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Genomes and Genes | M KimuraSummaryAffiliation: National Institute of Genetics Country: Japan Publications
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Publications
Formation of a carboxy-terminal domain phosphatase (Fcp1)/TFIIF/RNA polymerase II (pol II) complex in Schizosaccharomyces pombe involves direct interaction between Fcp1 and the Rpb4 subunit of pol IIMakoto Kimura
Department of Molecular Genetics, National Institute of Genetics, Mishima, Shizuoka 411 8540, Japan
Mol Cell Biol 22:1577-88. 2002..This result indicates the importance of Fcp1-Rpb4 interaction for formation of the Fcp1/TFIIF/pol II complex in vivo...- Involvement of multiple subunit-subunit contacts in the assembly of RNA polymerase IIM Kimura
Department of Molecular Genetics, National Institute of Genetics, Mishima, Shizuoka 411 8540, Japan
Nucleic Acids Res 28:952-9. 2000..We propose a mechanism in which the assembly of RNA poly-merase II is stabilized through multiple subunit-subunit contacts... 
Intracellular contents and assembly states of all 12 subunits of the RNA polymerase II in the fission yeast Schizosaccharomyces pombeM Kimura
National Institute of Genetics, Department of Molecular Genetics, Mishima, Shizuoka, Japan
Eur J Biochem 268:612-9. 2001..In agreement with the biochemical analysis, the GFP-Rpb1 and GFP-Rpb3 fusions were present in the nuclei but the GFP-Rpb4 was detected in the cytoplasm as well as the nuclei...- The Rpb4 subunit of fission yeast Schizosaccharomyces pombe RNA polymerase II is essential for cell viability and similar in structure to the corresponding subunits of higher eukaryotesH Sakurai
Department of Molecular Genetics, National Institute of Genetics, Mishima, Shizuoka 411 8540, Japan
Mol Cell Biol 19:7511-8. 1999..However, S. pombe Rpb4 is closer in certain molecular functions to S. cerevisiae RPB4 than the eukaryotic RPB4 homologues... - Two large subunits of the fission yeast RNA polymerase II provide platforms for the assembly of small subunitsA Ishiguro
Department of Molecular Genetics, National Institute of Genetics, Shizuoka 411, Mishima, Japan
J Mol Biol 279:703-12. 1998..Direct contact of the two large subunits, Rpb1 and Rpb2, was also demonstrated by cross-linking... - RNA polymerase II subunits 2, 3, and 11 form a core subassembly with DNA binding activityM Kimura
Department of Molecular Genetics, National Institute of Genetics, Mishima, Shizuoka 411, Japan
J Biol Chem 272:25851-5. 1997..Both the Rpb2-Rpb3-Rpb11 complex and the free Rpb1 protein showed DNA binding activity, although the affinity was weaker compared with the intact RNA polymerase... - The two alpha subunits of Escherichia coli RNA polymerase are asymmetrically arranged and contact different halves of the DNA upstream elementK Murakami
Department of Molecular Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
Proc Natl Acad Sci U S A 94:1709-14. 1997..The results clearly indicated that the two alpha subunits bind in tandem to two helix turns of the rrnBP1 UP element, and that the beta'-associated alpha subunit is bound to the promoter-distal region... - Subunits of yeast RNA polymerases: structure and functionA Ishihama
Department of Molecular Genetics, National Institute of Genetics, Mishima, Shizuoka 411, Japan
Curr Opin Microbiol 1:190-6. 1998..These protein-protein interactions ultimately lead to control of the activity and specificity of the RNA polymerases... - Identification of the gene and the protein of RNA polymerase II subunit 9 (Rpb9) from the fission yeast Schizosacharomyces pombeH Sakurai
National Institute of Genetics, Department of Molecular Genetics, Shizuoka, Japan
Gene 221:11-6. 1998..After Western blot analysis using antibodies raised against the protein product of the newly isolated rpb9 gene, we found that the purified RNA polymerase II contains Rpb9... - Functional organization of two large subunits of the fission yeast Schizosaccharomyces pombe RNA polymerase II. Location of the catalytic sitesW A Wlassoff
