Kyushu University Academic Staff Educational and Research Activities Database
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Hironori Kawakami Last modified date:2018.07.17

Assistant Professor / Section of Pharmaceutical Care and Informatics
Department of Pharmaceutical Health Care and Sciences
Faculty of Pharmaceutical Sciences


Undergraduate School


E-Mail
Homepage
http://bunsei.phar.kyushu-u.ac.jp/
Phone
092-642-6644
Fax
092-642-6646
Academic Degree
PhD
Country of degree conferring institution (Overseas)
No
Field of Specialization
Biochemistry, Molecular Biology, Molecular Genetics, Computational Biology
Total Priod of education and research career in the foreign country
05years01months
Outline Activities
Working on chromosomal DNA replication and education.
Research
Research Interests
  • Chromosomal DNA replication
    keyword : Choromosomes, DNA replication
    2012.03.
Academic Activities
Reports
1. Tsutomu Katayama,Kazutoshi Kasho,Hironori Kawakami, The DnaA Cycle in Escherichia coli: Activation, Function and Inactivation of the Initiator Protein, Frontiers in Microbiology 8, 2496, 10.3389/fmicb.2017.02496, 2017.12.
2. Hironori Kawakami (corresponding author), Tsutomu Katayama, DnaA, ORC, and Cdc6: Similarity beyond the domains of life and diversity., Biochem. Cell Biol. 88(1), 49-62, 2010.02.
Papers
1. Yukari Sakiyama, Kazutoshi Kasho, Yasunori Noguchi, Hironori Kawakami, Tsutomu Katayama, Regulatory dynamics in the ternary DnaA complex for initiation of chromosomal replication in Escherichia coli, Nucleic Acids Res., doi:10.1093/nar/gkx914, doi:10.1093/nar/gkx914, 2017.10.
2. Masahiro Shimizu, Yasunori Noguchi, Yukari Sakiyama, Hironori Kawakami, Tsutomu Katayama, Shoji Takada, Near-atomic structural model for bacterial DNA replication initiation complex and its functional insights, Proc. Natl. Acad. Sci. U.S.A., doi:10.1073/pnas.1609649113, 113, 50, E8021-E8030, 2016.11, Upon DNA replication initiation in Escherichia coli, the initiator protein DnaA forms higher-order complexes with the chromosomal origin oriC and a DNA-bending protein IHF. Although tertiary structures of DnaA and IHF have previously been elucidated, dynamic structures of oriC-DnaA-IHF complexes remain unknown. Here, combining computer simulations with biochemical assays, we obtained models at almost-atomic resolution for the central part of the oriC-DnaA-IHF complex. This complex can be divided into three subcomplexes; the left and right subcomplexes include pentameric DnaA bound in a head-to-tail manner and the middle subcomplex contains only a single DnaA. In the left and right subcomplexes, DnaA ATPases associated with various cellular activities (AAA+) domain III formed helices with specific structural differences in interdomain orientations, provoking a bend in the bound DNA. In the left subcomplex a continuous DnaA chain exists, including insertion of IHF into the DNA looping, consistent with the DNA unwinding function of the complex. The intervening spaces in those subcomplexes are crucial for DNA unwinding and loading of DnaB helicases. Taken together, this model provides a reasonable near-atomic level structural solution of the initiation complex, including the dynamic conformations and spatial arrangements of DnaA subcomplexes..
3. Hironori Kawakami (corresponding author), Eiji Ohashi, Toshiki Tsurimoto, Tsutomu Katayama, Rapid purification and characterization of mutant origin recognition complexes in Saccharomyces cerevisiae, Front. Microbiol., 7, 521, 2016.04.
4. Hironori Kawakami (corresponding author), Eiji Ohashi, Shota Kanamoto, Toshiki Tsurimoto, Tsutomu Katayama, Specific binding of eukaryotic ORC to DNA replication origins depends on highly conserved basic residues, Sci. Rep., 5, 14929, 2015.10.
5. Yasunori Noguchi, Yukari Sakiyama, Hironori Kawakami, Tsutomu Katayama, The Arg fingers of key DnaA protomers are oriented inward within the replication origin oriC and stimulate DnaA subcomplexes in the initiation complex, J. Biol. Chem., 290, 33, 20295-20312, 2015.08.
