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Journal of Biochemistry

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https://www.readbyqxmd.com/read/29228300/dna-synthesis-by-fragment-assembly-using-extra-cellular-dna-delivered-by-artificial-controlled-horizontal-transfer
#1
Shinya Kaneko, Hiromi Fukushima, Misako Nakahama, Satomi Asano, Yasumasa Miyazaki, Yasunori Aizawa, Mitsuhiro Itaya
DNA synthesis in the Bacillus subtilis cells has become possible using extra-cellular DNA. Generally, purified DNAs in a test tube have been required to introduce into the host cells for molecular cloning technology in the laboratory. We have developed a cell lysis technique for natural transformation using stable extra-cellular plasmid DNAs, in which the extra-cellular plasmid DNAs are released from lysed Escherichia coli cells. DNA synthesis then proceeds by fragment assembly using the stable extracellular DNAs, without biochemical purification...
December 7, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/29228282/proteolytic-inactivation-of-adamts13-by-plasmin-in-human-plasma-risk-of-thrombotic-thrombocytopenic-purpura
#2
Yongchol Shin, Haruki Miyake, Kenshi Togashi, Ryuichi Hiratsuka, Kana Endou-Ohnishi, Yasutada Imamura
Thrombotic thrombocytopenic purpura (TTP) is caused by inactivation of a von Willebrand factor (VWF)-cleaving enzyme, ADAMTS13, which leads to platelet-rich thrombi comprising unusually large VWF multimers. We have found that ADAMTS13 can bind to the inactivated form of plasmin. In addition, plasmin cleaves purified ADAMTS13 into several fragments and inactivates it. Hence, we hypothesized that activation of plasminogen to plasmin becomes a new-onset factor for TTP due to ADAMTS13 inactivation. Plasmin was added exogenously or activated from plasminogen by streprokinase addition in HP...
December 7, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/29228210/cholesterol-blocks-spontaneous-insertion-of-membrane-proteins-into-liposomes-of-phosphatidylcholine
#3
Shota Nakamura, Sonomi Suzuki, Hiroaki Saito, Ken-Ichi Nishiyama
Spontaneous insertion of membrane proteins into liposomes formed from E. coli polar phospholipids is blocked by diacylglycerol (DAG) at a physiological level. We found that cholesterol also blocks this spontaneous insertion, although a much larger amount is necessary for sufficient blockage. Reversely, sphingomyelin enhanced the spontaneous insertion. DAG at a physiological level was found not to block spontaneous insertion into liposomes formed from phosphatidylcholine (PC), while non-physiologically high concentrations of DAG reduced it...
December 7, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/29211891/osw2-is-required-for-proper-assembly-of-glucan-and-or-mannan-layers-of-the-yeast-spore-wall
#4
Hua-Ping Pan, Ning Wang, Hiroyuki Tachikawa, Xiao-Dong Gao, Hideki Nakanishi
OSW2 is a meiotically-induced gene required for spore wall formation. osw2Δ spores are sensitive to ether treatment. Except for this phenotype, the mutants do not show obvious sporulation defects; thus, its function remains elusive. We found that deletion of both OSW2 and CHS3 results in a synthetic sporulation defect. The spore wall is composed of four layers, and chs3Δ spores lack the outer two (chitosan and dityrosine) layers. Thus, Osw2 is involved in the assembly of the inner (glucan and mannan) layers...
December 1, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/29186552/regulation-of-the-epithelial-barrier-by-post-translational-modifications-of-tight-junction-membrane-proteins
#5
Kenta Shigetomi, Junichi Ikenouchi
Body and organ surfaces in multicellular organisms are covered with a sheet of epithelial cells. The tight junction (TJ) is an adhesive structure that seals the gap between epithelial cells and functions as a selective barrier to prevent the entry of antigens and pathogenic microbes from the extracellular environment. Several transmembrane proteins that constitute the TJ (claudin, occludin, tricellulin, and angulin) have been identified. As over-expression of these proteins does not enlarge TJs or enhance epithelial barrier function, it remains unclear how TJ membrane proteins are regulated to modulate the amount of TJ and the strength of the epithelial barrier...
