Kyushu University Academic Staff Educational and Research Activities Database
List of Papers
Kota Mayanagi Last modified date:2019.07.30

Assistant Professor / Department of Molecular and Structural Biology / Medical Institute of Bioregulation


Papers
1. Kouta Mayanagi,Kazumi Saikusa, Naoyuki Miyazaki,Satoko Akashi, Kenji Iwasaki, Yoshifumi Nishimura, Kosuke Morikawa, Yasuo Tsunaka, Structural visualization of key steps in nucleosome reorganization by human FACT, Scientific Reports, 10.1038/s41598-019-46617-7., 9, 1, 10183, 2019.07.
2. Takashima N, Ishino S, Oki K, Takafuji M, Yamagami T, Matsuo R, Mayanagi K, Ishino Y., Elucidating functions of DP1 and DP2 subunits from the Thermococcus kodakarensis family D DNA polymerase, Extremophiles, 10.1007/s00792-018-1070-3, 23, 1, 161-172, 2019.01.
3. Kouyama K, Mayanagi K, Nakae S, Nishi Y, Miwa M, Shirai T, Single-particle analysis of full-length human poly(ADP-ribose) polymerase 1, Biophys Physicobiol, 10.2142/biophysico.16.0_59, 16, 59-67, 2019.02.
4. Kouta Mayanagi, Sonoko Ishino, Tsuyoshi Shirai, Takuji Oyama, Shinichi Kiyonari, Daisuke Kohda, Kosuke Morikawa Yoshizumi Ishino , Direct visualization of DNA baton pass between replication factors bound to PCNA, Scientific Repots, 10.1038/s41598-018-34176-2, 8, 1, 16209, 2018.11, In Eukarya and Archaea, the lagging strand synthesis is accomplished mainly by three key factors, DNA polymerase (Pol), flap endonuclease (FEN), and DNA ligase (Lig), in the DNA replication process. These three factors form important complexes with proliferating cell nuclear antigen (PCNA), thereby constructing a platform that enable each protein factor to act successively and smoothly on DNA. The structures of the Pol-PCNA-DNA and Lig-PCNA-DNA complexes alone have been visualized by single particle analysis. However, the FEN-PCNA-DNA complex structure remains unknown. In this report, we for the first time present this tertiary structure determined by single particle analysis. We also successfully visualized the structure of the FEN-Lig-PCNA-DNA complex, corresponding to a putative intermediate state between the removal of the DNA flap by FEN and the sealing of the nicked DNA by Lig. This structural study presents the direct visualization of the handing-over action, which proceeds between different replication factors on a single PCNA clamp bound to DNA. We detected a drastic conversion of the DNA from a bent form to a straight form, in addition to the dynamic motions of replication factors in the switching process.
5. Mayanagi K, Ishino S Takafuji M, Mitsuoka K, Shirai T, Kiyonari S, Nishida H, Kohda D, Morikawa K, Ishino Y., Switching mechanism of DNA replication fork complex revealed by single particle analysis, European Microscopy Congress , 3, 57-58, Vol3, 57-58, 2016.12.
6. Aramaki S, Mayanagi K, Aoyama K, Yasunaga T, Revealing the intracellular ultrastructure of filopodia with cryo-electron tomography, Microscopy (Oxf), 63 Suppl 1: i33-i34, 2016.07.
7. Aramaki S, Mayanagi K, Jin M, Aoyama K, Yasunaga T, Filopodia formation by crosslinking of F-actin with fascin in two different binding manners, Cytoskeleton, 10.1002/cm.21309, 73(7):365-74, 2016.06.
8. Takekawa N, Terahara N, Kato T, Gohara M, Mayanagi K, Hijikata A, Onoue Y, Kojima S, Shirai T, Namba K, Homma M, The tetrameric MotA complex as the core of the flagellar motor stator from hyperthermophilic bacterium, Scientific Reports, 10.1038/srep31526, 6:31526, 2016.08.
9. Nakae S, Hijikata A, Tsuji T, Yonezawa K, Kouyama KI, Mayanagi K, Ishino S, Ishino Y, Shirai T, Structure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease, Structure, 24, 1960-1971, 24, 1960-1971, 2016.07, Archaeal NucS nuclease was thought to degrade the single-stranded region of branched DNA, which contains flapped and splayed DNA. However, recent findings indicated that EndoMS, the orthologous enzyme of NucS, specifically cleaves double-stranded DNA (dsDNA) containing mismatched bases. In this study, we determined the structure of the EndoMS-DNA complex. The complex structure of the EndoMS dimer with dsDNA unexpectedly revealed that the mismatched bases were flipped out into binding sites, and the overall architecture most resembled that of restriction enzymes. The structure of the apo form was similar to the reported structure of Pyrococcus abyssi NucS, indicating that movement of the C-terminal domain from the resting state was required for activity. In addition, a model of the EndoMS-PCNA-DNA complex was preliminarily verified with electron microscopy. The structures strongly support the idea that EndoMS acts in a mismatch repair pathway..
