Since 2010
• Miyake, Y., Inaba, T., Watanabe, H., Teramoto, J., Yamamoto, K. and Ishihama, A. (2019). Regulatory roles of pyruvate-sensing two-component system PyrSR (YpdAB) in Escherichia coli K-12. FEMS Microbiol Lett 366(2). doi: 10.1093/femsle/fnz009.
• Shimada, T., Yamamoto, K., Nakano, M., Watanabe, H., Schleheck, D. and Ishihama, A. (2018). Regulatory role of CsqR (YihW) in transcription of the genes for catabolism of the anionic sugar sulfoquinovose (SQ) in Escherichia coli K-12. Microbiology 165(1):78-89. doi: 10.1099/mic.0.000740.
• Yamanaka, Y., Winardhi, R. S., Yamauchi, E., Nishiyama, S. I., Sowa, Y., Yan, J., Kawagishi, I., Ishihama, A. and Yamamoto, K. (2018). The dimerization site-2 of the bacterial DNA-binding protein H-NS is required for gene silencing and stiffened nucleoprotein filament formation. J Biol Chem 293(24):9496-9505. doi: 10.1074/jbc.RA117.001425.
• Yamamoto, K., Yamanaka, Y., Shimada, T., Sarkar, P., Yoshida, M., Bharadwaj, N., Watanabe, H., Taira, Y., Chatterji, D. and Ishihama, A. (2018). Altered distribution of RNA polymerase lacking the omega subunit within the prophages along the Escherichia coli K-12 genome. mSystems 3(1). pii: e00172-17. doi: 10.1128/mSystems.00172-17.
• Shimada, T., Momiyama, E., Yamanaka, Y., Watanabe, H., Yamamoto, K. and Ishihama, A. (2017). Regulatory role of XynR (YagI) in catabolism of xylonate in Escherichia coli K-12. FEMS Microbiol Lett 364(22). doi: 10.1093/femsle/fnx220.
• Urano, H., Yoshida, M., Ogawa, A., Yamamoto, K., Ishihama, A. and Ogasawara, H. (2017). Cross-regulation between two common ancestral response regulators, HprR and CusR, in Escherichia coli. Microbiology 163(2):243-252. doi: 10.1099/mic.0.000410.
• Takada, H., Shimada, T., Dey, D., Quyyum, M. Z., Nakano, M., Ishiguro, A., Yoshida, H., Yamamoto, K., Sen, R. and Ishihama, A. (2016). Differential regulation of rRNA and tRNA transcription from the rRNA-tRNA composite operon in Escherichia coli. PLoS One 11(12):e0163057. doi: 10.1371/journal.pone.0163057.
• Yoshida, K., Sakamoto, A., Terui, Y., Takao, K., Sugita, Y., Yamamoto, K., Ishihama, A., Igarashi, K. and Kashiwagi, K. (2016). Effect of spermidine analogues on cell growth of Escherichia coli polyamine requiring mutant MA261. PLoS One 11(7):e0159494. doi: 10.1371/journal.pone.0159494. eCollection 2016.
• Yamanaka, Y., Shimada, T., Yamamoto, K. and Ishihama, A. (2016). Transcription factor CecR (YbiH) regulates a set of genes affecting the sensitivity of Escherichia coli against cefoperazone and chloramphenicol. Microbiology 162(7):1253-64. doi: 10.1099/mic.0.000292.
• Shimada, T., Takada, H., Yamamoto, K. and Ishihama, A. (2015). Expanded roles of two-component response regulator OmpR in Escherichia coli: genomic SELEX search for novel regulation targets. Genes Cells 20(11):915-31. doi: 10.1111/gtc.12282.
• Kinoshita-Kikuta, E., Kinoshita, E., Eguchi, Y., Yanagihara, S., Edahiro, K., Inoue, Y., Taniguchi, M., Yoshida, M., Yamamoto, K., Takahashi, H., Sawasaki, T., Utsumi, R. and Koike, T. (2015). Functional characterization of the receiver domain for phosphorelay control in hybrid sensor kinases. PLoS One 10(7):e0132598. doi:10.1371/journal.pone.0132598.
