Experts and Doctors on escherichia coli in Ikoma, Nara, Japan

Summary

Locale: Ikoma, Nara, Japan
Topic: escherichia coli

Top Publications

  1. Arifuzzaman M, Oshima T, Mori H. The ATPase domain of HscC (DnaK homolog) is essential for interfering sigma70 activity in E. coli. FEMS Microbiol Lett. 2004;230:99-104 pubmed
    ..These results indicate that the ATPase domain of HscC rather than the substrate-binding domain is important for determining its functional specificity. ..
  2. Uchida K, Furukohri A, Shinozaki Y, Mori T, Ogawara D, Kanaya S, et al. Overproduction of Escherichia coli DNA polymerase DinB (Pol IV) inhibits replication fork progression and is lethal. Mol Microbiol. 2008;70:608-22 pubmed publisher
    ..Because the brake operates when cells have excess DinB, as they do under stress conditions, it may serve as a checkpoint that modulates replication to safeguard genome stability. ..
  3. Ohtsu I, Wiriyathanawudhiwong N, Morigasaki S, Nakatani T, Kadokura H, Takagi H. The L-cysteine/L-cystine shuttle system provides reducing equivalents to the periplasm in Escherichia coli. J Biol Chem. 2010;285:17479-87 pubmed publisher
    ..These findings led us to propose that the inducible L-cysteine/L-cystine shuttle system plays an important role in oxidative stress tolerance through providing a reducing equivalent to the periplasm in E. coli...
  4. Yanagihara F, Yoshida S, Sugaya Y, Maki H. The dnaE173 mutator mutation confers on the alpha subunit of Escherichia coli DNA polymerase III a capacity for highly processive DNA synthesis and stable binding to primer/template DNA. Genes Genet Syst. 2007;82:273-80 pubmed
  5. Furukohri A, Nishikawa Y, Akiyama M, Maki H. Interaction between Escherichia coli DNA polymerase IV and single-stranded DNA-binding protein is required for DNA synthesis on SSB-coated DNA. Nucleic Acids Res. 2012;40:6039-48 pubmed publisher
    ..We speculate that at the primer/template junction, Pol IV interacts with the tail of the nearest SSB tetramer on the template, and that this interaction allows the polymerase to travel along the template while disassembling SSB...
  6. Nakagawa A, Oshima T, Mori H. Identification and characterization of a second, inducible promoter of relA in Escherichia coli. Genes Genet Syst. 2006;81:299-310 pubmed
    ..These data suggest that transient expression from the relAP2 promoter is controlled by several global regulators. This may account for the complex regulation of relA expression in Escherichia coli. ..
  7. Nakayashiki T, Mori H. Genome-wide screening with hydroxyurea reveals a link between nonessential ribosomal proteins and reactive oxygen species production. J Bacteriol. 2013;195:1226-35 pubmed publisher
    ..These mutants increased the copy number of the p15A-based plasmid and exhibited reduced basal levels of SOS response. The data suggest that nonessential proteins indirectly affect the DNA-damaging process...
  8. Nakajima K, Furutani I, Tachimoto H, Matsubara H, Hashimoto T. SPIRAL1 encodes a plant-specific microtubule-localized protein required for directional control of rapidly expanding Arabidopsis cells. Plant Cell. 2004;16:1178-90 pubmed
    ..These observations suggest that SPR1 is a plant-specific MT-localized protein required for the maintenance of growth anisotropy in rapidly elongating cells. ..
  9. Oshima T, Aiba H, Masuda Y, Kanaya S, Sugiura M, Wanner B, et al. Transcriptome analysis of all two-component regulatory system mutants of Escherichia coli K-12. Mol Microbiol. 2002;46:281-91 pubmed
    ..The compiled data are avail-able at our website (http://ecoli.aist-nara.ac.jp/xp_analysis/ 2_components). ..

