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Journal of Biochemistry

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https://www.readbyqxmd.com/read/30321347/identification-of-a-common-epitope-in-the-sequences-of-col4a1-and-col6a1-recognised-by-monoclonal-antibody-141
#1
Takamichi Sato, Ryo Takano, Naoko Takahara, Kazuhiro Tokunaka, Kan Saiga, Arihiro Tomura, Hidemitsu Sugihara, Toshihiko Hayashi, Yasutada Imamura, Makoto Morita
Identification of a type IV collagen α1 polypeptide in non-triple helical form [NTH α1(IV)], possibly involved in angiogenesis, introduces the further possibility of the existence of non-triple helical forms of other collagen chains. We previously reported that an anti-NTH α1(IV) monoclonal antibody #141 recognises not only NTH α1(IV) but also a novel non-triple helical collagen polypeptide NTH α1(VI) encoded by COL6A1. In this study, we identified the recognition sequence in order to better understand the properties of antibody #141 and provide clues regarding the biological function of the two non-triple helical molecules...
October 13, 2018: Journal of Biochemistry
https://www.readbyqxmd.com/read/30304445/the-er-exit-sites-are-specialized-er-zones-for-the-transport-of-cargo-proteins-from-the-er-to-the-golgi-apparatus
#2
Kazuo Kurokawa, Akihiko Nakano
The endoplasmic reticulum (ER) is a multifunctional organelle, including secretory protein biogenesis, lipid synthesis, drug metabolism, Ca2+ signaling, and so on. Since the ER is a single continuous membrane structure, it includes distinct zones responsible for its different functions. The export of newly synthesized proteins from the ER is facilitated via coat protein complex II (COPII)-coated vesicles, which form in specialized zones within the ER, called the ER exit sites (ERES) or transitional ER. In this review, we highlight recent advances in our understanding of the structural organization of ERES, the correlation between the ERES and Golgi organization, and the faithful cargo transport mechanism from the ERES to the Golgi...
October 10, 2018: Journal of Biochemistry
https://www.readbyqxmd.com/read/30304349/circrna_001569-promotes-cell-proliferation-through-absorbing-mir-145-in-gastric-cancer
#3
Fengqian Shen, Peijie Liu, Ning Li, Zhenying Yi, Xiaojing Tie, Yan Zhang, Ling Gao, Zhiqiao Xu
Gastric cancer severely threatens human life, while its pathogenesis is still unclear. The present study was to explore the potential pathogenic mechanism underlying gastric cancer. Real-time PCR was performed to detect the expression of circRNA_001569 and miR-145; western blot was performed to detect the expression of NR4A2. Cell cycle and apoptosis was determined using flow cytometry, and cell viability was determined using Cell counting kit-8 (CCK-8) assay. Luciferase reporter assay was carried out to validate the relationship between miR-145 and NR4A2...
October 9, 2018: Journal of Biochemistry
https://www.readbyqxmd.com/read/30295825/application-of-machine-learning-algorithms-for-the-differential-diagnosis-of-peroxisomal-disorders
#4
Pammi Subhashini, Sampangi Jaya Krishna, Ganni Usha Rani, Nooguri Sushma Chander, Gummadi Maheshwar Reddy, Shaik Mohammad Naushad
We have established diagnostic thresholds of very long-chain fatty acids (VLCFA) for the differential diagnosis of peroxisomal disorders using the machine learning tools. The plasma samples of 131 controls and 90 cases were tested for VLCFA using Gas chromatography-Mass spectrometry following stable isotope dilution. This data was used to construct association rules and for recursive partitioning. The C26/22 in healthy controls ranged between 0.008 - 0.01. The C26 levels between 1.61 - 3.34 µmol/L and C26/C22 between 0...
October 8, 2018: Journal of Biochemistry
https://www.readbyqxmd.com/read/30295876/pikfyve-accelerates-phagosome-acidification-through-activation-of-trpml1-while-arrests-aberrant-vacuolation-independent-of-the-ca2-channel
#5
Yuri Isobe, Kiyomi Nigorikawa, Go Tsurumi, Shinya Takemasu, Shunsuke Takasuga, Satoshi Kofuji, Kaoru Hazeki
PIKfyve phosphorylates PtdIns(3)P to PtdIns(3,5)P2. One of the best characterized effector downstream of PtdIns(3,5)P2 is a lysosomal Ca2+ channel, TRPML1. Although it has been reported that TRPML1 is involved in phagosome-lysosome fusion, the relevance of the Ca2+ channel in phagosome acidification has been denied. In this paper, however, we demonstrated that the phagosome acidification was dependent on TRPML1. Based on the classical idea that FITC-fluorescence is highly sensitive to acidic pH, we could estimate the phagosome acidification by time laps imaging...
