| 1. |
Suzuki, S., Kurosawa, N., Yamagami, T., Matsumoto, S., Numata, T., Ishino, S., and Ishino, Y., Genetic and Biochemical Characterizations of aLhr1 Helicase in the Thermophilic Crenarchaeon Sulfolobus acidocaldarius., Catalysts, 12, 2022.04, アーキアのDNAポリメラーゼとGINSが結合することを示した。. |
| 2. |
Oki, K., Nagata, M., Yamagami, T., Numata, T., Ishino, S., Oyama, O., and Ishino, Y. , Family D DNA polymerase interacts with GINS to promote CMG-helicase in the archaeal replisome. , Nucleic Acids Res. , 49, 2021.06, Genomic DNA replication requires replisome assembly. We show here the molecular mechanism by which CMG (GAN-MCM-GINS)-like helicase cooperates with the family D DNA polymerase (PolD) in Thermococcus kodakarensis. The archaeal GINS contains two Gins51 subunits, the C-terminal domain of which (Gins51C) interacts with GAN. We discovered that Gins51C also interacts with the N-terminal domain of PolD's DP1 subunit (DP1N) to connect two PolDs in GINS. The two replicases in the replisome should be responsible for leading- and lagging-strand synthesis, respectively. Crystal structure analysis of the DP1N-Gins51C-GAN ternary complex was provided to understand the structural basis of the connection between the helicase and DNA polymerase. Site-directed mutagenesis analysis supported the interaction mode obtained from the crystal structure. Furthermore, the assembly of helicase and replicase identified in this study is also conserved in Eukarya. PolD enhances the parental strand unwinding via stimulation of ATPase activity of the CMG-complex. This is the first evidence of the functional connection between replicase and helicase in Archaea. These results suggest that the direct interaction of PolD with CMG-helicase is critical for synchronizing strand unwinding and nascent strand synthesis and possibly provide a functional machinery for the effective progression of the replication fork.. |
| 3. |
Oki, K., Yamagami, T., Nagata, M., Mayanagi, K., Shirai T., Adachi, N., Numata, T., Ishino, S., and Ishino, Y., DNA polymerase D temporarily connects primase to the CMG-like helicase before interacting with proliferating cell nuclear antigen., Nucleic Acids Res., 49, 4599-4612, 2021.04, The eukaryotic replisome is comprised of three family-B DNA polymerases (Polα, δ and ϵ). Polα forms a stable complex with primase to synthesize short RNA-DNA primers, which are subsequently elongated by Polδ and Polϵ in concert with proliferating cell nuclear antigen (PCNA). In some species of archaea, family-D DNA polymerase (PolD) is the only DNA polymerase essential for cell viability, raising the question of how it alone conducts the bulk of DNA synthesis. We used a hyperthermophilic archaeon, Thermococcus kodakarensis, to demonstrate that PolD connects primase to the archaeal replisome before interacting with PCNA. Whereas PolD stably connects primase to GINS, a component of CMG helicase, cryo-EM analysis indicated a highly flexible PolD-primase complex. A conserved hydrophobic motif at the C-terminus of the DP2 subunit of PolD, a PIP (PCNA-Interacting Peptide) motif, was critical for the interaction with primase. The dissociation of primase was induced by DNA-dependent binding of PCNA to PolD. Point mutations in the alternative PIP-motif of DP2 abrogated the molecular switching that converts the archaeal replicase from de novo to processive synthesis mode.. |
| 4. |
Takagi, S., Yamagami, T., Takeda, K., and Takagi, T., Helical configuration of lutein aggregate dispersed in liposomes of phosphatidyl choline and digalactocyldiglyceride, Agric. Biol. Chem., 51, 1567-1572, 1987.10. |
| 5. |
Yamagami T, Funatsu G., Purification and some properties of three chitinases from the seeds of rye (Secale cereale), Biosci Biotechnol Biochem. , 57, 4, 643-647, 1993.04. |
| 6. |