10. Kozo Takeuchi, Tatsuya Nishino, Kota Mayanagi, Naoki Horikoshi, Akihisa Osakabe, Hiroaki Tachiwana, Tetsuya Hori, Hitoshi Kurumizaka, Tatsuo Fukagawa, The centromeric nucleosome-like CENP-T-W-S-X complex induces positive supercoils into DNA, Nucleic Acids Research, 10.1093/nar/gkt1124, 42, 3, 1644-1655, 2014.02, The centromere is a specific genomic region upon which the kinetochore is formed to attach to spindle microtubules for faithful chromosome segregation. To distinguish this chromosomal region from other genomic loci, the centromere contains a specific chromatin structure including specialized nucleosomes containing the histone H3 variant CENP-A. In addition to CENP-A nucleosomes, we have found that centromeres contain a nucleosome-like structure comprised of the histone-fold CENP-T-W-S-X complex. However, it is unclear how the CENP-T-W-S-X complex associates with centromere chromatin. Here, we demonstrate that the CENP-T-W-S-X complex binds preferentially to ∼ 100 bp of linker DNA rather than nucleosome-bound DNA. In addition, we find that the CENP-T-W-S-X complex primarily binds to DNA as a (CENP-T-W-S-X)2 structure. Interestingly, in contrast to canonical nucleosomes that negatively supercoil DNA, the CENP-T-W-S-X complex induces positive DNA supercoils. We found that the DNA-binding regions in CENP-T or CENP-W, but not CENP-S or CENP-X, are required for this positive supercoiling activity and the kinetochore targeting of the CENP-T-W-S-X complex. In summary, our work reveals the structural features and properties of the CENP-T-W-S-X complex for its localization to centromeres..
11. Naoyuki Kuwabara, Yasuto Murayama, Hiroshi Hashimoto, Yuuichi Kokabu, Mitsunori Ikeguchi, Mamoru Sato, Kouta Mayanagi, Hiroshi Iwasaki and Toshiyuki Shimizu., Mechanistic insights into the activation of the Rad51-mediated strand exchange from the structure of a recombination activator, Swi5-Sfr1 complex., Structure, 20, 3, 440–449, 2012.03.
12. Hiromi Ogino, Sonoko Ishino, Kouta Mayanagi, Gyri Teien Haugland, Nils-Kare Birkeland, Akihiko Yamagishi and Yoshizumi Ishino, The GINS complex from the thermophilic archaeon, Thermoplasma acidophilum may function as a homotetramer in DNA replication, Extremophiles, 10.1007/s00792-011-0383-2, 15, 529-539, 2011.06.
13. Ohnishi K, Nakahira K, Unzai S, Mayanagi K, Hashimoto H, Shiraki K, Honda T, Yanagihara I, , Relationship between heat-induced fibrillogenicity and hemolytic activity of thermostable direct hemolysin and a related hemolysin of Vibrio parahaemolyticus, FEMS MicroBiol Lett. , 318, 1, 10-17, 2011.05.
14. Takuji Oyama, Sonoko Ishino, Seiji Fujino, Hiromi Ogino, Tsuyoshi Shirai, Kouta Mayanagi, Mihoko Saito, Naoko Nagasawa, Yoshizumi Ishino and Kosuke Morikawa, Architectures of archaeal GINS complexes, essential DNA replication initiation factors, BMC Biology, 10.1186/1741-7007-9-28, 9, 28, 2011.04.
15. Mayanagi K, Kiyonari S, Nishida H, Saito M, Kohda D, Ishino Y, Shirai T, Morikawa K, , Architecture of the DNA polymerase B-proliferating cell nuclear antigen (PCNA)-DNA ternary complex. , PNAS, 108, 5, 1845-1849, (Corresponding Author), 2011.02.
16. Yanagihara I, Nakahira K, Yamane T, Kaieda S, Mayanagi K, Hamada D, Fukui T, Ohnishi K, Kajiyama S, Shimizu T, Sato M, Ikegami T, Ikeguchi M, Honda T, Hashimoto H., Structure and functional characterization of Vibrio parahaemolyticus thermostable direct hemolysin (TDH), JBC, 285, 21, 16267-16274, 2010.05.