October 6, 2018: Journal of Biochemistry
https://www.readbyqxmd.com/read/30295852/creg1-promotes-uncoupling-protein-1-expression-and-brown-adipogenesis-in-vitro
#6
Tatsuya Kusudo, Michihiro Hashimoto, Naoya Kataoka, Yongxue Li, Aya Nozaki, Hitoshi Yamashita
Brown adipocytes play a critical role for adaptive thermogenesis to regulate body temperature in cold or to circumvent diet-induced obesity. In the present study, we investigated the role of cellular repressor of E1A-stimulated genes 1 (CREG1) on brown adipogenesis and uncoupling protein 1 (UCP1) expression by using in vitro culture models. In murine mesenchymal stem cell line C3H10T1/2, Creg1 mRNA expression significantly increased in a time-dependent manner along with Ucp1 mRNA induction in brown adipogenesis...
October 6, 2018: Journal of Biochemistry
https://www.readbyqxmd.com/read/30289529/specific-mutations-in-presenilin-1-cause-conformational-changes-in-%C3%AE-secretase-to-modulate-amyloid-beta-trimming
#7
So Imai, Tetsuo Cai, Chika Yoshida, Taisuke Tomita, Eugene Futai
γ-Secretase generates amyloid beta peptides (Aβ) from amyloid precursor protein (APP) through multistep cleavages, such as endoproteolysis (ε-cleavage) and trimming (γ-cleavage). Familial Alzheimer's disease (FAD) mutations within the catalytic subunit protein of presenilin 1 (PS1) decrease γ-cleavage, resulting in the generation of toxic, long Aβs. Reducing long Aβ levels has been proposed as an AD therapeutic strategy. Previously, we identified PS1 mutations that are active in the absence of nicastrin (NCT) using a yeast γ-secretase assay...
October 5, 2018: Journal of Biochemistry
https://www.readbyqxmd.com/read/30289493/thioredoxin-o-mediated-reduction-of-mitochondrial-alternative-oxidase-in-the-thermogenic-skunk-cabbage-symplocarpus-renifolius
#8
Yui Umekawa, Kikukatsu Ito
Thermogenesis in plants involves significant increases in their cyanide-resistant mitochondrial alternative oxidase (AOX) capacity. Because AOX is a non-proton-motive ubiquinol oxidase, the dramatic drop in free energy between ubiquinol and oxygen is dissipated as heat. In the thermogenic skunk cabbage (Symplocarpus renifolius), SrAOX is specifically expressed in the florets. Although SrAOX harbors conserved cysteine residues, the details of the mechanisms underlying its redox regulation are poorly understood...
October 5, 2018: Journal of Biochemistry
https://www.readbyqxmd.com/read/30256974/long-non-coding-rna-linc00662-promotes-cell-invasion-and-contributes-to-cancer-stem-cell-like-phenotypes-in-lung-cancer-cells
#9
Wenjing Gong, Yi Su, Yan Liu, Ping Sun, Xiumei Wang
Long non-coding RNAs (lncRNAs) is essential in regulation of cancer cell and cancer stem cells (CSCs) behavior. Linc00662 is a newly identified human lung cancer related lncRNA. In the present study, we aimed to explore the function of Linc00662 in human lung cancer. The expression level of Linc00662 was analyzed by qRT-PCR. Cell metastasis and invasive ability were detected by transwell and scratch wound healing assays. The stemness of CSCs was shown by tumorsphere formation assay and flow cytometry. The interaction between Linc00662 and Lin28 was confirmed by RNA immunoprecipitation and RNA pulldown assay...
September 26, 2018: Journal of Biochemistry
https://www.readbyqxmd.com/read/30247576/cleaved-pgam5-is-released-from-mitochondria-depending-on-proteasome-mediated-rupture-of-the-outer-mitochondrial-membrane-during-mitophagy
#10
Ayane Yamaguchi, Hayate Ishikawa, Mana Furuoka, Masashi Yokozeki, Noriyuki Matsuda, Susumu Tanimura, Kohsuke Takeda
PGAM5 is a unique type of protein phosphatase that exists in mitochondria. It has been shown to exist in the inner mitochondrial membrane through its transmembrane domain and to be cleaved within the transmembrane domain upon mitochondrial dysfunction. However, its submitochondrial localization remains controversial; many researchers claim that PGAM5 localizes to the outer mitochondrial membrane based on the findings that PGAM5 associates with many cytoplasmic proteins. Here, we found that cleaved PGAM5 was released from mitochondria during mitophagy, a selective form of autophagy specific for mitochondria, and that the release was inhibited by proteasome inhibitors in HeLa cells stably expressing the E3 ubiquitin ligase Parkin...