November 24, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/29186467/biological-functions-of-sulfoglycolipids-and-the-emars-method-for-identification-of-co-clustered-molecules-in-the-membrane-microdomains
#6
Koichi Honke
Two major sulfoglycolipids, sulfatide (SO3-3Gal-ceramide) and seminolipid (SO3-3Gal-alkylacylglycerol) exist in mammals. Sulfatide is abundant in the myelin sheath and seminolipid is unique to the spermatogenic cells. The carbohydrate moiety of sulfatide and seminolipid is identical and synthesized by common enzymes: ceramide galactosyltransferase (CGT) and cerebroside sulfotransferase (CST). We have purified CST homogenously, cloned the CST gene, and generated CST-knockout mice. CST-null mice completely lack sulfoglycolipids all over the body...
November 23, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/29165574/histone-variants-essential-actors-in-the-male-genome-programing
#7
Naghmeh Hoghoughi, Sophie Barral, Alexandra Vargas, Sophie Rousseaux, Saadi Khochbin
Prior to its transmission to the offspring, the male genome has to be tightly compacted. A genome-scale histone eviction and the subsequent repackaging of DNA by protamines direct this essential genome condensation step. The requirement for male germ cells to undergo such a dramatic and unique genome reorganization explains why these cells express the largest number of histone variants, including many testis-specific ones. Indeed, an open chromatin, nucleosome instability and a facilitated process of histone disassembly are direct consequences of the presence of these histone variants in the chromatin of male germ cells...
November 20, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/29161429/crosstalk-between-the-microbiome-and-epigenome-messages-from-bugs
#8
Yufeng Qin, Paul A Wade
Mammals exist in a complicated symbiotic relationship with their gut microbiome, which is postulated to have broad impacts on host health and disease. As omics-based technologies have matured, the potential mechanisms by which the microbiome affects host physiology are being addressed. The gut microbiome, which provides environmental cues, can modify host cell responses to stimuli through alterations in the host epigenome and, ultimately, gene expression. Increasing evidence highlights microbial generation of bioactive compounds that impact the transcriptional machinery in host cells...
November 17, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/29161414/structural-diversity-of-the-nucleosome
#9
Masako Koyama, Hitoshi Kurumizaka
In eukaryotes, genomic DNA is compacted in chromatin, which generally suppresses transcription, replication, repair, and recombination. The fundamental unit of chromatin is the nucleosome, whose structure was first determined at atomic resolution in 1997. However, recent findings have revealed that the nucleosome is not a structurally homogenous entity. Nucleosomes containing histone variants often have subtle but clear differences in their structural and functional characteristics, as compared to the canonical nucleosome...
November 17, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/29136173/high-levels-of-gsk-3%C3%AE-signaling-reduce-osteogenic-differentiation-of-stem-cells-in-osteonecrosis-of-femoral-head
#10
Lu Huang, Ying Wang, Yangzi Jiang, Yan Wu, Changchang Hu, Hongwei Ouyang
Osteonecrosis of the femoral head (ONFH) is a common but intractable disease. In this study, we investigated the mechanisms regulating alterations in mesenchymal stem cell (MSC) differentiation in ONFH. Five patients who were diagnosed with ONFH were enrolled in this study. BMSCs were isolated from the osteonecrotic zone in the femoral head (FH-pMSCs) and from the normal zone in the pelvis (hMSCs) of the same patient. Morphology, cell proliferation, and expression of mediators of the Wnt signaling pathway were evaluated...
November 10, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/29092074/characterization-of-redundant-trnailes-with-cau-and-uau-anticodons-in-lactobacillus-plantarum
#11
Chie Tomikawa, Sylvie Auxilien, Vincent Guérineau, Yuya Yoshioka, Kiyo Miyoshi, Hiroyuki Hori, Dominique Fourmy, Kazuyuki Takai, Satoko Yoshizawa
In most eubacteria, the minor AUA isoleucine codon is decoded by tRNAIle2, which has a lysidine (L) in the anticodon loop. The lysidine is introduced by tRNAIle-lysidine synthetase (TilS) through post-transcriptional modification of cytidine to yield an LAU anticodon. Some bacteria, Lactobacillus plantarum for example, possess two tRNAIle2(UAU) genes in addition to, two tRNAIle2(CAU) genes and the tilS gene. tRNA expression from all these genes would generate redundancy in a tRNA that decodes a rare AUA codon...
