Akira Ishihama

Summary

Affiliation: Hosei University
Country: Japan

Publications

  1. pmc A novel regulator RcdA of the csgD gene encoding the master regulator of biofilm formation in Escherichia coli
    Tomohiro Shimada
    Department of Frontier Bioscience and Research Center for Micro Nano Technology, Hosei University, Koganei, Tokyo, 184 8584, Japan
    Microbiologyopen 1:381-94. 2012
  2. pmc Novel roles of cAMP receptor protein (CRP) in regulation of transport and metabolism of carbon sources
    Tomohiro Shimada
    Department of Frontier Bioscience, Hosei University, Koganei, Tokyo, Japan
    PLoS ONE 6:e20081. 2011
  3. pmc The whole set of constitutive promoters recognized by RNA polymerase RpoD holoenzyme of Escherichia coli
    Tomohiro Shimada
    Department of Frontier Biosience, Hosei University, Koganai, Tokyo, Japan Micro Nano Technology Research Center, Hosei University, Koganai, Tokyo, Japan Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuda, Yokohama, Japan
    PLoS ONE 9:e90447. 2014
  4. pmc Prokaryotic genome regulation: a revolutionary paradigm
    Akira Ishihama
    Department of Frontier Bioscience and Micro Nano Technology Research Center, Hosei University, Koganei, Tokyo 184 8584, Japan
    Proc Jpn Acad Ser B Phys Biol Sci 88:485-508. 2012
  5. doi request reprint Prokaryotic genome regulation: multifactor promoters, multitarget regulators and hierarchic networks
    Akira Ishihama
    Department of Frontier Bioscience, Hosei University, Koganei, Tokyo 184 8584, Japan
    FEMS Microbiol Rev 34:628-45. 2010
  6. pmc Role of the biofilm master regulator CsgD in cross-regulation between biofilm formation and flagellar synthesis
    Hiroshi Ogasawara
    Department of Frontier Bioscience, Hosei University, Koganei, Tokyo 184 8584, Japan
    J Bacteriol 193:2587-97. 2011
  7. pmc The uncharacterized transcription factor YdhM is the regulator of the nemA gene, encoding N-ethylmaleimide reductase
    Yoshimasa Umezawa
    Department of Frontier Bioscience, Hosei University, Koganei, Tokyo 184 8584, Japan
    J Bacteriol 190:5890-7. 2008
  8. doi request reprint The transcription regulator AllR senses both allantoin and glyoxylate and controls a set of genes for degradation and reutilization of purines
    Akiko Hasegawa
    Department of Frontier Bioscience, Hosei University, Koganei, Tokyo, Japan
    Microbiology 154:3366-78. 2008
  9. pmc The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions
    Tomohiro Shimada
    Department of Frontier Bioscience and Micro Nano Technology Research Centre, Hosei University, Koganei, Tokyo 184 8584, Nippon Institute for Biological Science, Ome, Tokyo 198 0024, Japan
    Nucleic Acids Res 36:3950-5. 2008
  10. pmc PdhR (pyruvate dehydrogenase complex regulator) controls the respiratory electron transport system in Escherichia coli
    Hiroshi Ogasawara
    Department of Frontier Bioscience, Hosei University, Kajino cho 3 7 2, Koganei, Tokyo 184 8584, Japan
    J Bacteriol 189:5534-41. 2007

Collaborators

Detail Information

Publications38

  1. pmc A novel regulator RcdA of the csgD gene encoding the master regulator of biofilm formation in Escherichia coli
    Tomohiro Shimada
    Department of Frontier Bioscience and Research Center for Micro Nano Technology, Hosei University, Koganei, Tokyo, 184 8584, Japan
    Microbiologyopen 1:381-94. 2012
    ....
  2. pmc Novel roles of cAMP receptor protein (CRP) in regulation of transport and metabolism of carbon sources
    Tomohiro Shimada
    Department of Frontier Bioscience, Hosei University, Koganei, Tokyo, Japan
    PLoS ONE 6:e20081. 2011
    ..One unique regulation mode is that a single and the same CRP molecule bound within intergenic regions often regulates both of divergently transcribed operons...