National Institute of Genetics, Department of Molecular Genetics, Mishima, Shizuoka 411 8540, Japan
J Biol Chem 274:5104-13. 1999..All these regions include the conserved sequences of RNA polymerases, and the catalytic site of Rpb2 belongs to an NH2-terminal part of its conserved sequence H... - Functional map of the alpha subunit of Escherichia coli RNA polymerase: amino acid substitution within the amino-terminal assembly domainM Kimura
Department of Molecular Genetics, National Institute of Genetics, Shizuoka, Japan
J Mol Biol 254:342-9. 1995..Isolation of two mutants, alpha-K86A and alpha-V173A, both forming alpha 2 beta but not alpha 2 beta beta' complex, confirmed our previous conclusion that two separated regions participate in beta'-binding... - Studies of Schizosaccharomyces pombe TFIIE indicate conformational and functional changes in RNA polymerase II at transcription initiationKazuhiro Hayashi
Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565 0871, Japan
Genes Cells 10:207-24. 2005.... - Tfg3, a subunit of the general transcription factor TFIIF in Schizosaccharomyces pombe, functions under stress conditionsMakoto Kimura
Gene Engineering Division, BioResource Center, RIKEN Institute of Physical and Chemical Research, Tsukuba, Ibaraki 305 0074, Japan and Nippon Institute for Biological Science, Ome, Tokyo 198 0024, Japan
Nucleic Acids Res 32:6706-15. 2004..Taken together, we propose that Tfg3 is involved in transcriptional regulation under stress conditions, in particular, at high temperatures... - Glyceraldehyde-3-phosphate dehydrogenase and actin associate with RNA polymerase II and interact with its Rpb7 subunitHiroshi Mitsuzawa
Department of Molecular Genetics, National Institute of Genetics, Mishima, Shizuoka 411 8540, Japan
FEBS Lett 579:48-52. 2005..In addition, GAPDH was affinity-purified from S. pombe extract by using an Rpb4/Rpb7-coupled column. We also identified actin as a pol II-associated protein and revealed the interaction between actin and Rpb7... - AtNFXL1, an Arabidopsis homologue of the human transcription factor NF-X1, functions as a negative regulator of the trichothecene phytotoxin-induced defense responseTomoya Asano
Division of Functional Genomics, Advanced Science Research Center, Kanazawa University, 13 1 Takaramachi, Kanazawa 920 0934, Japan
Plant J 53:450-64. 2008..tomato strain DC3000 (Pst DC3000). Taken together, these results indicate that AtNFXL1 plays an important role in the trichothecene response, as well as the general defense response in Arabidopsis... 
IRF2-binding protein-1 is a JDP2 ubiquitin ligase and an inhibitor of ATF2-dependent transcriptionMakoto Kimura
Gene Engineering Division, RIKEN, 3 1 1 Koyadai, Tsukuba, Ibaraki, Japan
FEBS Lett 582:2833-7. 2008..As anticipated from the presence of a RING-finger domain, IRF2-BP1 enhanced the polyubiquitination of JDP2. Moreover, IRF2-BP1 repressed ATF2-mediated transcriptional activation from a CRE-containing promoter...- Crystal structure of archaeal toxin-antitoxin RelE-RelB complex with implications for toxin activity and antitoxin effectsHisanori Takagi
Laboratory of Biochemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka 812 8581, Japan
Nat Struct Mol Biol 12:327-31. 2005..Site-directed mutagenesis suggests that Arg85, in the C-terminal region, is strongly involved in the functional activity of aRelE, whereas Arg40, Leu48, Arg58 and Arg65 play a modest role in the toxin's activity... - Characterization of genes encoding metal tolerance proteins isolated from Nicotiana glauca and Nicotiana tabacumYoshinori Shingu
Environmental Plant Research Group, Plant Science Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