17. Hirokazu. Nishida, Kouta. Mayanagi, Shinichi. Kiyonari, Yuichi. Sato, Takuji. Oyama, Yoshizumi. Ishino, Kosuke. Morikawa, Structural determinant for switching between the polymerase and exonuclease modes in the PCNA-replicative DNA polymerase complex, PNAS, 106, 20693-20698, 2009.11.
18. Masayuki Oda, Susumu Uchiyama, Masanori Noda, Yoshinori Nishi, Maiko Koga, Kouta Mayanagi, Carol V. Robinson, Kiichi Fukui, Yuji Kobayashi, Kosuke Morikawa, and Takachika Azuma, Effects of antibody affinity and antigen valence on molecular forms of immune complexes., Molecular Immunology, 47, 357-364, 2009.10.
19. Kouta Mayanagi, Shinichi Kiyonari, Mihoko Saito, Tsuyoshi Shirai, Yoshizumi Ishino, Kosuke Morikawa, Mechanism of replication machinery assembly as revealed by the DNA ligase-PCNA-DNA complex architecture, PNAS, 106, 4647-4652, (Corresponding Author), 2009.03.
20. Takuji Oyama, Hayato Oka, Kouta Mayanagi, Tsuyoshi Shirai, Kyoko Matoba, Ryosuke Fujikane, Yoshizumi Ishino, Kosuke Morikawa,, Atomic structures and functional implications of the archaeal RecQ-like helicase Hjm, BMC Structural Biology, 9, 2, 2009.01.
21. Atsushi Miyagi, Yasuo Tsunaka, Takayuki Uchihashi, Kouta Mayanagi, Susumu Hirose, Kosuke Morikawa, and Toshio Ando., Visualization of intrinsically disordered regions of proteins by high-speed atomic force microscopy, Chemphyschem, 9, 13, 859-866, 2008.09.
22. Yasuto Murayama, Yumiko Kurokawa, Kouta Mayanagi, and Hiroshi Iwasaki, Formation and branch migration of Holliday junctions mediated by eukaryotic recombinases, Nature, 451, 7181, 1018-1021, 2008.02.
23. Yoshie Fujiwara, Kouta Mayanagi, and Kosuke Morikawa, Functional significance of octameric RuvA for a branch migration complex from Thermus thermophilus., BBRC, 366, 2, 426-431, 2007.12.
24. Kouta Mayanagi, Yoshie Fujiwara, Tomoko Miyata, and Kosuke Morikawa, Electron microscopic single particle analysis of a tetrameric RuvA/RuvB/Holliday junction DNA complex, BBRC, 365, 273-278, (Corresponding Author), 2007.11.
25. Daizo Hamada, Takashi Higurashi, Kouta Mayanagi, Tomoko Miyata, Takashi Fukui, Tetsuya Iida, Takeshi Honda, and Itaru Yanagihara, Tetrameric structure of Thermostable Direct Hemolysin from Vibrio parahaemolyticus revealed by Ultracentrifugation, Small Angle X-ray Scattering and Electron Microscopy, J. Mol. Biol., 365, 1, 187-195, 2006.09.
26. Tomoko Miyata, Hirofumi Suzuki, Takuji Oyama, Kouta Mayanagi, Yoshizumi Ishino, and Kosuke Morikawa, Open clamp structure in the clamp-loading complex visualized by electron microscopic image analysis. , PNAS, 10.1073/pnas.0506447102, 102, 39, 13795-13800, 2005.09.
27. Kyoko Matoba, Mitsuyoshi Yamazoe, Kouta Mayanagi, Kosuke Morikawa, Sota Hiraga, Comparison of MukB homodimer versus MukBEF complex molecular architectures by electron microscopy reveals a higher-order multimerization., BBRC, 333, 694-702, 2005.08.
28. Takahashi Fukui, Kentaro Shiraki, Daizo Hamada, Kojiro Hara, Tomoko Miyata, Shinsuke Fujiwara, Kouta Mayanagi, Keiko Yanagihara, Tetsuya Iida, Eiichiro Fukusaki, Tadayuki Imanaka, Takeshi Honda, and Itaru Yanagihara., Thermostable direct hemolysin of Vibrio parahaemolyticus is a bacterial reversible amyloid toxin., Biochemistry, 44, 29, 9825-9832, 2005.07.
29. Tomoko Miyata, Takuji Oyama, Kouta Mayanagi, Sonoko Ishino, Yoshizumi Ishino, and Kosuke Morikawa, The Clamp-loading Complex for Processive DNA Replication, Nature Struct. & Molec. Biol. , 10.1038/nsmb788, 11, 7, 632-636, 2004.06.
