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991.
Munehiro Uda Hiroaki Kawasaki Ayako Shigenaga Takeshi Baba Fumiyuki Yamakura 《Bioscience reports》2012,32(6):521-530
Nitration of tryptophan residues is a novel post-translational modification. In the present
study, we examined whether NO2Trp (nitrotryptophan)-containing proteins are produced in
the hippocampus and cerebellum of the adult rat under physiological conditions in
vivo. Using Western blot analysis with anti-6-NO2Trp-specific antibody, we found
many similar immunoreactive spots in the protein extracts from both regions. These spots were
subsequently subjected to trypsin digestion and LC-ESI-MS/MS (LC-electrospray ionization-tandem MS)
analysis. We identified several cytoskeletal proteins and glycolytic enzymes as
NO2Trp-containing proteins and determined the position of nitrated tryptophan residues
with significant ion score levels (P<0.05) in several proteins in both
regions. We also observed that the total amount of NO2Trp-containing proteins in the
cerebellum was significantly greater than that in the hippocampus (P<0.05).
Moreover, IP (immunoprecipitation) assays using anti-aldolase C antibody showed that the relative
intensity of immunostaining for NO2Trp over aldolase C was much higher in cerebellum than
in hippocampus. The amounts of nNOS (neuronal nitric oxide synthase) and eNOS (endothelial nitric
oxide synthase) were much greater in cerebellum than in hippocampus. This is the first evidence of
several specific sites of nitrated tryptophan in proteins under physiological conditions in
vivo. 相似文献
992.
Masai E Kamimura N Kasai D Oguchi A Ankai A Fukui S Takahashi M Yashiro I Sasaki H Harada T Nakamura S Katano Y Narita-Yamada S Nakazawa H Hara H Katayama Y Fukuda M Yamazaki S Fujita N 《Journal of bacteriology》2012,194(2):534-535
Sphingobium sp. strain SYK-6 is able to grow on an extensive variety of lignin-derived biaryls and monoaryls, and the catabolic genes for these compounds are useful for the production of industrially valuable metabolites from lignin. Here we report the complete nucleotide sequence of the SYK-6 genome which consists of the 4,199,332-bp-long chromosome and the 148,801-bp-long plasmid. 相似文献
993.
Matsuzawa T Mori K Kadowaki T Shimada M Tashiro K Kuhara S Inagawa H Soma G Takegawa K 《Journal of bacteriology》2012,194(5):1258-1259
Pantoea agglomerans is a gram-negative bacterium that grows symbiotically with various plants. Here we report the 4.8-Mb genome sequence of P. agglomerans strain IG1. The lipopolysaccharides derived from P. agglomerans IG1 have been shown to be effective in the prevention of various diseases, such as bacterial or viral infection, lifestyle-related diseases. This genome sequence represents a substantial step toward the elucidation of pathways for production of lipopolysaccharides. 相似文献
994.
Y Kimura T Hanami Y Tanaka MJ de Hoon T Soma M Harbers A Lezhava Y Hayashizaki K Usui 《Biochemistry》2012,51(31):6056-6067
Nucleic acid oligonucleotides are widely used in hybridization experiments for specific detection of complementary nucleic acid sequences. For design and application of oligonucleotides, an understanding of their thermodynamic properties is essential. Recently, exciton-controlled hybridization-sensitive fluorescent oligonucleotides (ECHOs) were developed as uniquely labeled DNA oligomers containing commonly one thymidine having two covalently linked thiazole orange dye moieties. The fluorescent signal of an ECHO is strictly hybridization-controlled, where the dye moieties have to intercalate into double-stranded DNA for signal generation. Here we analyzed the hybridization thermodynamics of ECHO/DNA duplexes, and thermodynamic parameters were obtained from melting curves of 64 ECHO/DNA duplexes measured by ultraviolet absorbance and fluorescence. Both methods demonstrated a substantial increase in duplex stability (ΔΔG°(37) ~ -2.6 ± 0.7 kcal mol(-1)) compared to that of DNA/DNA duplexes of the same sequence. With the exception of T·G mismatches, this increased stability was mostly unaffected by other mismatches in the position opposite the labeled nucleotide. A nearest neighbor model was constructed for predicting thermodynamic parameters for duplex stability. Evaluation of the nearest neighbor parameters by cross validation tests showed higher predictive reliability for the fluorescence-based than the absorbance-based parameters. Using our experimental data, a tool for predicting the thermodynamics of formation of ECHO/DNA duplexes was developed that is freely available at http://genome.gsc.riken.jp/echo/thermodynamics/ . It provides reliable thermodynamic data for using the unique features of ECHOs in fluorescence-based experiments. 相似文献
995.