Biochem Biophys Res Commun 331:675-80. 2005..In yeast, these proteins were shown to be located to vacuole membrane. These results suggest that the three MTPs operate by sequestering Zn and Co into vacuoles, thereby reducing the toxicity of these metals... - A wheat xylanase inhibitor gene, Xip-I, but not Taxi-I, is significantly induced by biotic and abiotic signals that trigger plant defenseTomoko Igawa
Laboratory for Remediation Research, Plant Science Center, RIKEN, Saitama
Biosci Biotechnol Biochem 69:1058-63. 2005..The different expression profiles of XIP- and TAXI-type genes suggest distinct roles in plant defense... - Protein-protein interactions in the subunits of ribonuclease P in the hyperthermophilic archaeon Pyrococcus horikoshii OT3Mayumi Kifusa
Laboratory of Biochemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka, Japan
Biosci Biotechnol Biochem 69:1209-12. 2005..In contrast, no interaction was detected between Ph1496p and the other four proteins. Co-immunoprecipitation analysis confirmed the interactions obtained by yeast two-hybrid assay... - Crystal structure of a ribonuclease P protein Ph1601p from Pyrococcus horikoshii OT3: an archaeal homologue of human nuclear ribonuclease P protein Rpp21Yoshimitsu Kakuta
Laboratory of Biochemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka 812 8581, Japan
Biochemistry 44:12086-93. 2005.... - A model transgenic cereal plant with detoxification activity for the estrogenic mycotoxin zearalenoneArisa Higa-Nishiyama
Laboratory for Remediation Research, Plant Science Center, RIKEN, 1-7-22 Suehiro, Kanagawa, Tsurumi, Yokohama 230-0045, Japan
Transgenic Res 14:713-7. 2005..g., wheat and maize) from contamination with the estrogenic mycotoxin... - In vitro reconstitution of the GTPase-associated centre of the archaebacterial ribosome: the functional features observed in a hybrid form with Escherichia coli 50S subunitsTakaomi Nomura
Institute of High Polymer Research, Faculty of Textile Science and Technology, Shinshu University, Ueda 386 8567, Japan
Biochem J 396:565-71. 2006..The results suggest that the archaebacterial proteins, including the Ph-L12 homodimer, are functionally accessible to eukaryotic translation factors... - The 1.48 A resolution crystal structure of the homotetrameric cytidine deaminase from mouseAik Hong Teh
Department of Life Science, Tokyo Institute of Technology, 4259 B 6 Nagatsuta cho, Midori ku, Yokohama, Kanagawa 226 8501, Japan
Biochemistry 45:7825-33. 2006..Implications for CDA-RNA interaction have also been considered... - Characterization of the archaeal ribonuclease P proteins from Pyrococcus horikoshii OT3Atsushi Terada
Laboratory of Biochemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Hakozaki 6-10-1, Higashi-ku, Fukuoka 812-8581
J Biochem (Tokyo) 140:293-8. 2006..Together, it is suggested that the P. horikoshii RNase P proteins are predominantly involved in optimization of the pRNA conformation, though they are individually dispensable for RNase P activity in vitro... - Crystal structure and functional analysis of an archaeal chromatin protein Alba from the hyperthermophilic archaeon Pyrococcus horikoshii OT3Kazumasa Hada
Laboratory of Structural Biology, Graduate School of Systems Life Sciences, Kyushu University, 6 10 1 Hakozaki, Fukuoka 812 8581, Japan
Biosci Biotechnol Biochem 72:749-58. 2008..These results suggest that PhoAlba contributes little to the catalytic activity of P. horikoshii RNase P... - Crystal structures of the Nicotiana glutinosa ribonuclease NT in complex with nucleoside monophosphatesShin Kawano
Laboratory of Biochemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Hakozaki 6-10-1, Higashi-ku, Fukuoka 812-8581
J Biochem (Tokyo) 140:375-81. 2006..The nucleotide binding modes in these complexes would provide a clue to elucidation of structural basis for the broad base specificity for RNase NT... - Conferring cadmium resistance to mature tobacco plants through metal-adsorbing particles of tomato mosaic virus vectorYoshinori Shingu
Environmental Plant Research Group, RIKEN Plant Science Center, Suehiro-cho 1-7-22, Tsurumi, Yokohama, 230-0045, Japan