• Yoshida, M., Ishihama, A. and Yamamoto, K. (2015) Crosstalk in promoter recognition between six NarL-family response regulators of Escherichia coli two-component system. Genes Cells 20(7):601-12. doi: 10.1111/gtc.12251.
• Sakamoto, A., Terui, Y., Yoshida, T., Yamamoto, T., Suzuki, H., Yamamoto, K., Ishihama, A., Igarashi, K. and Kashiwagi, K. (2015) Three Members of Polyamine Modulon under Oxidative Stress Conditions: Two Transcription Factors (SoxR and EmrR) and a Glutathione Synthetic Enzyme (GshA). PLoS One 10(4):e0124883. doi:10.1371/journal.pone.0124883.
• Urano, H., Umezawa, Y., Yamamoto, K., Ishihama, A., and Ogasawara, H. (2015). Cooperative regulation of the common target genes between hydrogen peroxide-response YedVW and copper-response CusSR in Escherichia coli. Microbiology 161(Pt 4):729-38. doi: 10.1099/mic.0.000026.
• Yamamoto, K., Nakano, M. and Ishihama, A. (2015). Regulatory role of transcription factor SutR (YdcN) in sulfur utilization in Escherichia coli. Microbiology 161(Pt 1):99-111. doi: 10.1099/mic.0.083550-0. (Editor’s choice)
• Yamanaka, Y., Oshima, T., Ishihama, A. and Yamamoto, K. (2014). Characterization of the YdeO Regulon in Escherichia coli. PLoS One 9(11): e111962. doi:10.1371/journal.pone.0111962
• Yamamoto, K., Nonaka, G., Ozawa, T., Takumi, K. and Ishihama, A. (2014). Induction of the Escherichia coli yijE gene expression by cystine. Biosci Biotechnol Biochem 27:1-5.
• Yamamoto, K., Watanabe, H. and Ishihama, A. (2014). Expression levels of transcription factors in Escherichia coli: growth phase- and growth condition-dependent variation of 90 regulators from 6 families. Microbiology 160(Pt 9):1903-1913. doi: 10.1099/mic.0.079889-0.
• Nakano, M., Ogasawara, H., Shimada, T., Yamamoto, K. and Ishihama, A. (2014). Involvement of cAMP-CRP in transcription activation and repression of the pck gene encoding PEP carboxykinase, the key enzyme of gluconeogenesis. FEMS Microbiol Lett 355(2):93-99. doi: 10.1111/1574-6968.
• Yamamoto, K. (2014). The hierarchic network of metal-response transcription factors in Escherichia coli. Biosci Biotechnol Biochem 78(5):737-747. doi: 10.1080/09168451.
• Kinoshita, E., Kinoshita-Kikuta, E., Shiba, A., Edahiro, K., Inoue, Y., Yamamoto, K., Yoshida, M. and Tohru Koike T. (2014). Profiling of protein thiophosphorylation by Phos-tag affinity electrophoresis: evaluation of adenosine 5’-O-(3-thiotriphosphate) as a phosphoryl donor in protein kinase reactions. Proteomics 14(6):668-79. doi: 10.1002/pmic.201300533.
• Shiratsuchi, A., Shimamoto, N., Nitta, M., Tuan, Tran Q., Firdausi, A., Gawasawa, M., Yamamoto, K., Ishihama, A. and Nakanishi, Y. (2013). Role for σ38 in Prolonged Survival of Escherichia coli in Drosophila melanogaster. J Immunol 192(2):666-75
• Shimada, K., Ogasawara, H., Yamada, K., Shimura, M., Kori, A., Shimada, T., Yamanaka, Y., Yamamoto, K. and Ishihama, A. (2013). Screening of promoter-specific transcription factors: multiple regulators for the sdiA gene involved in cell division control and quorum sensing. Microbiology 159(Pt 12):2501-12.
• Kurata, T., Katayama, A., Hiramatsu, M., Kiguchi, Y., Takeuchi, M., Watanabe, T., Ogasawara, H., Ishihama, A. and Yamamoto, K. (2013). Identification of the set of genes, including non-annotated morA, under the direct control of ModE in Escherichia coli. J Bacteriol 195(19):4496-505.
