Genomes and Genes
Experts and Doctors on escherichia coli in Tsuruoka, Yamagata, Japan
Locale: Tsuruoka, Yamagata, Japan
Topic: escherichia coli
- 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. ..
- 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; http://rna.iab.keio.ac.jp/), which integrates the data for previously identified sRNAs and the novel sRNAs found in this study. ..
- 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. ..
- 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. ..
- 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. ..
- 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. ..
- 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. ..
- 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. ..
- 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