Plant Biotechnol J 4:281-8. 2006..This shows the possible use of an artificial sink for metal tolerance and the advantage of employing a plant viral vector for phytoremediation... - Structural evidence for endocrine disruptor bisphenol A binding to human nuclear receptor ERR gammaAyami Matsushima
Laboratory of Structure Function Biochemistry, Department of Chemistry, Research Education Centre of Risk Science, Faculty and Graduate School of Sciences, Kyushu University, Fukuoka 812 8581, Japan
J Biochem 142:517-24. 2007..Our results present the first evidence that the nuclear receptor forms complexes with the endocrine disruptor, providing detailed molecular insight into the interaction features... - Crystal structure of hyperthermophilic archaeal initiation factor 5A: a homologue of eukaryotic initiation factor 5A (eIF-5A)Min Yao
Division of Biological Science, Graduate School of Science, Hokkaido University, Sapporo 066 0810
J Biochem 133:75-81. 2003..These findings led to the speculation that the concave surface and loop L1 at the N-domain may be involved in RNA binding, while the opposite side of the concave surface in the C-domain may be involved in protein interaction... - A novel lactonohydrolase responsible for the detoxification of zearalenone: enzyme purification and gene cloningNaoko Takahashi-Ando
Laboratory for Remediation Research, Plant Science Centre, RIKEN, 2 1 Hirosawa, Wako, Saitama 351 0198, Japan
Biochem J 365:1-6. 2002..Zhd101 could be a promising genetic resource for in planta detoxification of the mycotoxin in important crops... - Molecular cloning of cDNAs encoding ribonuclease-related proteins in Nicotiana glutinosa leaves, as induced in response to wounding or to TMV-infectionNaomi Kurata
Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka, Japan
Biosci Biotechnol Biochem 66:391-7. 2002..In contrast, the expression of the NGR3 gene is induced after 48 h upon TMV infection... - Expression of Nicotiana glutinosa ribonucleases in Escherichia coliMadoka Hino
Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka, Japan
Biosci Biotechnol Biochem 66:910-2. 2002..Furthermore, kinetic parameters for RNase NW (Km, 0.778 mM and kcat, 1938 min(-1)) and RNase NGR3 (Km, 0.548 mM and kcat, 408 min(-1)) were calculated using GpU as a substrate... - Guanine binding site of the Nicotiana glutinosa ribonuclease NW revealed by X-ray crystallographyShin Kawano
Laboratory of Biochemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka 812-8581, Japan
Biochemistry 41:15195-202. 2002..Therefore, Gln12, Tyr17, Thr78, Leu79, and Phe89 are responsible for recognition of the guanine base by RNase NW, findings which provide insight into the manner in which RNase NW preferentially cleaves guanylic acid... - Crystal structures of the ribonuclease MC1 mutants N71T and N71S in complex with 5'-GMP: structural basis for alterations in substrate specificityTomoyuki Numata
Laboratory of Biochemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka 812 8581, Japan
Biochemistry 42:5270-8. 2003..Consequently, it can be concluded that amino acids at position 71 (RNase MC1 numbering) serve as one of the determinants for substrate specificity (or preference) in the RNase T2 fimily by changing the size and shape of the B2 site... - Reconstitution of archaeal ribonuclease P from RNA and four protein componentsYoshiaki Kouzuma
Laboratory of Biochemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Hakozaki 6-10-1, Higashi-ku, 812-8581, Fukuoka, Japan
Biochem Biophys Res Commun 306:666-73. 2003..The present data will pave the way for the elucidation of the reaction mechanism for archaeal as well as eukaryotic RNase P... - Characterization of functional domains of the hemolytic lectin CEL-III from the marine invertebrate Cucumaria echinataYoshiaki Kouzuma
Laboratory of Biochemistry, Faculty of Agriculture, Graduate School, Kyushu University, Hakozaki 6 10 1 Higashi ku, Fukuoka 812 8581