  3. pmc The whole set of constitutive promoters recognized by RNA polymerase RpoD holoenzyme of Escherichia coli
    Tomohiro Shimada
    Department of Frontier Biosience, Hosei University, Koganai, Tokyo, Japan Micro Nano Technology Research Center, Hosei University, Koganai, Tokyo, Japan Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuda, Yokohama, Japan
    PLoS ONE 9:e90447. 2014
    ..The list of constitutive promoters provides the community resource toward estimation of the inducible promoters that operate under various stressful conditions in nature. ..
  4. pmc Prokaryotic genome regulation: a revolutionary paradigm
    Akira Ishihama
    Department of Frontier Bioscience and Micro Nano Technology Research Center, Hosei University, Koganei, Tokyo 184 8584, Japan
    Proc Jpn Acad Ser B Phys Biol Sci 88:485-508. 2012
    ..The most complex network was identified in the regulation cascades of transcription of two master regulators for planktonic growth and biofilm formation...
  5. doi request reprint Prokaryotic genome regulation: multifactor promoters, multitarget regulators and hierarchic networks
    Akira Ishihama
    Department of Frontier Bioscience, Hosei University, Koganei, Tokyo 184 8584, Japan
    FEMS Microbiol Rev 34:628-45. 2010
    ..The multifactor promoters and the multitarget transcription factors can be assembled into complex networks of transcription regulation, forming hierarchical networks...
  6. pmc Role of the biofilm master regulator CsgD in cross-regulation between biofilm formation and flagellar synthesis
    Hiroshi Ogasawara
    Department of Frontier Bioscience, Hosei University, Koganei, Tokyo 184 8584, Japan
    J Bacteriol 193:2587-97. 2011
    ..Taking these findings together, we propose that the cell motility for planktonic growth is repressed by CsgD, thereby promoting the switch to biofilm formation...
  7. pmc The uncharacterized transcription factor YdhM is the regulator of the nemA gene, encoding N-ethylmaleimide reductase
    Yoshimasa Umezawa
    Department of Frontier Bioscience, Hosei University, Koganei, Tokyo 184 8584, Japan
    J Bacteriol 190:5890-7. 2008
    ..This is an addition to the mode of controlling activity of transcription factors by alkylation with chemical agents...
  8. doi request reprint The transcription regulator AllR senses both allantoin and glyoxylate and controls a set of genes for degradation and reutilization of purines
    Akiko Hasegawa
    Department of Frontier Bioscience, Hosei University, Koganei, Tokyo, Japan
    Microbiology 154:3366-78. 2008
    ..On the other hand, when glyoxylate is accumulated, AllR is inactivated for derepression of the pathway for energy production. RutR, the master regulator for pyrimidines and arginine, is also involved in this pathway-switching control...
  9. pmc The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions
    Tomohiro Shimada
    Department of Frontier Bioscience and Micro Nano Technology Research Centre, Hosei University, Koganei, Tokyo 184 8584, Nippon Institute for Biological Science, Ome, Tokyo 198 0024, Japan
    Nucleic Acids Res 36:3950-5. 2008
    ..We suggest that either RutR has yet undiscovered function or that evolution has been slow to eliminate non-functional DNA sites for RutR because they do not have an adverse effect on cell fitness...
  10. pmc PdhR (pyruvate dehydrogenase complex regulator) controls the respiratory electron transport system in Escherichia coli
    Hiroshi Ogasawara
    Department of Frontier Bioscience, Hosei University, Kajino cho 3 7 2, Koganei, Tokyo 184 8584, Japan
    J Bacteriol 189:5534-41. 2007
    ..Taken together, we propose that PdhR is a master regulator for controlling the formation of not only the PDH complex but also the respiratory electron transport system...
