Korea Research Institute of Bioscience and Biotechnology
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R-catcher, a potent molecular tool to unveil the arginylome
No full textProtein arginylation is a critical regulator of a variety of biological processes. The ability to uncover the global arginylation pattern and its associated signaling pathways would enable us to identify novel disease targets. Here, we report the development of a tool able to capture the N-terminal arginylome. This tool, termed R-catcher, is based on the ZZ domain of p62, which was previously shown to bind N-terminally arginylated proteins. Mutating the ZZ domain enhanced its binding specificity and affinity for Nt-Arg. R-catcher pulldown coupled to LC-MS/MS led to the identification of 59 known and putative arginylated proteins. Among these were a subgroup of novel ATE1-dependent arginylated ER proteins that are linked to diverse biological pathways, including cellular senescence and vesicle-mediated transport as well as diseases, such as Amyotrophic Lateral Sclerosis and Alzheimer's disease. This study presents the first molecular tool that allows the unbiased identification of arginylated proteins, thereby unlocking the arginylome and provide a new path to disease biomarker discovery.
Identification and characterization of a novel, cold-adapted D-xylobiose- and D-xylose-releasing endo-β-1,4-xylanase from an antarctic soil bacterium, Duganella sp. PAMC 27433
No full textEndo-β-1,4-xylanase is a key enzyme in the degradation of β-1,4-d-xylan polysaccharides through hydrolysis. A glycoside hydrolase family 10 (GH10) endo-β-1,4-xylanase (XylR) from Duganella sp. PAMC 27433, an Antarctic soil bacterium, was identified and functionally characterized. The XylR gene (1122-bp) encoded an acidic protein containing a single catalytic GH10 domain that was 86% identical to that of an uncultured bacterium BLR13 endo-β-1,4-xylanase (ACN58881). The recombinant enzyme (rXylR: 42.0 kDa) showed the highest beechwood xylan-degrading activity at pH 5.5 and 40 °C, and displayed 12% of its maximum activity even at 4 °C. rXylR was not only almost completely inhibited by 5 mM N-bromosuccinimide or metal ions (each 1 mM) including Hg2+, Ca2+, or Cu2+ but also significantly suppressed by 1 mM Ni2+, Zn2+, or Fe2+. However, its enzyme activity was upregulated (>1.4-fold) in the presence of 0.5% Triton X-100 or Tween 80. The specific activities of rXylR toward beechwood xylan, birchwood xylan, oat spelts xylan, and p-nitrophenyl-β-d-cellobioside were 274.7, 103.2, 35.6, and 365.1 U/mg, respectively. Enzymatic hydrolysis of birchwood xylan and d-xylooligosaccharides yielded d-xylose and d-xylobiose as the end products. The results of the present study suggest that rXylR is a novel cold-adapted d-xylobiose- and d-xylose-releasing endo-β-1,4-xylanase.
3,4,5-Trihydroxycinnamic acid exerts anti-inflammatory effects on TNF-α/IFN-γ-stimulated HaCaT cells
No full text3,4,5？Trihydroxycinnamic acid (THCA) exhibits anti？inflammatory activity in acute or chronic inflammatory disorders, such as acute lung injury and asthma. The present study investigated the anti？inflammatory activity of THCA in a tumor necrosis factor？α/interferon？γ (TI) mixture？stimulated human keratinocyte cell line. The results of ELISA and reverse transcription？quantitative PCR revealed that THCA reduced the secretion and mRNA expression levels of interleukin (IL)？6; IL？8; thymus and activation？regulated chemokine; macrophage？derived chemokine; regulated upon activation, normal T cell expressed and secreted; and monocyte chemoattractant protein？1 in TI mixture？stimulated HaCaT cells. In addition, the results of western blot analysis demonstrated that THCA exerted inhibitory activity on the activation of AKT, ERK and nuclear factor？κB in TI mixture？stimulated HaCaT cells. Furthermore, THCA upregulated the expression levels of heme oxygenase？1 and NAD(P)H:quinone oxidoreductase 1, and the activation of nuclear factor erythroid 2？related factor 2 in HaCaT cells. These results demonstrated that THCA may exhibit anti？inflammatory activity in activated HaCaT cells.