Glutamate excitotoxicity is implicated in chronic neurological disorders and acute CNS insults and causes neuronal degeneration including axons. The molecular mechanism underlying excitotoxicity-induced axon degeneration is poorly understood. Recently, we found that components of the dynein-dynactin complex that governs microtubule-dependent retrograde transport play important roles in modulating the process of excitotoxicity-induced neurodegeneration. Here we used hippocampal cultures and searched for pathways that function in concert with the components of the dynein-dynactin complex and identified microtubule stabilization as a cooperative pathway to suppress axon degeneration. We find that overexpression of p150Glued, a major component of the dynactin complex, and microtubule stabilization cooperatively suppress axon degeneration. The protective effect of p150Glued is dependent on the C-terminal region as excitotoxicity-induced C-terminal truncated form of p150Glued was unable to interact with APP cargo and altered the localization of APP in neurites when overexpressed. C-terminal truncation of p150Glued is not rescued by microtubule stabilization suggesting that the downstream effects of p150Glued and microtubule stabilization to protect axon degeneration are mutually exclusive. 相似文献
996.
OsGEN-L has a 5'-flap endonuclease activity and plays an essential role in rice microspore development. The Class 4 RAD2/XPG family nucleases, including OsGEN-L, were recently found to have resolving activity for the Holliday junction (HJ), the intermediate of DNA strand recombination. In this study, we performed a detailed characterization of OsGEN-L, as a structure-specific endonuclease. Highly purified OsGEN-L was prepared as the full-length protein for in vitro endonuclease assays using various structured DNAs, and the 5'-flap endonuclease activity, which is stimulated in a PCNA-dependent manner, was demonstrated. In addition, the in vitro HJ resolving activity of OsGEN-L represents the first such activity originating from plant cells. OsGEN-L cleaved HJ at symmetrically related sites of the branch point. However, the two branched strands seemed to be cleaved individually, and not cooperatively, by each OsGEN-L monomer protein. The substrate specificity suggests that OsGEN-L functions in multiple processes of DNA metabolism in rice cells. 相似文献
997.
Kuwahara T Tonegawa R Ito G Mitani S Iwatsubo T 《The Journal of biological chemistry》2012,287(10):7098-7109
α-Synuclein is causative for autosomal dominant familial Parkinson disease and dementia with Lewy bodies, and the phosphorylation of α-synuclein at residue Ser-129 is a key posttranslational modification detected in Parkinson disease/dementia with Lewy bodies lesions. However, the role of Ser-129 phosphorylation on the pathogenesis of Parkinson disease/dementia with Lewy bodies remains unclear. Here we investigated the neurotoxicity of Ser-129-substituted α-synuclein in the transgenic Caenorhabditis elegans (Tg worm) model of synucleinopathy. Tg worms pan-neuronally overexpressing nonphosphorylatable (S129A) α-synuclein showed severe defects including motor dysfunction, growth retardation, and synaptic abnormalities. In contrast, Tg worms expressing phosphorylation mimic (S129D) α-synuclein exhibited nearly normal phenotypes. Biochemical fractionation revealed that the level of membrane-bound α-synuclein was significantly increased in S129A-α-synuclein Tg worms, whereas S129D- as well as A30P-α-synuclein displayed lower membrane binding properties. Furthermore, A30P/S129A double mutant α-synuclein did not cause neuronal dysfunction and displayed low membrane binding property. In human neuroblastoma SH-SY5Y cells, localization of S129A-α-synuclein to membranes was significantly increased. Finally, gene expression profiling of S129A-Tg worms revealed a dramatic up-regulation of Daf-16/FOXO pathway genes, which likely act against the dysfunction caused by S129A-α-synuclein. These results imply a role of Ser-129 phosphorylation of α-synuclein in the attenuation of α-synuclein-induced neuronal dysfunction and downstream stress response by lowering the membrane binding property. 相似文献
998.