More Information

Publications24

  1. Arifuzzaman M, Oshima T, Nakade S, Mori H. Characterization of HscC (Hsc62), homologue of Hsp70 in Escherichia coli: over-expression of HscC modulates the activity of house keeping sigma factor sigma70. Genes Cells. 2002;7:553-66 pubmed
    ..In addition, the co-purification analysis showed that sigma70 co-eluted with HscC. These results indicate that HscC forms a complex with sigma70 and may function as its negative modulator. ..
  2. Sugaya Y, Ihara K, Masuda Y, Ohtsubo E, Maki H. Hyper-processive and slower DNA chain elongation catalysed by DNA polymerase III holoenzyme purified from the dnaE173 mutator mutant of Escherichia coli. Genes Cells. 2002;7:385-99 pubmed
    ..A link between the proofreading and chain elongation processes was suggested. ..
  3. Kawano M, Kanaya S, Oshima T, Masuda Y, Ara T, Mori H. Distribution of repetitive sequences on the leading and lagging strands of the Escherichia coli genome: comparative study of Long Direct Repeat (LDR) sequences. DNA Res. 2002;9:1-10 pubmed
    ..Adaptation of individual LDRs to E. coli genome is also discussed on the basis of codon usage. ..
  4. Shimizu T, Toumoto A, Ihara K, Shimizu M, Kyogoku Y, Ogawa N, et al. Crystal structure of PHO4 bHLH domain-DNA complex: flanking base recognition. EMBO J. 1997;16:4689-97 pubmed
    ..The residues involved in the E-box recognition are His5, Glu9 and Arg13, as already reported for bHLH/Zip proteins MAX and USF, and are different from those recognized by bHLH proteins MyoD and E47, although PHO4 is a bHLH protein. ..
  5. Itoh T, Matsuda H, Mori H. Phylogenetic analysis of the third hsp70 homolog in Escherichia coli; a novel member of the Hsc66 subfamily and its possible co-chaperone. DNA Res. 1999;6:299-305 pubmed
    ..A further database search revealed that two dnaJ homologs, ybeS and ybeV, were located on the opposite strand near hscC. Consequently, E. coli seems to have three gene clusters composed of DnaK and DnaJ homologs. ..
  6. Seki M, Akiyama M, Sugaya Y, Ohtsubo E, Maki H. Strand asymmetry of +1 frameshift mutagenesis at a homopolymeric run by DNA polymerase III holoenzyme of Escherichia coli. J Biol Chem. 1999;274:33313-9 pubmed
  7. Nawata M, Tsutsumi H, Kobayashi Y, Unzai S, Mine S, Nakamura T, et al. Heat-induced native dimerization prevents amyloid formation by variable domain from immunoglobulin light-chain REI. FEBS J. 2017;284:3114-3127 pubmed publisher
    ..Structural data are available in the Protein Data Bank under the accession numbers 5XP1 and 5XQY. ..
  8. Mori T, Nakamura T, Okazaki N, Furukohri A, Maki H, Akiyama M. Escherichia coli DinB inhibits replication fork progression without significantly inducing the SOS response. Genes Genet Syst. 2012;87:75-87 pubmed
    ..We conclude that DinB impedes replication fork progression in a way that does not activate RecA, in contrast to obstructive DNA lesions and dysfunctional replication machinery...
  9. Nakahigashi K, Takai Y, Kimura M, Abe N, Nakayashiki T, Shiwa Y, et al. Comprehensive identification of translation start sites by tetracycline-inhibited ribosome profiling. DNA Res. 2016;23:193-201 pubmed publisher
    ..In summary, we showed that ribosome profiling upon translation inhibition by tetracycline offers a simple, reliable and comprehensive experimental tool for precise annotation of translation start sites of expressed genes in bacteria. ..
  10. Furukohri A, Goodman M, Maki H. A dynamic polymerase exchange with Escherichia coli DNA polymerase IV replacing DNA polymerase III on the sliding clamp. J Biol Chem. 2008;283:11260-9 pubmed publisher
    ..Our study suggests a model in which the interaction between pol III* and the beta clamp is mediated by pol IV to ensure that DNA replication proceeds with minimal interruption. ..
  11. Yoshimura M, Oshima T, Ogasawara N. Involvement of the YneS/YgiH and PlsX proteins in phospholipid biosynthesis in both Bacillus subtilis and Escherichia coli. BMC Microbiol. 2007;7:69 pubmed publisher
    ..PlsX and YgiH also, however, play important roles in E. coli growth, possibly by regulating the intracellular concentration of acyl-ACP. These proteins are therefore important targets for development of new antibacterial agents...
  12. Katoh A, Uenohara K, Akita M, Hashimoto T. Early steps in the biosynthesis of NAD in Arabidopsis start with aspartate and occur in the plastid. Plant Physiol. 2006;141:851-7 pubmed
    ..An analysis of functional green fluorescent protein-fused constructs and in vitro assays of uptake into isolated chloroplasts demonstrated that these three enzymes are located in the plastid. ..
  13. Sakai A, Kita M, Tani Y. Recent progress of vitamin B6 biosynthesis. J Nutr Sci Vitaminol (Tokyo). 2004;50:69-77 pubmed
    ..These studies provided important clues of B6 biosynthesis, but the entire picture of the B6 biosynthetic pathway remains unclear. ..
  14. Mori H, Isono K, Horiuchi T, Miki T. Functional genomics of Escherichia coli in Japan. Res Microbiol. 2000;151:121-8 pubmed
    ..coli published in the past, and analyses of the data from a bio-informatics point of view. Thus, we aim at reaching complete understanding of this model organism in the near future. ..
  15. Yamaguchi Y, Nakamura T, Kusano T, Sano H. Three Arabidopsis genes encoding proteins with differential activities for cysteine synthase and beta-cyanoalanine synthase. Plant Cell Physiol. 2000;41:465-76 pubmed
    ..thaliana seedlings were subjected to various stresses, including nutrient deprivation. In vivo targeting experiments indicated that AtcysD1 and AtcysD2 are cytoplasmic isozymes, and AtcysC1 is a mitochondrial isozyme. ..