Experts and Doctors on escherichia coli in Tsuruoka, Yamagata, Japan


Locale: Tsuruoka, Yamagata, Japan
Topic: escherichia coli

Top Publications

  1. Zhao J, Baba T, Mori H, Shimizu K. Global metabolic response of Escherichia coli to gnd or zwf gene-knockout, based on 13C-labeling experiments and the measurement of enzyme activities. Appl Microbiol Biotechnol. 2004;64:91-8 pubmed
    ..There was also a negative correlation between the fluxes through malic enzyme and isocitrate dehydrogenase in the mutants; and a positive correlation was found between the fluxes through malic enzyme and phosphoenolpyruvate carboxylase. ..
  2. Sato A, Soga T, Igarashi K, Takesue K, Tomita M, Kanai A. GTP-dependent RNA 3'-terminal phosphate cyclase from the hyperthermophilic archaeon Pyrococcus furiosus. Genes Cells. 2011;16:1190-9 pubmed publisher
    ..furiosus). The possible roles of Pf-Rtc and the importance of terminal phosphate structures in RNA are discussed...
  3. Zhao J, Baba T, Mori H, Shimizu K. Effect of zwf gene knockout on the metabolism of Escherichia coli grown on glucose or acetate. Metab Eng. 2004;6:164-74 pubmed
  4. Ohtani N, Yanagawa H, Tomita M, Itaya M. Identification of the first archaeal Type 1 RNase H gene from Halobacterium sp. NRC-1: archaeal RNase HI can cleave an RNA-DNA junction. Biochem J. 2004;381:795-802 pubmed
    ..It is likely that the archaeal Type 1 RNase H plays a role in the removal of the last ribonucleotide of the RNA primer from the Okazaki fragment during DNA replication...
  5. Saito N, Robert M, Kitamura S, Baran R, Soga T, Mori H, et al. Metabolomics approach for enzyme discovery. J Proteome Res. 2006;5:1979-87 pubmed
    ..Our approach should be broadly applicable and useful for enzyme discovery in any system. ..
  6. Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl F, Kerner M, et al. Protein abundance profiling of the Escherichia coli cytosol. BMC Genomics. 2008;9:102 pubmed publisher
    ..We show significant associations between the abundance of a protein and its properties and functions in the cell. In this way, we provide both data and novel insights into the role of protein concentration in this model organism. ..
  7. Masuda T, Saito N, Tomita M, Ishihama Y. Unbiased quantitation of Escherichia coli membrane proteome using phase transfer surfactants. Mol Cell Proteomics. 2009;8:2770-7 pubmed publisher
    ..Finally, this protocol was applied to quantitative analysis of guanosine tetra- and pentaphosphate-dependent signaling in E. coli wild-type and relA knock-out strains. ..
  8. Nakahigashi K, Toya Y, Ishii N, Soga T, Hasegawa M, Watanabe H, et al. Systematic phenome analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism. Mol Syst Biol. 2009;5:306 pubmed publisher
    ..The emergence of an alternative pathway not requiring any changes in gene expression, but rather relying on the accumulation of an intermediate metabolite may be a novel mechanism mediating the robustness of these metabolic networks. ..
  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. ..

More Information


  1. Yang C, Hua Q, Baba T, Mori H, Shimizu K. Analysis of Escherichia coli anaplerotic metabolism and its regulation mechanisms from the metabolic responses to altered dilution rates and phosphoenolpyruvate carboxykinase knockout. Biotechnol Bioeng. 2003;84:129-44 pubmed
    ..Combining the measurement data of in vivo fluxes, metabolite concentrations and enzyme activities, the in vivo regulations of PEP carboxykinase flux, PEP carboxylation, and glyoxylate shunt in E. coli are discussed. ..
  2. Shinhara A, Matsui M, Hiraoka K, Nomura W, Hirano R, Nakahigashi K, et al. Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli. BMC Genomics. 2011;12:428 pubmed publisher
    ..coli genome. We constructed the Escherichia coli Small RNA Browser (ECSBrowser;, which integrates the data for previously identified sRNAs and the novel sRNAs found in this study. ..
  3. Toya Y, Ishii N, Nakahigashi K, Hirasawa T, Soga T, Tomita M, et al. 13C-metabolic flux analysis for batch culture of Escherichia coli and its Pyk and Pgi gene knockout mutants based on mass isotopomer distribution of intracellular metabolites. Biotechnol Prog. 2010;26:975-92 pubmed publisher
    ..Furthermore, ATP production was the primary objective function in the Pgi mutant. This study demonstrates how cells adjust their metabolism in response to environmental changes and/or genetic perturbations in the batch cultivation. ..
  4. Tsuchiya D, Shimizu N, Tomita M. Cooperativity of two active sites in bacterial homodimeric aconitases. Biochem Biophys Res Commun. 2009;379:485-8 pubmed publisher
    ..In conjunction with the dissociable homodimer of AcnB, the catalytic property could affect the intracellular metabolic process involving the Krebs cycle. ..
  5. Tsuchiya D, Shimizu N, Tomita M. Versatile architecture of a bacterial aconitase B and its catalytic performance in the sequential reaction coupled with isocitrate dehydrogenase. Biochim Biophys Acta. 2008;1784:1847-56 pubmed publisher
    ..Connecting the two proteins by a flexible linker yielded a locally high concentration to promote the weak protein-protein interaction. The versatile architecture of AcnB may alter the metabolic process involving the Krebs cycle. ..
  6. Ishii N, Suga Y, Hagiya A, Watanabe H, Mori H, Yoshino M, et al. Dynamic simulation of an in vitro multi-enzyme system. FEBS Lett. 2007;581:413-20 pubmed
    ..coli glycolytic enzymes. Thus, the results indicate that kinetic parameters can be determined without using an undesirable tuning process. ..
  7. Itoh A, Ohashi Y, Soga T, Mori H, Nishioka T, Tomita M. Application of capillary electrophoresis-mass spectrometry to synthetic in vitro glycolysis studies. Electrophoresis. 2004;25:1996-2002 pubmed
    ..This approach is likely useful for the synthesis of natural products requiring complex sequential biocatalytic reactions. ..
  8. Hua Q, Yang C, Oshima T, Mori H, Shimizu K. Analysis of gene expression in Escherichia coli in response to changes of growth-limiting nutrient in chemostat cultures. Appl Environ Microbiol. 2004;70:2354-66 pubmed
    ..Independent of the growth rate, 92 genes were identified as being differentially expressed. Genes tightly related to the culture conditions were highlighted, some of which may be used to characterize nutrient-limited growth. ..
  9. Hua Q, Yang C, Baba T, Mori H, Shimizu K. Responses of the central metabolism in Escherichia coli to phosphoglucose isomerase and glucose-6-phosphate dehydrogenase knockouts. J Bacteriol. 2003;185:7053-67 pubmed