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FEBS Open Bio

Sumera Perveen, Naeem Rashid, Xiao-Feng Tang, Tadayuki Imanaka, Anastassios C Papageorgiou
Anthranilate phosphoribosyltransferase (TrpD) is involved in tryptophan biosynthesis, catalyzing the transfer of a phosphoribosyl group to anthranilate, leading to the generation of phosphoribosyl anthranilate. TrpD belongs to the phosphoribosyltransferase (PRT) superfamily and is the only member of the structural class IV. X-ray structures of TrpD from seven species have been solved to date. Here, functional and structural characterization of a recombinant TrpD from hyperthermophilic archaeon Thermococcus kodakarensis KOD1 (TkTrpD) was carried out...
August 2017: FEBS Open Bio
Ko On Lee, Young-Joo Yun, Iktae Kim, Jeong-Yong Suh
The bacterial phosphotransferase system is central to sugar uptake and phosphorylation. Enzyme I (EI), the first enzyme of the system, autophosphorylates as a dimer using phosphoenolpyruvate (PEP), but it is not clearly understood how dimerization activates the enzyme activity. Here, we show that EI dimerization is important for proper conformational transitions and the domain association required for the autophosphorylation. EI(G356S) with reduced dimerization affinity and lower autophosphorylation activity revealed that significantly hindered conformational transitions are required for the phosphoryl transfer reaction...
August 2017: FEBS Open Bio
Liqin Wang, Daniel Xing, Adriana Le Van, Ann E Jerse, Shuishu Wang
Effective vaccines are urgently needed to combat gonorrhea, a common sexually transmitted bacterial infection, for which treatment options are diminishing due to rapid emergence of antibiotic resistance. We have used a rational approach to the development of gonorrhea vaccines, and genetically engineered nanoparticles to present antigenic peptides of Neisseria gonorrhoeae, the causative agent of gonorrhea. We hypothesized that the ferritin nanocage could be used as a platform to display an ordered array of N...
August 2017: FEBS Open Bio
Tatyana O Pleshakova, Kristina A Malsagova, Anna L Kaysheva, Arthur T Kopylov, Vadim Yu Tatur, Vadim S Ziborov, Sergey L Kanashenko, Rafael A Galiullin, Yuri D Ivanov
We report here the highly sensitive detection of protein in solution at concentrations from 10(-15) to 10(-18) m using the combination of atomic force microscopy (AFM) and mass spectrometry. Biospecific detection of biotinylated bovine serum albumin was carried out by fishing out the protein onto the surface of AFM chips with immobilized avidin, which determined the specificity of the analysis. Electrical stimulation was applied to enhance the fishing efficiency. A high sensitivity of detection was achieved by application of nanosecond electric pulses to highly oriented pyrolytic graphite placed under the AFM chip...
August 2017: FEBS Open Bio
Kenta Watanabe, Tsukasa Tominari, Michiko Hirata, Chiho Matsumoto, Junya Hirata, Gillian Murphy, Hideaki Nagase, Chisato Miyaura, Masaki Inada
Abnormalities of bone turnover are commonly observed in patients with chronic kidney disease (CKD), and the low-turnover bone disease is considered to be associated with low serum parathyroid hormone (PTH) levels and skeletal resistance to PTH. Indoxyl sulfate (IS) is a representative uremic toxin that accumulates in the blood of patients with CKD. Recently, we have reported that IS exacerbates low bone turnover induced by parathyroidectomy (PTX) in adult rats, and suggested that IS directly induces low bone turnover through the inhibition of bone formation by mechanisms unrelated to skeletal resistance to PTH...
August 2017: FEBS Open Bio
Bernadett Márkus, Zsuzsanna Pató, Zsolt Sarang, Réka Albert, József Tőzsér, Goran Petrovski, Éva Csősz
Proliferative vitreoretinopathy (PVR) develops as a complication of retinal detachment surgery and represents a devastating condition leading to serious vision loss. A good animal model that permits extensive functional studies and drug testing is crucial in finding better therapeutic modalities for PVR. A previously established mouse model, using dispase injection, was analyzed from the proteomic point of view, examining global protein profile changes by 2D electrophoresis, image analysis and HPLC-tandem mass spectrometry-based protein identification...
August 2017: FEBS Open Bio
Takuya Hasegawa, Ryohei Adachi, Hitoshi Iwakata, Takayoshi Takeno, Koji Sato, Toshiyuki Sakamaki
We previously reported that microRNA-205 (miR-205) is downregulated by overexpression of the receptor tyrosine kinase ErbB2 and that ectopic transfection of miR-205 precursor decreases ErbB2 tumorigenicity in soft agar. In this study, we further analyzed the regulatory mechanisms linking ErbB2 overexpression and miR-205 downregulation. In ErbB2-overexpressing breast epithelial cells, miR-205 expression was significantly increased by treatment with MEK inhibitor U0126 or PD98059, Raf-1 inhibitor ZM-336372, and ERK inhibitor SCH772984, but PI3K inhibitor LY294002 and p38 MAPK inhibitor SB203580 had no effect...