30. Norikazu Yabuta, Naoko Kajimura, Kouta Mayanagi, Michio Sato, Takahito Gotow, Yasuo Uchiyama, Yukio Ishimi and Hiroshi Nojima, Mammalian Mcm2/4/6/7 complex forms a toroidal structure, Genes to Cells, 8, 5, 413-421, 2003.05.
31. Kyoko Matoba, Kouta Mayanagi, Syo Nakasu, Akihiko Kikuchi, and Kosuke Morikawa, Three-dimensional electron microscopy of the reverse gyrase from Sulfolobus tokodaii, BBRC, 297, 4, 749-755, 2002.10.
32. Kazuhiro Yamada, Tomoko Miyata, Daisuke Tsuchiya, Takuji Oyama, Yoshie Fujiwara, Takayuki Ohnishi, Hiroshi Iwasaki, Hideo Shinagawa, Mariko Ariyoshi, Kouta Mayanagi, and Kosuke Morikawa, Crystal structure of the RuvA-RuvB complex: A structural basis for the Holliday junction migrating motor machinery, Mollecular Cell, 10, 3, 671-681, 2002.09.
33. Naoko Kajimura, Matsuyo Yamazaki, Kosuke Morikawa, Akio Yamazaki, and Kouta Mayanagi, Three-dimensional structure of non-activated cGMP phosphodiesterase 6 and comparison of its image with those of activated forms, J. Struct. Biol., 139, 1, 27-38, (Corresponding Author), 2002.07.
34. Kozo Hamada, Tomoko Miyata, Kouta Mayanagi, Junji Hirota and Katsuhiko Mikoshiba, Two-state conformational changes in Inositol 1,4,5-trisphosphate receptor regulated by calcium, J. Biol. Chem., 277, 24, 21115-21118, 2002.04.
35. Han, Y.-W., Iwasaki, H., Miyata, T., Mayanagi, K., Yamada, K., Morikawa, K., and Shinagawa, H, A unique beta-hairpin protruding from AAA+ ATPase domain of RuvB motor protein is involved in the interaction with RuvA DNA recognition protein for branch migration of Holliday junctions, J. Biol. Chem., 276, 37, 35024-35028, 2001.06.
36. Narita, A., Yasunaga, T., Ishikawa, T., Mayanagi, K., and Wakabayashi, T, Ca2+-induced switching of troponin and tropomyosin on actin filaments as revealed by electron cryo-microscopy, J. Mol. Biol., 308, 2, 241-261, 2001.04.
37. Mayanagi, K., Miyata, T., Oyama, T., Ishino, Y., and Morikawa, K, Three-dimensional electron microscopy of the clamp loader small subunit from Pyrococcus furiosus, J. Struct. Biol., 134, 1, 35-45, (Corresponding Author), 2001.04.
38. Yamada, K., Kunishima, N., Mayanagi, K., Ohnishi, T., Nishino, T., Iwasaki, H., Shinagawa, H., and Morikawa. K., Crystal structure of the Holliday junction migration motor protein RuvB from Thermus thermophilus HB8, Proc. Natl. Acad. Sci. U S A, 98, 4, 1442-1447, 2001.02.
39. Komori, K., Miyata, T., DiRuggiero, J., Holley-Shanks, R., Hayashi, I., Cann, I.K., Mayanagi, K., Shinagawa, H., Ishino. Y, Both RadA and RadB are involved in homologous recombination in Pyrococcus furiosus, J Biol Chem., 275, 43, 33782-33790, 2000.10.
40. Miyata, T., Yamada, K., Iwasaki, H., Shinagawa, H., Morikawa, K., and Mayanagi. K, Two different oligomeric states of the RuvB branch migration motor protein as revealed by electron microscopy, J. Struct. Biol., 131, 2, 83-89, (Corresponding Author), 2000.08.
41. Mayanagi, K., Ishikawa, T., Toyoshima, C., Inoue, Y., and Nakazato, K, Three-dimensional electron microscopy of the photosystem II core complex, J. Struct. Biol. , 123, 3, 211-224, 1998.11.
42. Yasuaki Hiromasa, Yoichi Aso, Kouta Mayanagi, Yorinao Inoue, Tetsuro Fujisawa, Koji Meno, and Tatzuo Ueki, Guanidine hydrochloride- induced changes of the E2 inner core of the Bacillus stearothermophilus pyruvate dehydrogenase complex, J. Biochem., 123, 4, 564-567, 1998.04.
43. Shinohara, S., Yamagishi, K., Ohdachi, S., Ejiri, A., Mayanagi, K., Shimazu, Y., and Miyamoto, K, Wall conditioning and its effect on RFP plasma performance in REPUTE-1, Plasma Physics and Controlled Fusion, 34, 627-633, 1992.05.