October 30, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/29092071/the-regulation-mechanisms-of-ahr-by-molecular-chaperone-complex
#12
Ikuru Kudo, Miki Hosaka, Asami Haga, Noriko Tsuji, Yuhtaroh Nagata, Hirotaka Okada, Kana Fukuda, Yuka Kakizaki, Tomoya Okamoto, Ewa Grave, Hideaki Itoh
The AhR, so called the dioxin receptor, is a member of the nuclear receptor superfamily. The ligand-free AhR forms a cytosolic protein complex with the molecular chaperone HSP90, co-chaperone p23, and XAP2 in the cytoplasm. Following ligand binding like 2, 3, 7, 8-tetrachlorodibenzo-p-dioxin (TCDD), the AhR translocates into the nucleus. Although it has been reported that HSP90 regulates the translocation of the AhR to the nucleus, the precise activation mechanisms of the AhR have not yet been fully understood...
October 28, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/29087477/detection-of-protonated-non-watson-crick-base-pairs-using-electrospray-ionization-mass-spectrometry
#13
Riyoko Ishida, Hideo Iwahashi
Many studies have shown that protonated nucleic acid base pairs are involved in a wide variety of nucleic acid structures. However, little information is available on relative stability of hemiprotonated self- and non-self-dimers at monomer level. We used electrospray ionization mass spectrometry (ESI-MS) to evaluate the relative stability under various concentrations of hydrogen ion. These enable conjecture of the formation of protonated non-Watson-Crick base pairs based on DNA and RNA base sequence. In the present study, we observed that ESI-MS peaks corresponded to respective self-dimers for all examined nucleosides except for adenosine...
October 26, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/29069453/kinetic-characterization-of-substrate-binding-sites-of-thermostable-trna-methyltransferase-trmb
#14
Chie Tomikawa, Kazuyuki Takai, Hiroyuki Hori
TrmB is a eubacterial tRNA methyltransferase which catalyzes the formation of N 7-methylguanosine at position 46 (m 7 G46) in tRNA consuming S-adenosyl-L-methionine (AdoMet) as the methyl group donor during the reaction. Previously, we purified TrmB from Aquifex aeolicus , a hyper-thermophilic eubacterium, and clarified the recognition sites in tRNA. Furthermore, we reported that an additional C-terminal region of A. aeolicus TrmB is required for protein stability at high temperatures. In the current study, we devised a new purification method to remove contaminating RNA completely...
October 23, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/29069440/tight-interaction-of-eef2-in-the-presence-of-stm1-on-ribosome
#15
Hikari Hayashi, Riku Nagai, Taisho Abe, Miki Wada, Koichi Ito, Nono Takeuchi-Tomita
The stress-related protein Stm1 interacts with ribosomes, and is implicated in repressing translation. Stm1 was previously studied both in vivo and in vitro by cell-free translation systems using crude yeast lysates, but its precise functional mechanism remains obscure. Using an in vitro reconstituted translation system, we now show that Stm1 severely inhibits translation through its N-terminal region, aa 1 to 107, and this inhibition is antagonized by eEF3. We found that Stm1 stabilizes eEF2 on the 80S ribosome in the GTP-bound form, independently of eEF2's diphthamide modification, a conserved post-translational modification at the tip of domain IV...
