• Microbiology and Biotechnology Letters
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• v.46 no.4
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• pp.334-345
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• 2018

Spore-forming Bacillus species are commercially available probiotic formulations for application in humans. They have health benefits and help prevent disease in hosts by combating entero-pathogens and ameliorating antibiotic-associated diarrhea. However, the molecular and cellular mechanisms of these benefits remain unclear. Here, we report the draft genome of a potential probiotic strain of Bacillus clausii B106. We mapped and compared the probiotic profile of B106 with other reference genomes. The draft genome analysis of B106 revealed the presence of ADI pathway genes, indicating its ability to tolerate acidic pH and bile salts. Genes encoding fibronectin binding proteins, enolase, as well as a gene cluster involved in the biosynthesis of exopolysaccharides underscored the potential of B106 to adhere to the intestinal epithelium and colonize the human gut. Genes encoding bacteriocins were also detected, indicating the antimicrobial ability of this isolate. The presence of genes encoding vitamins, including Riboflavin, Folate, and Biotin, also indicated the health-promoting ability of B106. Resistance of B106 to multiple antibiotics was evident from the presence of genes encoding resistance to chloramphenicol, ${\beta}$-lactams, Vancomycin, Tetracycline, fluoroquinolones, and aminoglycosides. The findings indicate the significance of B. clausii B106 administration during antibiotic treatment and its potential value as a probiotic strain to replenish the health-promoting and disease-preventing gut flora following antibiotic treatment.

• Genomics & Informatics
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• v.19 no.4
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• pp.43.1-43.12
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• 2021

Campylobacter jejuni is one of the most prevalent organisms associated with foodborne illness across the globe causing campylobacteriosis and gastritis. Many proteins of C. jejuni are still unidentified. The purpose of this study was to determine the structure and function of a non-annotated hypothetical protein (HP) from C. jejuni. A number of properties like physiochemical characteristics, 3D structure, and functional annotation of the HP (accession No. CAG2129885.1) were predicted using various bioinformatics tools followed by further validation and quality assessment. Moreover, the protein-protein interactions and active site were obtained from the STRING and CASTp server, respectively. The hypothesized protein possesses various characteristics including an acidic pH, thermal stability, water solubility, and cytoplasmic distribution. While alpha-helix and random coil structures are the most prominent structural components of this protein, most of it is formed of helices and coils. Along with expected quality, the 3D model has been found to be novel. This study has identified the potential role of the HP in 2-methylcitric acid cycle and propionate catabolism. Furthermore, protein-protein interactions revealed several significant functional partners. The in-silico characterization of this protein will assist to understand its molecular mechanism of action better. The methodology of this study would also serve as the basis for additional research into proteomic and genomic data for functional potential identification.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.127-127
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• 2017

Aluminum is the most abundant metallic element in the Earth's crust and considered as the most limiting factor for plant productivity in acidic soils. The inhibition of root growth is recognized as the primary effect of Al toxicity. Seeds of wheat cv. Keumkang (Korean cultivar) were germinated on petridish for 5 days and then transferred hydroponic apparatus which was treated with $0{\mu}M$ $AlCl_3$ (control), $100{\mu}M$ $AlCl_3$ and $150{\mu}M$ $AlCl_3$ for 5 days. The length of roots, shoots and fresh weight of wheat seedlings were decreased under aluminum stress. The concentrations of $K^+$, $Mg^{2+}$ and $Ac^{2+}$ were decreased whereas $Al^{3+}$ and $P_2O_5{^-}$ concentration was increased under aluminum stress. Using confocal microscopy, the fluorescence intensity of aluminum was increased with morin staining. In this study, a proteome analysis was performed to identify proteins, which is responsible to aluminum stress in wheat roots. In 10-day-old seedlings, proteins were extracted from roots and separated by 2-DE, stained by CBB. Using image analysis, a total of 47 differentially expressed protein spots were selected, whereas 19 protein spots were significantly up-regulated such as s-adenosylmethionine, oxalate oxidase, malate dehydrogenase, cysteine synthase, ascorbate peroxidase and 28 protein spots were significantly down-regulated such as heat shock protein 70, o-methytransferase 4, enolase, amylogenin by aluminum stress following protein spots analyzed by LTQ-FTICR mass spectrometry. The results provide the global picture of Al toxicity-induced alterations of protein profiles in wheat roots, and identify the Al toxicity-responsive proteins related to various biological processes that may provide some novel clues about plant Al tolerance.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.61 no.4
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• pp.227-234
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• 2016

