202 research outputs found
RecJ 型エキソヌクレアーゼの構造機能解析
No full textThis research was originally published in The Journal of Biological Chemistry. Taisuke Wakamatsu, Yoshiaki Kitamura, Yutaro Kotera, Noriko Nakagawa, Seiki Kuramitsu, and Ryoji Masui. Structure of RecJ Exonuclease Defines Its Specificity for Single-stranded DNA. Journal of Biological Chemistry. 2010; VOL. 285, NO. 13, pp. 9762–9769. © the American Society for Biochemistry and Molecular Biology. http://www.jbc.org/content/285/13/9762.abstractThis research was originally published in The Journal of Biological Chemistry. Taisuke Wakamatsu, Kwang Kim, Yuri Uemura, Noriko Nakagawa, Seiki Kuramitsu and Ryoji Masui. Role of RecJ-like Protein with 5′-3′ Exonuclease Activity in Oligo(deoxy)nucleotide Degradation. Journal of Biological Chemistry. 2011; VOL. 286, NO. 4, pp. 2807–2816 © the American Society for Biochemistry and Molecular Biology. http://www.jbc.org/content/286/4/2807.abstrac
Purification, Molecular Cloning, and Catalytic Activity of Schizosaccharomyces pombe Pyridoxal Reductase -A POSSIBLE ADDITIONAL FAMILY IN THE ALDO-KETO REDUCTASE SUPERFAMILY-
No full textCytoplasmic factors that control nuclear behavior in mammalian oocytes: A re-evaluation of studies performed as a student of Yoshio Masui
No full textStudies performed by the author in the laboratory of Dr Yoshio Masui are reviewed and interpreted in the light of subsequent findings. The first series of studies indicated that that chromosome condensation during meiotic maturation of mouse oocytes is controlled initially by a stable protein that decays during maturation and subsequently by an unstable protein synthesized after germinal vesicle breakdown. Cyclin B is present in immature oocytes, becomes partially degraded near metaphase I and then re-accumulates, suggesting that this may be protein whose activity was inferred from the original results. The second series of experiments indicated that factors which appear in the oocyte cytoplasm during maturation are able to remodel the sperm into metaphase-like chromosomes, and that the supply of these factors is limited. Recent work indicates that these factors are required for the assembly of histones onto the sperm DNA, and has identified two molecular species, mNAP-1 and NPM-3, known to promote replication-independent chromatin assembly in somatic cells, that are expressed in oocyte
Inactivation of the DNA repair genes mutS, mutL or the anti-recombination gene mutS2 leads to activation of vitamin B1 biosynthesis genes.
No full textOxidative stress generates harmful reactive oxygen species (ROS) that attack biomolecules including DNA. In living cells, there are several mechanisms for detoxifying ROS and repairing oxidatively-damaged DNA. In this study, transcriptomic analyses clarified that disruption of DNA repair genes mutS and mutL, or the anti-recombination gene mutS2, in Thermus thermophilus HB8, induces the biosynthesis pathway for vitamin B(1), which can serve as an ROS scavenger. In addition, disruption of mutS, mutL, or mutS2 resulted in an increased rate of oxidative stress-induced mutagenesis. Co-immunoprecipitation and pull-down experiments revealed previously-unknown interactions of MutS2 with MutS and MutL, indicating that these proteins cooperatively participate in the repair of oxidatively damaged DNA. These results suggested that bacterial cells sense the accumulation of oxidative DNA damage or absence of DNA repair activity, and signal the information to the transcriptional regulation machinery for an ROS-detoxifying system
Mass spectrometry-based cancer biomarker discovery
No full textThe aim of the projects in this thesis was to identify biomarkers for clear cell renal cell carcinomas (ccRCC) and head and neck/oral squamous cell carcinoma (HNOSCC), using quantitative or qualitative proteomics. Comparative analysis of cancerous and normal tissue homogenates, or secretome analysis of cancer cell cultures using liquid chromatography - mass spectrometry (LC-MS) and immunoassay techniques, allowed the identification of different types of biomarkers: diagnostic or prognostic, biofluid- or tissue-based. Chapter 1 of this thesis provides general information on cancer and cancer biomarker discovery. Chapter 2 gives a brief introduction to the techniques used in this work and theories behind them. Chapters 3 - 5 are papers that resulted from the cancer biomarker discovery research performed here, and Chapter 6 contains the conclusions, the author's comments and the final remarks. The papers on the identification of biomarkers for different diseases, to which the author of this thesis contributed, are listed in the Appendix
A specific single-stranded DNA induces a distinct conformational change in the nucleoid-associated protein HU
No full textAbstractIn prokaryotic cells, genomic DNA forms an aggregated structure with various nucleoid-associated proteins (NAPs). The functions of genomic DNA are cooperatively modulated by NAPs, of which HU is considered to be one of the most important. HU binds double-stranded DNA (dsDNA) and serves as a structural modulator in the genome architecture. It plays important roles in diverse DNA functions, including replication, segregation, transcription and repair. Interestingly, it has been reported that HU also binds single-stranded DNA (ssDNA) regardless of sequence. However, structural analysis of HU with ssDNA has been lacking, and the functional relevance of this binding remains elusive.In this study, we found that ssDNA induced a significant change in the secondary structure of Thermus thermophilus HU (TtHU), as observed by analysis of circular dichroism spectra. Notably, this change in secondary structure was sequence specific, because the complementary ssDNA or dsDNA did not induce the change. Structural analysis using nuclear magnetic resonance confirmed that TtHU and this ssDNA formed a unique structure, which was different from the previously reported structure of HU in complex with dsDNA. Our data suggest that TtHU undergoes a distinct structural change when it associates with ssDNA of a specific sequence and subsequently exerts a yet-to-be-defined function
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