tropical and tropical countries, as well as in Korea. However, the mechanism of TYLCV infection remains unclear, although the function of each viral component has been identified. TYLCV C4 codes for a small protein involved in various cellular functions, including symptom determination, gene silencing, viral movement, and induction of the plant defense response. In this study, through yeast-two hybrid screenings, we identified TYLCV C4-interacting host proteins from both healthy and symptom-exhibiting tomato tissues, to determine the role of TYLCV C4 proteins in the infection processes. Comparative analyses of 28 proteins from healthy tissues and 36 from infected tissues showing interactions with TYLCV C4 indicated that TYLCV C4 mainly interacts with host proteins involved in translation, ubiquitination, and plant defense, and most interacting proteins differed between the two tissues but belong to similar molecular functional categories. Four proteins-two ribosomal proteins, S-adenosyl-L-homocysteine hydrolase, and 14-3-3 family protein-were detected in both tissues. Furthermore, the identified proteins in symptom-exhibiting tissues showed greater involvement in plant defenses. Some are key regulators, such as receptor-like kinases and pathogenesis-related proteins, of plant defenses. Thus, TYLCV C4 may contribute to the suppression of host defense during TYLCV infection and be involved in ubiquitination for viral infection.

• Journal of Ginseng Research
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• v.43 no.3
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• pp.482-487
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• 2019

Background: The mixed-cultivation of different Panax ginseng cultivars can cause adverse effects on stability of yield and quality. K-1 is a superior cultivar with good root shape and stronger disease resistance. DNA markers mined from functional genes are clearly desirable for K-1, as they may associate with major traits and can be used for marker-assisted selection to maintain the high quality of Korean ginseng. Methods: Five genes encoding pathogenesis-related (PR) proteins of P. ginseng were amplified and compared for polymorphism mining. Primary, secondary, and tertiary structures of PR5 protein were analyzed by ExPASy-ProtParam, PSSpred, and I-TASSER methods, respectively. A coding single nucleotide polymorphism (SNP)-based specific primer was designed for K-1 by introducing a destabilizing mismatch within the 3' end. Allele-specific polymerase chain reaction (PCR) and real-time allele-specific PCR assays were conducted for molecular discrimination of K-1 from other cultivars and landraces. Results: A coding SNP leading to the modification of amino acid residue from aspartic acid to asparagine was exploited in PR5 gene of K-1 cultivar. Bioinformatics analysis showed that the modification of amino acid residue changed the secondary and tertiary structures of the PR5 protein. Primer KSR was designed for specific discrimination of K-1 from other ginseng cultivars and landraces. The developed real-time allele-specific PCR assay enabled easier automation and accurate genotyping of K-1 from a large number of ginseng samples. Conclusion: The SNP marker and the developed real-time allele-specific PCR assay will be useful not only for marker-assisted selection of K-1 cultivar but also for quality control in breeding and seed programs of P. ginseng.

• Journal of Microbiology and Biotechnology
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• v.14 no.3
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• pp.553-562
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• 2004

To investigate protective activity in pepper plants, which were pre-inoculated with arbuscular mycorrhizal (AM) fungi Glomus intra radices (Gi), against pathogenic strain Phytophthora capsici (Pc), pathogenesis-related (PR) proteins and antioxidant enzymes were examined. The growth of root and shoot was the highest in peppers inoculated with G. intraradices, compared with non-inoculated control plants and those challenged by the pathogen with and without mycorrhizae after nine days of infection. Mycorrhizal colonization rate was reduced by about 10% in pathogen-challenged plants, but disease pressure was reduced. The activities of PR proteins, $\beta$-1- 3-glucanase and chitinase, were increased in Pc-treated plants compared to Gi+Pc-treated plants in leaves, but those in roots were suppressed. Superoxide dismutase activity and $H_2O_2${/TEX> content in Gi+Pc and Pc-treated plants were gradually increased in leaves. However, those in roots continuously increased up to 5 days, and then decreased dramatically. Peroxidase activity in leaves and roots increased after P. capsici infection both in plants inoculated with or without G. intraradices. These results suggest that AM fungi, G. intra radices, potentially act as one of the protective agents against plant pathogens. Changes of PR proteins and antioxidative enzymes in mycorrhizae-inoculated pepper appear to be regulated differently in leaves and roots by pathogen infection.

• Proceedings of the Korean Biophysical Society Conference
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• 2003.06a
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• pp.64-64
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• 2003

In growing number of diseases it has been shown that the aggregation of specific proteins has an important role in the pathogenesis of the disorder. This has been demonstrated in structural detail with the liver cirrhosis of ${\alpha}$$_1$-antitrypsin deficiency, and it is now believed that similar protein aggregation underlies many neurodegenerative disorders such as autosomal dominant Parkinson disease, prion diseases, Alzheimer disease, Huntington disease.

• Genomics & Informatics
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• v.17 no.1
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• pp.2.1-2.12
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• 2019

Chronic obstructive pulmonary disease (COPD) is a type of progressive lung disease, featured by airflow obstruction. Recently, a comprehensive analysis of the transcriptome in lung tissue of COPD patients was performed, but the heterogeneity of the sample was not seriously considered in characterizing the mechanistic dysregulation of COPD. Here, we established a new transcriptome analysis pipeline using a deconvolution process to reduce the heterogeneity and clearly identified that these transcriptome data originated from the mild or moderate stage of COPD patients. Differentially expressed or co-expressed genes in the protein interaction subnetworks were linked with mitochondrial dysfunction and the immune response, as expected. Computational protein localization prediction revealed that 19 proteins showing changes in subcellular localization were mostly related to mitochondria, suggesting that mislocalization of mitochondria-targeting proteins plays an important role in COPD pathology. Our extensive evaluation of COPD transcriptome data could provide guidelines for analyzing heterogeneous gene expression profiles and classifying potential candidate genes that are responsible for the pathogenesis of COPD.

• The Plant Pathology Journal
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• v.21 no.3
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• pp.195-206
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• 2005

Spatial and temporal expression of pathogenesis-related (PR) gene and proteins has been recognized as inducible defense response in pepper plants. Gene expression and/or protein accumulation of PR-1, $\beta-1,3-glucanase$ and chitinase was predominantly found in pepper plants during the inoculations by Xanthomonas campestris pv. vesicatoria, Phytophthora capsici and Colletotrichum coccodes. PR-1 and chitinase genes were also induced in pepper plants in response to environmental stresses, such as high salinity and drought. PR-1 and chitinase gene expressions by biotic and abiotic stresses were regulated by their own promoter regions containing several stress-related cis-acting elements. Overexpression of pepper PR-1 or chitinase genes in heterogeneous transgenic plants showed enhanced disease resistance as well as environmental stress tolerances. In this review, we focused on the putative function of pepper PR-1, $\beta-1,3-glucanase$ and chitinase proteins and/or genes at the biochemical, molecular and cytological aspects.