In this study, we analyzed seed storage proteins in order to investigate the main factors related to the eating quality of japonica and tongil-type rice varieties. Sensory evaluation was performed by a trained panel to assess the appearance (color and glossiness), flavor, taste, stickiness, texture, and overall score of nine japonica and three tongil-type rice cultivars. Moreover, the pattern of variation in rice storage proteins was examined by electrophoresis of protein extracts. The electrophoretic pattern of rice proteins showed 16.4 kDa albumin, 26.4 kDa globulin, 34-39 kDa and 21-22 kDa glutelin, and 14.3 kDa prolamin. In terms of storage protein, the varietal differences between japonica and tongil-type rice were found in albumin, globulin, and the ${\alpha}-1$, and ${\alpha}-2$ sub-units of acidic glutelin. Furthermore, the overall sensory evaluation score was observed to be positively correlated with albumin ($0.495^{**}$) and globulin ($0.567^{**}$), and negatively correlated with ${\alpha}-1$ glutelin ($-0.612^{**}$). Therefore, the results indicated that albumin, globulin, and ${\alpha}-1$ glutelin can affect the eating quality of japonica and tongil-type rice varieties, with the latter having lower eating quality than the former.

• Parasites, Hosts and Diseases
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• v.56 no.5
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• pp.409-418
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• 2018

Acanthamoeba spp. are free-living protozoa that are opportunistic pathogens for humans. Cysteine proteases of Acanthamoeba have been partially characterized, but their biochemical and functional properties are not clearly understood yet. In this study, we isolated a gene encoding cysteine protease of A. castellanii (AcCP) and its biochemical and functional properties were analyzed. Sequence analysis of AcCP suggests that this enzyme is a typical cathepsin L family cysteine protease, which shares similar structural characteristics with other cathepsin L-like enzymes. The recombinant AcCP showed enzymatic activity in acidic conditions with an optimum at pH 4.0. The recombinant enzyme effectively hydrolyzed human proteins including hemoglobin, albumin, immunoglobuins A and G, and fibronectin at acidic pH. AcCP mainly localized in lysosomal compartment and its expression was observed in both trophozoites and cysts. AcCP was also identified in cultured medium of A. castellanii. Considering to lysosomal localization, secretion or release by trophozoites and continuous expression in trophozoites and cysts, the enzyme could be a multifunctional enzyme that plays important biological functions for nutrition, development and pathogenicity of A. castellanii. These results also imply that AcCP can be a promising target for development of chemotherapeutic drug for Acanthamoeba infections.

• Journal of dental hygiene science
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• v.1 no.1
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• pp.7-11
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• 2001

Streptococcus mutans is one of the primary bacteria that cause dental caries which further result in plaque build up. Acid production resulted from carbohydrate metabolism can threaten survival of the bacteria. However some populations of S. mutans which are exposed to low acidic condition for a period of time would develop resistance and tolerance of cells to acidity that will enhance the chance of survival. Similar acid tolerances has been reported in case of Salmonella enterica serovar typhimurium, E. coli, Shigella flexneri. These acid tolerance responses(ATR) have been evolved in a similar manner as S. mutans. The protein produced in acidic condition has been proven to be important for ATR and confirmed by using chloramphenicol procedure. We hypothesize here that proteins synthesized in response to acid shock and other elements are important for ATR of cells. In this study we have confirmed that S. mutans developed acid tolerance and resistance against anaerobic condition. Mutational DNA analysis responsible for acid tolerance should be additionally required in the future. Since the development of acid tolerance that is essential for the survival of S. mutans and development of dental caries, ATR of S. mutans shoule be farther to prevent dental caries.

• Journal of Life Science
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• v.25 no.7
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• pp.833-838
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• 2015

Multidrug-resistant super bacterial, fungal, viral, and parasitic infections are major health threaten pathogens. However, to overcome the present healthcare situation, among the leading alternatives to current drugs are antimicrobial peptides (AMPs), which are abundantly produced via various species in nature. AMPs, small host defense proteins, are in charge of the innate immunity for the protection of multicellular organisms such as fish, amphibian, reptile, plants and animals from infection. The number of AMPs identified per year has increased steadily since the 1980s. Over 2,000 natural AMPs from bacteria, protozoa, fungi, plants, and animals have been listed into the antimicrobial peptide database (APD). The majority of these AMPs (>86%) possess 11–50 amino acids with a net charge from 0 to +7 and hydrophobic percentages between 31–70%. This report classified AMP into several categories including biological source, biological functions, peptide properties, covalent bonding pattern, and 3D structure. AMP functions not only antimicrobial activity but facilitates cell biological activity such as chemotatic activity. In addition, fibroblastic reticular cell (FRC) originated from mouse lymph node stroma induced the expression of AMP in inflammatory condition. AMP induced from FRC contained whey acidic protein (WAP) domain. It suggests that the classification of AMP will be done by protein domain.