6. Ozaki, S., Matsuda, Y., Keyamura, K., Kawakami, H., Noguchi, Y., Kasho, K., Nagata, K., Masuda, T., Sakiyama, Y., Katayama, T., A replicase clamp-binding protein with a dynamin motif promotes colocalization of nascent DNA strands and equipartitioning of chromosomes in Escherichia coli, Cell Reports, 4, 5, 985-995, 2013.09.
7. Sun, J., Evrin, C., Samel, S., Fernández-Cid, A., Riera, A., Kawakami, H., Stillman, B., Speck, C., Li, H., Cryo-EM structure of a helicase loading intermediate containing ORC-Cdc6-Cdt1-MCM2-7 bound to DNA, Nat. Struct. Mol. Biol., 10.1038/nsmb.2629, 20, 8, 944-951, 2013.08.
8. Sun, J., Kawakami, H. (joint first author), Speck, C., Zech, J., Stillman, B., and Li, H. , Cdc6-induced conformational changes in ORC bound to origin DNA revealed by cryo-electron microscopy, Structure, 20, 3, 534-544, 2012.03.
9. Fujimitsu Kazuyuki, Masayuki Su'etsugu, Yoko Yamaguchi, Kensaku Mazda, Nisi Fu, Hironori Kawakami, Tsutomu Katayama, Modes of over-initiation, dnaA gene expression and the inhibition of cell division in a novel cold-sensitive hda mutant in Escherichia coli., J. Bacteriol., 190, 15, , 5368-5381, 2008.08.
10. Shogo Ozaki, Hironori Kawakami, Kenta Nakamura, Norie Fujikawa, Wataru Kagawa, Sam-Yong Park, Shigeyuki Yokoyama, Hitoshi Kurumizaka, Tsutomu Katayama, A common mechanism for the ATP-DnaA-dependent formation of open complexes at the replication origin., J. Biol. Chem., 283, 13, 8351-8362, 2008.03.
11. Kawakami, H., Ozaki, S., Suzuki, S., Nakamura, K., Senriuchi, T., Su'etsugu, M., Fujimitsu, K., Katayama, T., The exceptionally tight affinity of DnaA for ATP/ADP requires a unique aspartic acid residue in the AAA+ sensor 1 motif, Mol. Microbiol., in press, 2006.01.
12. Kawakami, H., Su'etsugu, M., Katayama, T., An isolated Hda-clamp complex is functional in the regulatory inactivation of DnaA and DNA replication, J. Struct. Biol., 156(1), 220-229, 2006.10.
13. Kawakami, H., Keyamura K., Katayama, T., Formation of an ATP-DnaA-specific initiation complex requires DnaA arginine 285, a conserved motif in the AAA+ protein family, J. Biol. Chem., 10.1074/jbc.M502764200, 280, 29, 27420-27430, 280(29) 27420-27430, 2005.07.
14. Masayuki Su'etsugu, Toh-ru Shimuta, Takuma Ishida, Hironori Kawakami, Tsutomu Katayama, Protein associations in DnaA-ATP hydrolysis mediated by the replicase clamp-Hda complex, J. Biol. Chem., 10.1074/jbc.M412060200, 280, 8, 6528-6536, 280(8) 6528-6536, 2005.02.
15. Kawakami, H., Iwura, T., Takata, M., Sekimizu, K., Hiraga, S., Katayama, T., Arrest of cell division and nucleoid partition by genetic alterations in the sliding clamp of the replicase and in DnaA, Mol. Genet. Genomics, 10.1007/s004380100546, 266, 2, 167-179, 266(2) 167-179, 2001.10.
16. Su'etsugu, M., Kawakami, H. (joint first author), Kurokawa, K., Kubota, T., Takata, M., Katayama, T., DNA replication-coupled inactivation of DnaA protein in vitro: a role for DnaA arginine-334 of the AAA+ Box VIII motif in ATP hydrolysis, Mol. Microbiol., 10.1046/j.1365-2958.2001.02378.x, 40, 2, 376-386, 40(2) 376-386, 2001.04.
Presentations
1. Hironori Kawakami, Takeaki Chichibu, Eiji Ohashi, Shota Kanamoto, Toshiki Tsurimoto, Tsutomu Katayama, Multifaceted approach of Orc1 to DNA is the primary determinant of specific recognition of replication origins by ORC, The 10th 3R symposium, 2016.11.
2. Kawakami, H., Sun, J., Zech, J., Speck, C., Li, H., Stillman, B., Conformational transition of a nucleoprotein complex at a yeast chromosomal replication origin revealed by cryo-electron microscopy, Kyushu University – Pusan University Joint Seminar, 2012.09.
Membership in Academic Society
  • The Molecular Biology Society of Japan
  • The Japanese Biochemical Society
  • The Genetics Society of Japan
  • The Japanese Society for Bioinformatics