Satoshi N. Suzuki Masae I. Ishihara Masahiro Nakamura Shin Abe Tsutom Hiura Kosuke Homma Motoki Higa Daisuke Hoshino Kazuhiko Hoshizaki Hideyuki Ida Ken Ishida Motohiro Kawanishi Kazutaka Kobayashi Koichiro Kuraji Shigeo Kuramoto Takashi Masaki Kaoru Niiyama Mahoko Noguchi Haruto Nomiya Satoshi Saito Takeshi Sakai Michinori Sakimoto Hitoshi Sakio Tamotsu Sato Hirofumi Shibano Mitsue Shibata Maki Suzuki Atsushi Takashima Hiroshi Tanaka Masahiro Takagi Naoaki Tashiro Naoko Tokuchi Toshiya Yoshida Yumiko Yoshida 《Ecological Research》2012,27(6):989-990
This data paper reports litter fall data collected in a network of 21 forest sites in Japan. This is the largest litter fall data set freely available in Japan to date. The network is a part of the Monitoring Sites 1000 Project launched by the Ministry of the Environment, Japan. It covers subarctic to subtropical climate zones and the four major forest types in Japan. Twenty-three permanent plots in which usually 25 litter traps were installed were established in old-growth or secondary natural forests. Litter falls were collected monthly from 2004, and sorted into leaves, branches, reproductive structures and miscellaneous. The data provide seasonal patterns and inter-annual dynamics of litter falls, and their geographical patterns, and offer good opportunities for meta-analyses and comparative studies among forests. 相似文献
999.
Ishibashi N Himeno K Fujita K Masuda Y Perez RH Zendo T Wilaipun P Leelawatcharamas V Nakayama J Sonomoto K 《Bioscience, biotechnology, and biochemistry》2012,76(5):947-953
Enterocins NKR-5-3A, B, C, and D were purified from the culture supernatant of Enterococcus faecium NKR-5-3 and characterized. Among the four purified peptides, enterocin NKR-5-3A (5242.3 Da) was identical to brochocin A, produced by Brochothrix campestris ATCC 43754, in mature peptides, and its putative synergistic peptide, enterocin NKR-5-3Z, was found to be encoded in ent53Z downstream of ent53A, encoding enterocin NKR-5-3A. Enterocin NKR-5-3B (6316.4 Da) showed a broad antimicrobial spectrum, and enterocin NKR-5-3C (4512.8 Da) showed high activity against Listeria. Enterocin NKR-5-3D (2843.5 Da), showing high homology to an inducing peptide produced by Lactobacillus sakei 5, induced the production of the enterocins. The enterocins showed different antimicrobial spectra and intensities. E. faecium NKR-5-3 concomitantly produced enterocins NKR-5-3A, B, C, and D which probably belong to different classes of bacteriocins. Furthermore, NKR-5-3 production was induced by enterocin NKR-5-3D. 相似文献
1000.
Watanabe I Harada K Matsui T Miyasaka H Okuhata H Tanaka S Nakayama H Kato K Bamba T Hirata K 《Bioscience, biotechnology, and biochemistry》2012,76(5):1015-1017
The garden plant portulaca (Portulaca oleracea cv.) efficiently removes bisphenol A (BPA), an endocrine-disrupting chemical, from a hydroponic solution, but the molecular mechanisms underlying BPA metabolism by portulaca remain unclear. In this study, BPA metabolites converted by portulaca were analyzed by liquid chromatography coupled with tandem mass spectrometry. We observed the hydroxylation of BPA and the oxidization of it to quinone. Polyphenol oxidases are likely to contribute to BPA degradation by portulaca. 相似文献