• Journal of Ginseng Research
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• v.41 no.3
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• pp.247-256
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• 2017

Background: KG-135, a standardized formulation enriched with Rk1, Rg3, and Rg5 ginsenosides, has been shown to inhibit various types of cancer cells; however, the underlying mechanisms are not fully understood. In this study, we explored its effects in A549 human lung cancer cells to investigate the induction of Forkhead Class box O3a (FOXO3a) and autophagy. Methods: Cell viability was determined by sulforhodamine B staining. Apoptosis and cell cycle distribution were analyzed using flow cytometry. The changes of protein levels were determined using Western blot analysis. Autophagy induction was monitored by the formation of acidic vesicular organelles stained with acridine orange. Results: KG-135 effectively arrested the cells in G1 phase with limited apoptosis. Accordingly, a decrease of cyclin-dependent kinase-4, cyclin-dependent kinase-6, cyclin D1, and phospho-retinoblastoma protein, and an increase of p27 and p18 proteins were observed. Intriguingly, KG-135 increased the tumor suppressor FOXO3a and induced the accumulation of autophagy hallmark LC3-II and acidic vesicular organelles without an increase of the upstream marker Beclin-1. Unconventionally, the autophagy adaptor protein p62 (sequestosome 1) was increased rather than decreased. Blockade of autophagy by hydroxychloroquine dramatically potentiated KG-135-induced FOXO3a and its downstream (FasL) ligand accompanied by the cleavage of caspase-8. Meanwhile, the decrease of Bcl-2 and survivin, as well as the cleavage of caspase-9, were also drastically enhanced, resulting in massive apoptosis. Conclusion: Besides arresting the cells in G1 phase, KG-135 increased FOXO3a and induced an unconventional autophagy in A549 cells. Both the KG-135-activated extrinsic FOXO3a/FasL/caspase-8 and intrinsic caspase-9 apoptotic pathways were potentiated by blockade of autophagy. Combination of KG-135 and autophagy inhibitor may be a novel strategy as an integrative treatment for cancers.

• BMB Reports
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• v.34 no.1
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• pp.73-79
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• 2001

Transcriptional activation domains are known to be inherently "unstructured" with no tertiary structure. A recent NMR study, however, has shown that the transactivation domain in human p53 is populated with an amphipathic helix and two nascent turns. This suggests that the presence of such local secondary structures within the overall "unstructured" structural framework is a general feature of acidic transactivation domains. These pre-existing local structures in p53, formed selectively by positional conserved hydrophobic residues that are known to be critical for transcriptional activity, thus appear to constitute the specific structural motifs that regulate recognition of the p53 transactivation domain by target proteins. Here, we report the results of a NMR structural comparison between the native human p53 transactivation domain and an inactive mutant (22L,23W$\rightarrow$22R,23S). Results show that the mutant has an identical overall structural topology as the native protein, to the extent that the amphipathic helix formed by the residues 18T 26L within the native p53 transactivating domain is preserved in the double mutant. Therefore, the lack of transcriptional activity in the double mutant should be ascribed to the disruption of the essential hydrophobic contacts between the p53 transactivation domain and target proteins due to the (22L,23W$\rightarrow$22R,23S) mutation.

• Journal of the Korea Organic Resources Recycling Association
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• v.5 no.2
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• pp.47-56
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• 1997

To examine of possibility protein recycling of shaving scraps contained chrome generated from manufacturing process of leather, the characteristics of hydrolyzed protein that differently treated with MgO as alkaline agent were investigated. In alkaline hydrolysis of saving scraps treated with MgO, MgO had to be treated over 5.0% to maintain over pH 8.0 that is insoluble of chrome. Under the condition of alkaline treated with MgO, the solubility of chrome is low with about 60%. The average molecular weight of hydrolyzed proteins from shaving scraps treated with MgO was about 80~100 KD. The amino acid contents of that were largely collagen proteins such as glycine, alanine and proline, and acidic amino acids such as aspartic acid and glutatamic acid. The contents of Mg, Ca and Na in hydrolyzed protein were too much as liquid fertilizer, and chrome contents was 30~40 ppm that largely decreased in comparing with raw materials (40,000~42,000 ppm).