  11. pmc A novel nucleoid protein of Escherichia coli induced under anaerobiotic growth conditions
    Jun Teramoto
    Department of Frontier Bioscience, Hosei University, Koganei, Tokyo 184 8584, Japan
    Nucleic Acids Res 38:3605-18. 2010
    ..We then propose that YgiP is a novel nucleoid protein of E. coli under anaerobiosis and propose to rename it Dan (DNA-binding protein under anaerobic conditions)...
  12. pmc Participation of regulator AscG of the beta-glucoside utilization operon in regulation of the propionate catabolism operon
    Yuji Ishida
    Department of Frontier Bioscience, Hosei University, Tokyo, Japan
    J Bacteriol 191:6136-44. 2009
    ..Taken together, these data suggest a metabolic link through interplay between the asc and prp operons...
  13. doi request reprint Regulation of the Escherichia coli csgD promoter: interplay between five transcription factors
    Hiroshi Ogasawara
    Department of Frontier Bioscience, Hosei University, Koganei, Tokyo 184 8584, Japan
    Microbiology 156:2470-83. 2010
    ..In addition, we propose a novel regulation model of this complex csgD promoter through cooperation between the two positive factors (OmpR-IHF and RstA-IHF) and also between the two negative factors (CpxR-H-NS)...
  14. ncbi request reprint RutR is the uracil/thymine-sensing master regulator of a set of genes for synthesis and degradation of pyrimidines
    Tomohiro Shimada
    Department of Frontier Bioscience and Micro Nano Technology Research Centre, Hosei University, Koganei, Tokyo 184 8584, Japan
    Mol Microbiol 66:744-57. 2007
    ..Altogether we propose that RutR is the pyrimidine sensor and the master regulator for a large set of the genes involved in the synthesis and degradation of pyrimidines...
  15. pmc Genomic SELEX search for target promoters under the control of the PhoQP-RstBA signal relay cascade
    Hiroshi Ogasawara
    Hosei University, Department of Frontier Bioscience, Kajino cho 3 7 2, Koganei, Tokyo 184 8584, Japan
    J Bacteriol 189:4791-9. 2007
    ..With these data taken together, we conclude that the expression of both asr and csgD is under the direct control of the PhoQP-RstBA signal relay cascade...
  16. doi request reprint Regulatory role of MlrA in transcription activation of csgD, the master regulator of biofilm formation in Escherichia coli
    Hiroshi Ogasawara
    Department of Frontier Bioscience, Hosei University, Tokyo, Japan
    FEMS Microbiol Lett 312:160-8. 2010
    ..The possible interplay between three activators was analysed in detail...
  17. doi request reprint Involvement of the ribose operon repressor RbsR in regulation of purine nucleotide synthesis in Escherichia coli
    Tomohiro Shimada
    Department of Frontier Bioscience, Hosei University, Koganei, Tokyo, Japan
    FEMS Microbiol Lett 344:159-65. 2013
    ..Taken together, we propose that RbsR is a global regulator for switch control between the de novo synthesis of purine nucleotides and its salvage pathway...
  18. pmc The Escherichia coli K-12 MntR miniregulon includes dps, which encodes the major stationary-phase DNA-binding protein
    Kaneyoshi Yamamoto
    Department of Frontier Bioscience and Research Center for Micro Nano Technology, Hosei University, Koganei, Tokyo 184 8584, Japan
    J Bacteriol 193:1477-80. 2011
    ..coli chromosome in vivo, and we report that MntR binds to only four targets, adjacent to the mntH, mntR, yebN, and dps genes. Unexpectedly, we found that dps expression is directly repressed by Mn(2+)-MntR...
  19. pmc Novel members of the Cra regulon involved in carbon metabolism in Escherichia coli
    Tomohiro Shimada
    Hosei University, Department of Frontier Bioscience, Koganei, Tokyo 184 8584, Japan
    J Bacteriol 193:649-59. 2011
    ..Taken together, we propose that Cra plays a key role in balancing the levels of the enzymes for carbon metabolism...