Modified MYOMI-14 Korean herbal formulations have protective effects against cyclophosphamide-induced male infertility in mice
No full textKorean herbal formulation, MYOMI-14, has been reported to improve the idiopathic male infertility condition with poor semen. In this study, four MYOMI formulations were modified from MYOMI-14 by reducing the number of constituents. We investigated the therapeutic effect of MYOMI formulations on cyclophosphamide-induced male infertility using mice model. Cyclophosphamide treatment significantly decreased body weight, testicular weight, sperm count, normal-shaped sperm rate and sperm motility compared to untreated control group, whereas MYOMI formulations restore the cyclophosphamide-induced dysfunction, as determined by increased sperm count and motility, and decreased abnormally shaped spermatozoa. In addition, treatment with MYOMI formulations reduced cyclophosphamide-induced apoptosis of germ cells and oxidative stress. MYOMI-treated mice also showed improved spermatogenesis as shown by the increased expression of spermatogenesis-related genes, as cAMP-responsive element modulator (CREM) and cAMP response element-binding (CREB) protein. Among the MYOMI formulations, MYOMI-7 showed better results in terms of recovering CP-induced damages to testis and improving the fertility. Taken together, this study is expected to make significant contribution to the literature by exploring various formulations that reduced constituents of MYOMI-14, a Korean herbal medicine, in treating CP-induced male infertility
N-acetyl-L-cysteine improves the developmental competence of bovine oocytes and embryos cultured in vitro by attenuating oxidative damage and apoptosis
No full textOxidative stress has been suggested to negatively affect oocyte and embryo quality and developmental competence, resulting in failure to reach full term. In this study, we investigated the effect of N-acetyl-L-cysteine (NAC), a cell-permeating antioxidant, on developmental competence and the quality of oocytes and embryos upon supplementation (0.1？10 mM) in maturation and culture medium in vitro using slaughterhouse-derived oocytes and embryos. The results show that treating oocytes with 1.0 mM NAC for 8 h during in vitro maturation attenuated the intracellular reactive oxygen species (ROS) (p < 0.05) and upregulated intracellular glutathione levels (p < 0.01) in oocytes. Interestingly, we found that NAC affects early embryonic development, not only in a dose-dependent, but also in a stage-specific, manner. Significantly (p < 0.05) decreased cleavage rates (90.25% vs. 81.46%) were observed during the early stage (days 0？2), while significantly (p < 0.05) increased developmental rates (38.20% vs. 44.46%) were observed during the later stage (from day 3) of embryonic development. In particular, NAC supplementation decreased the proportion of apoptotic blastomeres significantly (p < 0.05), resulting in enhanced hatching capability and developmental rates during the in vitro culture of embryos. Taken together, our results suggest that NAC supplementation has beneficial effects on bovine oocytes and embryos through the prevention of apoptosis and the elimination of oxygen free radicals during maturation and culture in vitro.
Phosphorylation of REPS1 at Ser709 by RSK attenuates the recycling of Transferrin receptor
No full textRalBP1 associated EPS domain containing 1 (REPS1) is conserved from Drosophila to humans and implicated in the endocytic system. However, an exact role of REPS1 remains largely unknown. Here, we demonstrated that mitogen activated protein kinase kinase (MEK)-p90 ribosomal S6 Kinase (RSK) signaling pathway directly phosphorylated REPS1 at Ser709 upon stimulation by epidermal growth factor (EGF) and amino acid. While REPS2 is known to be involved in the endocytosis of EGF receptor (EGFR), REPS1 knockout (KO) cells did not show any defect in the endocytosis of EGFR. However, in the REPS1 KO cells and the KO cells reconstituted with a non-phosphorylatable REPS1 (REPS1 S709A), the recycling of transferrin receptor (TfR) was attenuated compared to the cells reconstituted with wild type REPS1. Collectively, we suggested that the phosphorylation of REPS1 at S709 by RSK may have a role of the trafficking of TfR.