August 2017: FEBS Open Bio
Kunpeng Hu, Pinzhu Huang, Hui Luo, Zhicheng Yao, Qingliang Wang, Zhiyong Xiong, Jizong Lin, He Huang, Shilei Xu, Peng Zhang, Bo Liu
Mammalian-enabled (MENA) protein is an actin-regulatory protein that influences cell motility and adhesion. It is known to play a role in tumorigenicity of hepatocellular carcinoma (HCC) but the underlying molecular mechanism remains unknown. This study aimed to investigate the oncogenic potential of MENA and its capacity to regulate cancer stem cell (CSC)-like phenotypes in HCC cells. Real-time-PCR and western blot were used to assess mRNA and protein levels of target genes in human HCC tissue specimens and HCC cell lines, respectively...
August 2017: FEBS Open Bio
Prerna Sharma, Purnananda Guptasarma
The eight-stranded (β/α)8 barrel fold known as the Triosephosphate isomerase (TIM) barrel is the most commonly observed fold in enzymes, displaying an eightfold structural symmetry. The sequences and structures of different TIM barrel enzymes suggest that nature exploits the modularity inherent in the eightfold symmetry to generate enzymes with diverse enzymatic activities and, in certain cases, more than one catalytic activity per enzyme. Here, we report the discovery, verification, and characterization of such an additional activity, a novel endoglucanase/cellulase activity in what is otherwise a triosephosphate isomerase from the hyperthermophile archaeon Pyrococcus furiosus (PfuTIM)...
August 2017: FEBS Open Bio
Xinning Liu, Zhoude Zheng, Chuhong Chen, Simin Guo, Zhennan Liao, Yue Li, Ying Zhu, Haiying Zou, Jianyi Wu, Wenming Xie, Pixian Zhang, Liyan Xu, Bingli Wu, Enmin Li
SMYD3 is a member of the SET and myeloid-Nervy-DEAF-1 (MYND) domain-containing protein family of methyltransferases, which are known to play critical roles in carcinogenesis. Expression of SMYD3 is elevated in various cancers, including esophageal squamous cell carcinoma (ESCC), and is correlated with the survival time of patients with ESCC. Here, we dissect gene expression data, from a previously described KYSE150 ESCC cell line in which SMYD3 had been knocked down, by integration with the protein-protein interaction (PPI) network, to find the new potential biological roles of SMYD3 and subsequent target genes...
August 2017: FEBS Open Bio
Yudong Fu, Zhongcheng Zhou, Hua Wang, Peng Gong, Renpeng Guo, Jinmiao Wang, Xinyi Lu, Feng Qi, Lin Liu
Interferon-induced transmembrane protein 1 (IFITM1), a member of the IFITM protein family, is a component of a multimeric complex involved in the transduction of antiproliferation and cell adhesion signals. IFITM1 is thought to play a role in antiproliferation and immune surveillance, and has been shown to restrict infection by numerous viruses. It is highly expressed in human embryonic stem cells (hESCs) but its role in hESCs remains to be elucidated. In this study, knockout of IFITM1 mediated by CRISPR/Cas9 in hESCs did not affect self-renewal, pluripotency, telomerase activity or telomeres...
August 2017: FEBS Open Bio
Julie Anne Côté, Julie Lessard, Mélissa Pelletier, Simon Marceau, Odette Lescelleur, Julie Fradette, André Tchernof
Dedifferentiation of adipocytes contributes to the generation of a proliferative cell population that could be useful in cellular therapy or tissue engineering. Adipocytes can dedifferentiate into precursor cells to acquire a fibroblast-like phenotype using ceiling culture, in which the buoyancy of fat cells is exploited to allow them to adhere to the inner surface of a container. Ceiling culture is usually performed in flasks, which limits the ability to test various culture conditions. Using a new six-well plate ceiling culture approach, we examined the relevance of TGF-β signaling during dedifferentiation...
August 2017: FEBS Open Bio
Wei Huo, Min Du, Xinyan Pan, Xiaomin Zhu, Yu Gao, Zhimin Li
Hepatocellular carcinoma (HCC) is one of the most common causes of cancer-related death. Cytokines, including interleukin 24 (IL-24), play an important role in HCC. IL-24 inhibits HCC metastasis but the molecular mechanism by which this occurs is still unknown. MicroRNAs (miRNAs) are regulators of cancers including hepatocellular carcinoma (HCC). However, the role that miRNAs play in the regulation of IL-24 in HCC is unclear. The aim of this study was to investigate the effects of regulation of IL-24 by miR-203a-3p...