September 21, 2018: Journal of Biochemistry
https://www.readbyqxmd.com/read/30239818/generation-of-an-anti-desmoglein-3-antibody-without-pathogenic-activity-of-pemphigus-vulgaris-for-therapeutic-application-to-squamous-cell-carcinoma
#11
Shin-Ichi Funahashi, Shigeto Kawai, Etsuko Fujii, Kenji Taniguchi, Kiyotaka Nakano, Shumpei Ishikawa, Hiroyuki Aburatani, Masami Suzuki
It is ideal for the target antigen of a cytotoxic therapeutic antibody against cancer to be cancer-specific, but such antigens are rare. Thus an alternative strategy for target selection is necessary. DSG3 is highly expressed in lung squamous cell carcinoma, while it is well known that anti-DSG3 antibodies cause pemphigus vulgaris, an autoimmune disease. We evaluated DSG3 as a novel target by selecting an epitope that exerts efficacy against cancer with no pathogenic effects in normal tissues. Pathogenic anti-DSG3 antibodies induce skin blisters by inihibiting the cell-cell interaction in a Ca2+-dependent manner...
September 18, 2018: Journal of Biochemistry
https://www.readbyqxmd.com/read/30219914/emerging-impacts-of-biological-methylation-on-genetic-information
#12
Koichiro Kako, Jun-Dal Kim, Akiyoshi Fukamizu
The central dogma of molecular biology explains the fundamental flow of genetic information for life. Although genome sequence (DNA) itself is a static chemical signature, it includes multiple layers of information composed of messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA), and small RNAs, all of which are involved in protein synthesis, and is passing from parents to offspring via DNA. Methylation is a biologically important modification, because DNA, RNAs, and proteins, components of the central dogma, are methylated by a set of methyltransferases...
September 14, 2018: Journal of Biochemistry
https://www.readbyqxmd.com/read/30219851/goldfish-an-old-and-new-model-system-to-study-vertebrate-development-evolution-and-human-disease
#13
Yoshihiro Omori, Tetsuo Kon
The goldfish (Carassius auratus) is a domesticated cyprinid teleost closely related to the crucian carp. Goldfish domestication occurred in South China around 1,000 years ago. At least 180 variants and 70 genetically established strains are currently produced. These strains possess diverse phenotypes in body shape, coloration, scales, and fin, eye, and hood morphology. These include biologically interesting phenotypes that have not been observed in mutants of zebrafish or medaka. In addition, goldfish strains have been maintained in a non-wild environment for several hundreds of generations, and certain goldfish strains have phenotypes similar to some human diseases...
September 14, 2018: Journal of Biochemistry
https://www.readbyqxmd.com/read/30204891/the-hidden-nature-of-protein-translational-control-by-diphthamide-the-secrets-under-the-leather
#14
Kayoko Tsuda-Sakurai, Masayuki Miura
The protein translation elongation factor eEF2 undergoes a unique posttranslational modification called diphthamidation. eEF2 is an essential factor in protein translation, and the diphthamide modification has been a famous target of the diphtheria toxin for a long time. On the other hand, the physiological function of this rare modification in vivo remains unknown. Recent studies have suggested that diphthamide has specific functions for the cellular stress response and active proliferation. In this review, we summarize the history and findings of diphthamide obtained to date and discuss the possibility of a specific function for diphthamide in regulating protein translation...
September 11, 2018: Journal of Biochemistry
https://www.readbyqxmd.com/read/30204880/a-newly-isolated-pex7-binding-atypical-pts2-protein-p7bp2-is-a-novel-dynein-type-aaa-protein
#15
Hajime Niwa, Yasuhiro Miyauchi-Nanri, Kanji Okumoto, Satoru Mukai, Kentaro Noi, Teru Ogura, Yukio Fujiki
A newly isolated binding protein of peroxisomal targeting signal type 2 (PTS2) receptor Pex7, termed P7BP2, is transported into peroxisomes by binding to the longer isoform of Pex5p, Pex5pL, via Pex7p. The binding to Pex7p and peroxisomal localization of P7BP2 depends on the cleavable PTS2 in the N-terminal region, suggesting that P7BP2 is a new PTS2 protein. By search on human database, three AAA+ domains are found in the N-terminal half of P7BP2. Protein sequence alignment and motif search reveal that in the C-terminal region P7BP2 contains additional structural domains featuring weak but sufficient homology to AAA+ domain...