Phospholipid transfer function of PTPIP51 at mitochondria-associated ER membranes
No full textIn eukaryotic cells, mitochondria are closely tethered to the endoplasmic reticulum (ER) at sites called mitochondria-associated ER membranes (MAMs). Ca2+ ion and phospholipid transfer occurs at MAMs to support diverse cellular functions. Unlike those in yeast, the protein complexes involved in phospholipid transfer at MAMs in humans have not been identified. Here, we determine the crystal structure of the tetratricopeptide repeat domain of PTPIP51 (PTPIP51_TPR), a mitochondrial protein that interacts with the ER-anchored VAPB protein at MAMs. The structure of PTPIP51_TPR shows an archetypal TPR fold, and an electron density map corresponding to an unidentified lipid-like molecule probably derived from the protein expression host is found in the structure. We reveal functions of PTPIP51 in phospholipid binding/transfer, particularly of phosphatidic acid, in vitro. Depletion of PTPIP51 in cells reduces the mitochondrial cardiolipin level. Additionally, we confirm that the PTPIP51-VAPB interaction is mediated by the FFAT-like motif of PTPIP51 and the MSP domain of VAPB. Our findings suggest that PTPIP51 is a phospholipid transfer protein with a MAM-tethering function.
Real-time monitoring of geosmin based on an aptamer-conjugated graphene field-effect transistor
No full textIn this paper, we propose a novel field-effect transistor (FET) using graphene, which is a two-dimensional (2D) nanomaterial, capable of evaluating water quality, and immobilizing the surface of a graphene micropatterned transistor with a highly responsive bioprobe for a water contamination indicator, geosmin, with high selectivity. A high-quality bioprobe-immobilized graphene FET (GFET) was fabricated for the real-time monitoring of geosmin using a liquid-gate measurement configuration. Immobilization was confirmed by measuring the change in the electrical characteristics of the platform (slope of the current-voltage (I？V) curve) and fluorescence images. In addition, a selectivity test showed remarkable implementation of the highly sensitive sensing platform with an insignificant signal when a nontarget was added. Using the fabricated device, the linear range for geosmin detection was determined to be from 0.01 nM - 1 μM with a detection limit of 0.01 nM. In addition, geosmin concentrations as low as 10 nM could be determined from river water samples with the sensor platform. This sensor can be utilized to immediately determine the presence of odorous substances by analyzing a water supply source without additional pretreatment. Another advantage is that the sensor device is a promising tool that does not have special equipment that requirs careful maintenance. In addition, the device provides a new platform for detecting harmful substances in various water sources by varying the bioprobes that are empolyed.
Curcumin activates ROS signaling to promote pyroptosis in hepatocellular carcinoma HepG2 cells
No full textBackground/aim: Curcumin is a polyphenol that exerts a variety of pharmacological activities and plays an anti-cancer role in many cancer cells. It was recently reported that gasdermin E (GSDME) is involved in the progression of pyroptosis.
Materials and methods: HepG2 cells were treated with various concentrations of curcumin and cell viability was examined using MTT assay, apoptosis was analysed using flow cytometry, reactive oxygen species (ROS) levels using dihydroethidium, LDH release using an LDH cytotoxicity assay, and protein expression using western blot.
Results: Curcumin increased the expression of the GSDME N-terminus and proteins involved in pyrolysis, promoted HspG2 cell pyrolysis and increased intracellular ROS levels. Moreover, inhibition of the production of intracellular ROS with n-acetylcysteine (NAC) improved the degree of apoptosis and pyrolysis induced by curcumin.
Conclusion: Curcumin induces HspG2 cell death by increasing apoptosis and pyroptosis, and ROS play a key role in this process. This study improves our understanding of the potential anti-cancer properties of curcumin in liver cancer.