August 2017: FEBS Open Bio
Shufen Zhou, Dongjie Yao, Ling Guo, Ling Teng
Hyperacidity in the stomach is known to promote the progression of gastric cancer. The plant-derived chemotherapeutic curcumin is used to treat gastric cancer. The objective of this study was to investigate whether curcumin regulates gastrin-mediated acid secretion in suppressing gastric cancer. Gastric cancer cells were treated with 25 μm curcumin, followed by Annexin V/propidium iodide double-staining assay to evaluate cell apoptosis. Western blot analysis was used to analyze caspase-3 expression in response to curcumin treatment...
August 2017: FEBS Open Bio
Sonia Covaceuszach, Manuela Bozzi, Maria Giulia Bigotti, Francesca Sciandra, Petr Valeryevich Konarev, Andrea Brancaccio, Alberto Cassetta
Dystroglycan (DG), composed of α and β subunits, belongs to the dystrophin-associated glycoprotein complex. α-DG is an extracellular matrix protein that undergoes a complex post-translational glycosylation process. The bifunctional glycosyltransferase like-acetylglucosaminyltransferase (LARGE) plays a crucial role in the maturation of α-DG, enabling its binding to laminin. We have already structurally analyzed the N-terminal region of murine α-DG (α-DG-Nt) and of a pathological single point mutant that may affect recognition of LARGE, although the structural features of the potential interaction between LARGE and DG remain elusive...
August 2017: FEBS Open Bio
Geunho Lee, Hyun Beom Lee, Byung Hwa Jung, Hojung Nam
Mass spectrometry (MS) data are used to analyze biological phenomena based on chemical species. However, these data often contain unexpected duplicate records and missing values due to technical or biological factors. These 'dirty data' problems increase the difficulty of performing MS analyses because they lead to performance degradation when statistical or machine-learning tests are applied to the data. Thus, we have developed missing values preprocessor (mvp), an open-source software for preprocessing data that might include duplicate records and missing values...
July 2017: FEBS Open Bio
Marcelo Y Icimoto, Juliana C Ferreira, César H Yokomizo, Larissa V Bim, Alyne Marem, Joyce M Gilio, Vitor Oliveira, Iseli L Nantes
Thimet oligopeptidase (EC, TOP) is a cytosolic mammalian zinc protease that can process a diversity of bioactive peptides. TOP has been pointed out as one of the main postproteasomal enzymes that process peptide antigens in the MHC class I presentation route. In the present study, we describe a fine regulation of TOP activity by hydrogen peroxide (H2O2). Cells from a human embryonic kidney cell line (HEK293) underwent an ischemia/reoxygenation-like condition known to increase H2O2 production. Immediately after reoxygenation, HEK293 cells exhibited a 32% increase in TOP activity, but no TOP activity was observed 2 h after reoxygenation...
July 2017: FEBS Open Bio
João Leandro, Anne J Stokka, Knut Teigen, Ole A Andersen, Torgeir Flatmark
Mammalian phenylalanine hydroxylase (PAH) is a key enzyme in l-phenylalanine (l-Phe) metabolism and is active as a homotetramer. Biochemical and biophysical work has demonstrated that it cycles between two states with a variably low and a high activity, and that the substrate l-Phe is the key player in this transition. X-ray structures of the catalytic domain have shown mobility of a partially intrinsically disordered Tyr(138)-loop to the active site in the presence of l-Phe. The mechanism by which the loop dynamics are coupled to substrate binding at the active site in tetrameric PAH is not fully understood...
July 2017: FEBS Open Bio
Puji Rahayu, Lia Agustina, Raymond R Tjandrawinata
Wound healing is a complex biological process that involves integration of hemostasis, inflammation, proliferation and tissue remodeling. An extract of pineapple (Ananas comosus) stem demonstrates several therapeutics properties, including acceleration of wound healing. Tacorin is a water crude extract derived from the stem of A. comosus with high protein content. The effect of tacorin on wound healing in vivo was examined using rats with an induced injury. Wound closure was faster with tacorin treatment than in the untreated group...
July 2017: FEBS Open Bio
Takako Mukai, Miki Egawa, Tamaki Takeuchi, Hitoshi Yamashita, Tatsuya Kusudo
Nonalcoholic fatty liver disease (NAFLD) is increasing in prevalence worldwide and has been identified as a risk factor for cirrhosis and hepatocellular carcinoma. However, there is no effective pharmacologic treatment for NAFLD. FABP1 is a liver-specific fatty acid-binding protein (FABP) that plays important roles in intracellular lipid metabolism in the liver. We investigated the effect of repression of FABP1 expression on NAFLD, using adenovirus-mediated silencing of FABP1. FABP1 knockdown in the liver decreased the liver weight and hepatic triglyceride (TG) accumulation...
July 2017: FEBS Open Bio
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