September 11, 2018: Journal of Biochemistry
https://www.readbyqxmd.com/read/30184107/function-of-the-amino-terminal-region-of-human-mcm4-in-helicase-activity
#16
Xuan Wang, Yukio Ishimi
The amino-terminal region of eukaryotic MCM4 is characteristic of the presence of a number of phosphorylation sites for CDK and DDK, suggesting that the region plays regulatory roles in the MCM2-7 helicase function. However, the roles are not fully understood. We analyzed the role of the amino-terminal region of human MCM4 by using MCM4/6/7 helicase as a model for MCM2-7 helicase. First we found that deletion of 35 amino acids at the amino-terminal end resulted in inhibition of DNA helicase activity of the MCM4/6/7 complex...
September 4, 2018: Journal of Biochemistry
https://www.readbyqxmd.com/read/30165670/c1d-is-not-directly-involved-in-the-repair-of-uv-damaged-dna-but-protects-cells-from-oxidative-stress-by-regulating-gene-expressions-in-human-cell-lines
#17
Takeshi Tomita, Katsuaki Ieguchi, Morichika Takita, Fujiko Tsukahara, Masayuki Yamada, Jean-Marc Egly, Yoshiro Maru
A small nuclear protein, C1D, has roles in various cellular processes, transcription regulation, genome stability surveillance, DNA repair, and RNA processing, all of which are required to maintain the host life cycles. In the previous report, C1D directly interacts with XPB, a component of the nucleotide excision repair complex, and C1D knockdown reduced cell survival of 27-1 cells, CHO derivative cells, after UV irradiation. To find out the role of C1D in UV damaged cells, we used human cell lines with siRNA or shRNA to knockdown C1D...
August 27, 2018: Journal of Biochemistry
https://www.readbyqxmd.com/read/30165618/metabolomics-approach-in-lung-tissue-of-septic-rats-and-the-interventional-effects-of-xuebijing-injection-using-uhplc-q-orbitrap-hrms
#18
Tanye Xu, Lin Zhou, Yingying Shi, Liwei Liu, Lihua Zuo, Qingquan Jia, Shuzhang Du, Jian Kang, Xiaojian Zhang, Zhi Sun
Sepsis is the dysregulated host response to an infection which leads to life-threatening organ dysfunction. Metabolomic profiling in bio-fluid or tissue is vital for elucidating the pathogenesis of sepsis and evaluating therapeutic effects of medication. In this study, an untargeted metabolomics approach was applied to study the metabolic changes in lung tissue of septic rats induced by cecal ligation and puncture (CLP) and investigate the treatment effects of Xubijing injection (XBJ). Metabolomics analyses were performed on ultra-high performance liquid chromatography-Q Exactive hybrid quadrupole-orbitrap high-resolution accurate mass spectrometry (UHPLC-Q-Orbitrap-HRMS) together with multivariate statistical analysis...
August 27, 2018: Journal of Biochemistry
https://www.readbyqxmd.com/read/30137333/organelle-zones-in-mitochondria
#19
Shigeomi Shimizu
The recent development of scientific imaging techniques have lead to the identification of various novel organellar functions. Most of these functions are perfomred in limited areas within organelles. These local functional organelle regions are referred to as "zones". In mitochondria, there are various types of zones exist, including the apoptosis zone, necrosis zone, mitophagy zone, mitochondrial-derived vesicle budding zone, innate immunity zone, etc. The membrane contact site between mitochondria and the endoplasmic reticulum, which is referred to as MAM, is also considered a zone...
August 23, 2018: Journal of Biochemistry
https://www.readbyqxmd.com/read/30107464/hsp90-inhibitor-at-533-blocks-hsv-1-nuclear-egress-and-assembly
#20
Feng Li, Fujun Jin, Yiliang Wang, Danlin Zheng, Junwei Liu, Zhen Zhang, Rongze Wang, Dong Dong, Kai Zheng, Yifei Wang
Heat shock protein 90 (Hsp90) has been identified as an essential host factor for the infection and replication of several viruses, including HSV-1. Recent works have clearly shown that Hsp90 plays a role in the early stages of HSV-1 infection, including nuclear import and DNA replication. However, the role of Hsp90 in the late stages of HSV-1 infection remains unclear. In this study, we found that Hsp90 was up-regulated during late viral infection. Treatment with the Hsp90 inhibitor AT-533 significantly decreased the intracellular and extracellular virus titer, and strongly inhibited nucleocapsid egress from the nucleus...
August 10, 2018: Journal of Biochemistry
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