• Pukklay, P., Nakanishi, Y., Nitta, M., Yamamoto, K., Ishihama, A. and Shiratsuchi A. (2013) Involvement of EnvZ-OmpR two-component system in virulence control of Escherichia coli in Drosophila melanogaster. Biochem Biophys Res Commun 438(2):306-11.
• Shimada, T., Katayama, Y., Kawakita, S., Ogasawara, H., Nakano, M., Yamamoto, K. and Ishihama, A. (2012) A novel regulator RcdA of the csgD gene encoding the master regulator of biofilm formation in Escherichia coli. Microbiologyopen. doi:10.1002/mbo3.42.
• Sakamoto, A., Terui, Y., Yamamoto, T., Kasahara, T., Nakamura, M., Tomitori, H., Yamamoto, K., Ishihama, A., Michael, A. J., Igarashi, K. and Kashiwagi, K. (2012). Enhanced biofilm formation and/or cell viability by polyamines through stimulation of response regulators UvrY and CpxR in the two-component signal transducing systems, and ribosome recycling factor. Int. J. Biochem. Cell Biol 44(11):1877-1886.
• Ogasawara, H., Shinohara, S., Yamamoto, K. and Ishihama, A. (2012). Novel regulation targets of the metal-response BasS-BasR two-component system of Escherichia coli. Microbiology 158(Pt 6), 1482-1492.
• Yamanaka, Y., Ishihama, A. and Yamamoto, K. (2012). Induction of YdeO, a regulator for acid resistance genes, by ultraviolet irradiation in Escherichia coli. Biosci. Biotechnol. Biochem. 76(6), 1236-1238.
• Terui, Y., Akiyama, M., Sakamoto, A., Tomitori, H., Yamamoto, K., Ishihama, A., Igarashi, K. and Kashiwagi, K. (2012) Increase in cell viability by polyamines through stimulation of the synthesis of ppGpp regulatory protein and omega protein of RNA polymerase in Escherichia coli. Int. J. Biochem. Cell Biol 44, 412–422.
• Nakano, M., Teramoto, J., Shimada, T., Yamamoto, K. and Ishihama, A. (2011). Single molecule analysis of transcription factor-DNA complexes using atomic force microscopy. Micro- and Nano-Mechatronics and Human Science, 2011 IEEE International Symposium on Nov. 2011 490-494, IEEE Robotics and Automation Society, USA.
• Yamamoto, K., Oshima, T., Nonaka, G., Ito, H. and Ishihama, A. (2011). Induction of the Escherichia coli cysK gene by genetic and environmental factors. FEMS Microbiol. Lett. 323(1), 88-95.
• Shimada, T., Fujita, N., Yamamoto, K. and Ishihama, A. (2011). Novel roles of cAMP receptor protein (CRP) in regulation of transport and metabolism of carbon sources. PLoS ONE 6(6), e20081.
• Ogasawara, H., Yamamoto, K. and Ishihama, A. (2011). Role of the biofilm master regulator CsgD in cross-regulation between biofilm formation and flagellar synthesis. J. Bacteriol. 193(10), 2587-97.
• Yamamoto, K., Ishihama, A., Busby, S. J. W. and Grainger, D. C. (2011). The Escherichia coli K-12 MntR mini-regulon includes dps that encodes the major stationary phase DNA-binding protein. J. Bacteriol. 193(6), 1477-80.
• Shimada, T., Yamamoto, K. and Ishihama, A. (2011). Novel members of the Cra regulon involved in carbon metabolism in Escherichia coli. J. Bacteriol. 193(3), 649-59.
• Ogasawara, H., Yamamoto, K., and Ishihama, A. (2010). Regulatory role of MlrA in transcription activation of csgD, the master regulator of biofilm formation in Escherichia coli. FEMS Microbiol Lett 312(2), 160-168.
• Terui, Y., Tabei, Y., Akiyama, M., Higashi, K., Tomitori, H., Yamamoto, K., Ishihama, A., Igarashi, K., and Kashiwagi, K. (2010). Ribosome modulation factor, an important protein for cell viability encoded by the polyamine modulon. J Biol Chem 285(37), 28698-28707.
• Ogasawara, H., Yamada, K., Kori, A., Yamamoto, K. and Ishihama, A. (2010). Regulation of the E. coli csgD promoter: Interplay between five transcription factors. Microbiology. 156(Pt 8), 2470-2483.