October 23, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/29069416/importance-of-the-positively-charged-residue-at-position-54-to-the-chaperoning-function-conformational-stability-and-amyloidogenic-nature-of-human-%C3%AE-a-crystallin
#16
Kazem Khoshaman, Reza Yousefi, Ali Niazi, Ahmad Oryan, Ali Akbar Moosavi-Movahedi, Boris I Kurganov
Arginine 54 (R54) in αA-Crystallin (αA-Cry) is highly conserved within different species. Recently, three missense mutations at this hot spot position have been reported to cause congenital cataract disorders. To investigate the impact of charge on structural and functional aspects of αA-Cry, R54 was individually substituted with lysine and aspartate. Replacement of R54 with the positively and negatively charged residues led to structural alteration and reduction in the protein conformational and proteolytic stability...
October 23, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/29069405/structural-analysis-of-neutral-glycosphingolipids-from-the-silkworm-bombyx-mori-and-the-difference-in-ceramide-composition-between-larvae-and-pupae
#17
Saki Itonori, Kyouhei Hashimoto, Mika Nakagawa, Masashi Harada, Takae Suzuki, Hisao Kojima, Masahiro Ito, Mutsumi Sugita
Glycosphingolipids (GSLs) from the silkworm Bombyx mori were identified and GSL expression patterns between larvae and pupae were compared. The structural analysis of neutral GSLs from dried pupae revealed the following predominant species: Glcβ1Cer, Manβ4Glcβ1Cer, GlcNAcβ3Manβ4Glcβ1Cer, Galβ3Manβ4Glcβ1Cer, GalNAcα4Galβ3Manβ4Glcβ1Cer, GlcNAcβ3Galβ3Manβ4Glcβ1Cer, Galα4Galβ3Manβ4Glcβ1Cer, and (GalNAcα4) 1-4 GalNAcα4Galβ3Manβ4Glcβ1Cer. Linear elongation of α4-GalNAc was observed at the non-reducing end of Galβ3Manβ4Glcβ1Cer with up to five GalNAc repeats...
October 23, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/29048484/adiponectin-suppression-of-late-inflammatory-mediator-hmgb1-induced-cytokine-expression-in-raw-264-macrophage-cells
#18
Mohamed Elfeky, Takeshi Yoneshiro, Yuko Okamatsu-Ogura, Kazuhiro Kimura
High mobility group protein B1 (HMGB1) is a late inflammatory mediator released from inflammatory cells when stimulated, resulting in exaggerating septic symptoms. We recently demonstrated that full-length adiponectin, a potent anti-inflammatory adipokine, inhibits lipopolysaccharide-induced HMGB1 release. However, the effects of adiponectin on HMGB1-induced exaggerating signals currently remain unknown. This study aimed to investigate the effects of adiponectin on the pro-inflammatory function of HMGB1 in RAW264 macrophage cells...
October 18, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/29040577/metabolomics-of-postprandial-plasma-alterations-a-comprehensive-japanese-study
#19
Takeo Moriya, Yoshinori Satomi, Hiroyuki Kobayashi
While endogenous metabolites in plasma can be used as clinical biomarkers, intra-day variations should be carefully considered. The postprandial effect is a large contributing factor and is dependent on regional features (e.g., meals, ethnicity). Thus, for clinical application, regional-specific postprandial baseline data are required. In this study, 10 healthy Japanese volunteers of different ages and genders ate the same meal, and blood samples were taken 30 min before and one hour after the meal challenge...
October 4, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/29036651/aureobasidium-pullulans-cultured-fluid-induces-il-18-production-leading-to-th1-polarization-during-influenza-a-virus-infection
#20
Daisuke Fujikura, Daisuke Muramatsu, Kochi Toyomane, Satoko Chiba, Takuji Daito, Atsushi Iwai, Takahisa Kouwaki, Masaaki Okamoto, Hideaki Higashi, Hiroshi Kida, Hiroyuki Oshiumi
Several microbial molecules with pathogen-associated molecular patterns stimulate host innate immune responses. The innate immune system plays a crucial role in activating acquired immune response via cytokine production and antigen presentation. Previous studies have shown that Aureobasidium pullulans-cultured fluid (AP-CF), which contains β-glucan, exhibits adjuvant activity and renders mice resistance to influenza A virus infection; however, the underlying mechanism remains elusive. In this study, we investigated the innate immune response to AP-CF...
October 3, 2017: Journal of Biochemistry
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