J Biochem 134:395-402. 2003..These results suggest that after binding to cell surface carbohydrate chains, CEL-III oligomerizes through C-terminal domains, leading to the formation of ion-permeable pores by hydrophobic interaction with the cell membrane... - In vitro phosphorylation of initiation factor 2 alpha (aIF2 alpha) from hyperthermophilic archaeon Pyrococcus horikoshii OT3Maino Tahara
Laboratory of Biochemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Hakozaki 6-10-1, Higashi-ku, Fukuoka 812-8581
J Biochem (Tokyo) 135:479-85. 2004..horikoshii. These findings suggest that aIF2 alpha, like eIF2 alpha in eukaryotes, plays a role in regulation of the protein synthesis in Archaea through phosphorylation and dephosphorylation... - Crystal structure of the regulatory subunit of archaeal initiation factor 2B (aIF2B) from hyperthermophilic archaeon Pyrococcus horikoshii OT3: a proposed structure of the regulatory subcomplex of eukaryotic IF2BYoshimitsu Kakuta
Laboratory of Biochemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka 812 8581, Japan
Biochem Biophys Res Commun 319:725-32. 2004..This structure suggests an architecture of the three subunits, alpha, beta, and delta, in the regulatory subcomplex within eIF2B... - Crystal structure of the ribonuclease P protein Ph1877p from hyperthermophilic archaeon Pyrococcus horikoshii OT3Hisanori Takagi
Laboratory of Biochemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka 812 8581, Japan
Biochem Biophys Res Commun 319:787-94. 2004..The results presented here provide an initial step for definite understanding of how archaeal and eukaryotic RNase Ps mediate substrate recognition and process 5'-leader sequence of pre-tRNA... - Metabolism of zearalenone by genetically modified organisms expressing the detoxification gene from Clonostachys roseaNaoko Takahashi-Ando
Laboratory for Remediation Research, Plant Science Center, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
Appl Environ Microbiol 70:3239-45. 2004..Environ. Microbiol. 68:3545-3549, 2002). An appropriate combination of a candidate host microbe and the codon-optimized synthetic gene may contribute significantly to establishing a mycotoxin detoxification system for food and feed... - Crystal structure of archaeal ribonuclease P protein Ph1771p from Pyrococcus horikoshii OT3: an archaeal homolog of eukaryotic ribonuclease P protein Rpp29Tomoyuki Numata
Laboratory of Biochemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka 812 8581, Japan
RNA 10:1423-32. 2004..These two potential sites for RNA binding are located in close proximity. The crystal structure of Ph1771p provides insight into the structure and function relationships of archaeal and eukaryotic RNase P... - Amino acids conserved at the C-terminal half of the ribonuclease T2 family contribute to protein stability of the enzymesKazumi Kimura
Laboratory of Biochemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Hakozaki 6-10-1, Fukuoka 812-8581, Japan
Biosci Biotechnol Biochem 68:1748-57. 2004..Taken together, it appeared that Tyr(101), Phe(102), Ala(105), Pro(125), Gly(127), Gly(144), Leu(162), Val(165), and Phe(190) conserved in the RNase T2 family play an important role in the stability of the proteins... - New TAXI-type xylanase inhibitor genes are inducible by pathogens and wounding in hexaploid wheatTomoko Igawa
Laboratory for Remediation Research, Plant Science Center, RIKEN, 1 7 22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230 0045, Japan
Plant Cell Physiol 45:1347-60. 2004..xylanases: it was also active against some spelt xylan-induced xylanases of F. graminearum. These features suggest that some, but not all, TAXI-type xylanase inhibitors have a role in plant defense... - On the interaction of ribosomal protein L5 with 5S rRNAKenta Iwasaki
Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka, Japan
Biosci Biotechnol Biochem 66:103-9. 2002....