  20. ncbi request reprint Characterization of CitA-CitB signal transduction activating genes involved in anaerobic citrate catabolism in Escherichia coli
    Kaneyoshi Yamamoto
    Department of Frontier Bioscience and Research Center for Micro Nano Technology, Hosei University, Koganei, Tokyo, Japan
    Biosci Biotechnol Biochem 73:346-50. 2009
    ..DNase-I footprinting assay indicated that CitB specifically bound on the intergenic region between the citA and citC genes. These results characterize the molecular mechanism of the CitA-CitB signal transduction system in E. coli...
  21. pmc Involvement of the leucine response transcription factor LeuO in regulation of the genes for sulfa drug efflux
    Tomohiro Shimada
    Department of Frontier Bioscience, Hosei University, Tokyo, Japan
    J Bacteriol 191:4562-71. 2009
    ..The results described herein indicate that the yjcRQP operon, one of the LeuO targets, is involved in sensitivity control against sulfa drugs. We propose to rename the yjcRQP genes the sdsRQP genes (sulfa drug sensitivity determinant)...
  22. pmc Involvement of cyclic AMP receptor protein in regulation of the rmf gene encoding the ribosome modulation factor in Escherichia coli
    Tomohiro Shimada
    Department of Frontier Bioscience, Hosei University, Koganei, Tokyo
    J Bacteriol 195:2212-9. 2013
    ..Taken together, we propose that CRP regulates transcription activation of the rmf gene for formation of 100S ribosome dimers. Physiological roles of CRP involvement in RMF production are discussed...
  23. doi request reprint Novel roles of LeuO in transcription regulation of E.‚ÄÉcoli genome: antagonistic interplay with the universal silencer H-NS
    Tomohiro Shimada
    Hosei University, Department of Frontier Bioscience, Koganei, Tokyo 184 8540, Japan INRA UMR1319 MICALIS, 78352 Jouy en Josas, France AgroParisTech UMR MICALIS, 91300 Massy, France
    Mol Microbiol 82:378-97. 2011
    ..Taken together we propose that LeuO is a major player in antagonistic interplay against the universal silencer H-NS...
  24. doi request reprint Single live-bacterial cell assay of promoter activity and regulation
    Jun Teramoto
    Department of Frontier Bioscience, Hosei University, Koganei, Tokyo, Japan
    Genes Cells 15:1111-22. 2010
    ..The heterogeneity in gcl promoter activity was, however, confirmed by Flow cytometry of suspension cultures. Our success provides an experimental system for the increased demand of single-cell biology in bacterial studies...
  25. doi request reprint Screening of promoter-specific transcription factors: multiple regulators for the sdiA gene involved in cell division control and quorum sensing
    Kaori Shimada
    Department of Frontier Bioscience, Hosei University, Koganei, Tokyo 184 8584, Japan
    Microbiology 159:2501-12. 2013
    ..Taken together, we propose that these TCS regulators repress transcription in vivo of the sdiA gene, ultimately leading to suppression of cell division. ..
  26. doi request reprint Novel regulator PgrR for switch control of peptidoglycan recycling in Escherichia coli
    Tomohiro Shimada
    Department of Frontier Bioscience, Hosei University, Koganei, Tokyo, Japan
    Genes Cells 18:123-34. 2013
    ..Taken together, we propose to rename YcjZ as PgrR (regulator of peptide glycan recycling)...
  27. doi request reprint Novel regulation targets of the metal-response BasS-BasR two-component system of Escherichia coli
    Hiroshi Ogasawara
    Department of Frontier Bioscience, Hosei University, Koganei, Tokyo, Japan
    Microbiology 158:1482-92. 2012
    ....
  28. ncbi request reprint Two modes of autoregulation of the murR repressor in Escherichia coli
    Daiki Ishii
    Department of Frontier Bioscience, Hosei University, Tokyo, Japan
    Biosci Biotechnol Biochem 73:2528-30. 2009
    ..We found that murR is stimulated in rich medium. This activation involves MurR and most of the IIBC components of the phosphotransferase system, suggesting auto-induction of murR by an activated form of MurR...
  29. pmc RodZ regulates the post-transcriptional processing of the Shigella sonnei type III secretion system
    Jiro Mitobe
    Department of Bacteriology I, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
    EMBO Rep 12:911-6. 2011
    ..Thus, we propose that RodZ is a new membrane-bound RNA-binding protein that provides a scaffold for post-transcriptional regulation...
  30. doi request reprint Induction of the Escherichia coli cysK gene by genetic and environmental factors
    Kaneyoshi Yamamoto
    Department of Frontier Bioscience and Research Center for Micro Nano Technology, Hosei University, Koganei, Tokyo, Japan
    FEMS Microbiol Lett 323:88-95. 2011
    ..Based on the findings, we constructed the high-level expression system of cysK...
  31. ncbi request reprint Involvement of cAMP-CRP in transcription activation and repression of the pck gene encoding PEP carboxykinase, the key enzyme of gluconeogenesis
    Masahiro Nakano
    Department of Frontier Bioscience and Research Center for Micro Nano Technology, Hosei University, Koganei, Tokyo, Japan
    FEMS Microbiol Lett 355:93-9. 2014
    ..Taken together, we propose that cAMP-CRP associated at downstream CRP box-2 plays as a repressor for pck transcription only in the presence of high levels of cAMP-CRP. ..
  32. ncbi request reprint Induction of YdeO, a regulator for acid resistance genes, by ultraviolet irradiation in Escherichia coli
    Yuki Yamanaka
    Department of Frontier Bioscience and Research Center for Micro Nano Technology, Hosei University, Tokyo, Japan
    Biosci Biotechnol Biochem 76:1236-8. 2012
    ..This required the evgA and gadE genes in vivo. YdeO, induced by UV, controls the expression of a total of 21 genes. This accompanies SOS response in E. coli...
  33. ncbi request reprint Host factor Ebp1: selective inhibitor of influenza virus transcriptase
    Ayae Honda
    Department of Frontier Bioscience and Micro Nano Technology Research Center, Hosei University, Koganei, Tokyo 184 8584, Japan
    Genes Cells 12:133-42. 2007
    ....
  34. ncbi request reprint [Differentiation of Escherichia coli during transition from exponential growth to stationary phase]
    Akira Ishihama
    Tanpakushitsu Kakusan Koso 51:958-65. 2006
  35. pmc Involvement of RNA-binding protein Hfq in the osmotic-response regulation of invE gene expression in Shigella sonnei
    Jiro Mitobe
    Department of Bacteriology, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
    BMC Microbiol 9:110. 2009
    ..To date, the molecular details of the regulation of TTSS expression in response to osmotic pressure are not known. In the current study, we investigated the mechanism of regulation of TTSS by osmotic pressure...
  36. ncbi request reprint Roles of cell division control factor SdiA: recognition of quorum sensing signals and modulation of transcription regulation targets
    Tomohiro Shimada
    Department of Frontier Bioscience, Hosei University, Koganei, Tokyo, 184 8584, Japan Research Center for Micro Nano Technology, Hosei University, Koganei, Tokyo, 184 8584, Japan Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuda, Yokohama, 226 8503, Japan
    Genes Cells 19:405-18. 2014
    ..Taken together, we propose that the spectrum of taget gene selection by SdiA is modulated in multiple modes depending on the interacting HSL-like signal molecules. ..
  37. ncbi request reprint Role of a non-natural beta-C-nucleotide unit in DNA as a template for DNA and RNA syntheses and as a substrate for nucleolytic digestion
    Saeko Aketani
    Department of Chemistry, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo ku, 113 0033, Tokyo, Japan
    Eur J Pharm Sci 20:43-51. 2003
    ..These findings provide a useful tool for the size control of products in the synthesis and degradation of nucleic acids...
  38. pmc The nucleoid-associated protein Dan organizes chromosomal DNA through rigid nucleoprotein filament formation in E. coli during anoxia
    Ci Ji Lim
    National University of Singapore, Graduate School for Integrative Sciences and Engineering, Singapore
    Nucleic Acids Res 41:746-53. 2013
    ..Formation of the nucleoprotein filament provides a basis in understanding how Dan may play roles in both chromosomal DNA protection and gene regulation...