Yamagami T, Funatsu G., The complete amino acid sequence of chitinase-c from the seeds of rye (Secale cereal), Biosci Biotechnol Biochem., 57, 11, 1854-1861, 1993.11. |
| 7. |
Yamagami T, Funatsu G., The complete amino acid sequence of chitinase-a from the seeds of rye (Secale cereal), Biosci Biotechnol Biochem., 58, 2, 322-329, 1994.02. |
| 8. |
Aso, Y., Yamamoto, K., Yoshinaga, T., Yamamoto, H., and Yamagami, T., Partial purification and characterzation of DOPA quinone imine conversion factor from larval hemolymph of the solkworm, Bambyx mori, Biosci. Biotech. Biochem., 59, 2, 277-281, 1995.02. |
| 9. |
Ohta M, Yamagami T, Funatsu G., Purification and characterization of two chitinases from the leaves of pokeweed (Phytolacca americana), Biosci Biotechnol Biochem., 59, 4, 656-661, 1995.04. |
| 10. |
Tanigawa M, Yamagami T, Funatsu G., The complete amino acid sequence of chitinase-B from the leaves of pokeweed (Phytolacca americana), Biosci Biotechnol Biochem., 59, 5, 841-847, 1995.05. |
| 11. |
Yamagami T, Funatsu G., Identification of the tryptophan residue located at the substrate-binding site of rye seed chitinase-c, Biosci Biotechnol Biochem., 59, 1076-1081, 1995.10. |
| 12. |
Yamagami T, Funatsu G., Limited proteolysis and reduction-carboxymethylation of rye seed chitinase-a: role of the chitin-binding domain in its chitinase action, Biosci Biotechnol Biochem., 60, 7, 1081-1086, 1996.07. |
| 13. |
Yamagami T, Funatsu G., Involvements of Trp23 in the Chitin-binding and of Trp131 in the Chitinase Activity of Rye Seed Chitinase-a, Biosci Biotechnol Biochem., 61, 11, 1819-1825, 1997.06. |
| 14. |
Yamagami, T., Mine, Y., Aso, Y., and Ishiguro, M., Purification and characterization of two chitinase isoforms from the bulbs of gladiolus (Gladiolus gandavensis), Biosci. Biotech. Biochem., 61, 11, 2140-2142, 1997.11. |
| 15. |
Yamagami, T. and G. Funatsu, Identification of the aspartic acid residue located at or near substrate-binding site of rye seed chitinase-c, Biosci. Biotechnol. Biochem., 10.1271/bbb.62.383, 62, 2, 383-385, 62, 383-3852, 1998.01. |
| 16. |
Yamagami, T., Y. Mine and M. Ishiguro, Complete amino acid sequence of chitinase-a from bulbs of gladiolus (Gladiolus gandavenis),, Biosci. Biotechnol. Biochem., 10.1271/bbb.62.386, 62, 2, 386-389, 62, 386-389, 1998.01. |
| 17. |
Yamagami, T., T. Taira, Y. Mine, Y. Aso and M. Ishiguro, Isolation and characterization of chitinase isoforms from the bulbs of four species of the genus tulipa, Biosci. Biotechnol. Biochem., 10.1271/bbb.62.584, 62, 3, 584-587, 62, 584-587, 1998.01. |
| 18. |
Yamagami, T. and M. Ishiguro, Complete amino acid sequence of chitinase-1 and -2 from bulbs of genus Tulipa,, Biosci. Biotechnol. Biochem., 10.1271/bbb.62.1253, 62, 6, 1253-1257, 62, 1253-1257, 1998.01. |
| 19. |
Yamagami T, Tanigawa M, Ishiguro M, Funatsu G., Complete amino acid sequence of chitinase-A from leaves of pokeweed (Phytolacca americana), Biosci Biotechnol Biochem., 62, 4, 825-828, 1998.04. |
| 20. |
Yamagami, T., G. Funatsu, and M. Ishiguro, Positions of disulfide bonds in rye (Secale cereale) seed chitinase-a, Biosci. Biotechnol. Biochem., 10.1271/bbb.64.1313, 64, 6, 1313-1316, 64, 1313-1316, 2000.01. |
| 21. |
Yamagami, T., K. Tsutsumi, and M. Ishiguro, Cloning, sequencing, and expression of the tulip bulb chitinase-1 cDNA, Biosci. Biotechnol. Biochem., 10.1271/bbb.64.1394, 64, 7, 1394-1401, 64, 1394-1401, 2000.01. |
| 22. |
Taira T., T. Yamagami, Y. Aso, M. Ishiguro, and M. Ishihara, Localization, accumulation, and antifungal activity of chitinases in rye seed,, Biosci. Biotechnol. Biochem., 10.1271/bbb.65.2710, 65, 12, 2710-2718, 65, 2710-2718, 2001.01. |
| 23. |
Ishiguro M., T. Yamagami, M. Tanigawa, K. Tsutsumi, G. Funatsu, T. Ohnuma, and Y. Aso,, Modification of tryptophan residues of plant class III chitinases involved in enzyme activity, J. Fac. Agr. Kyushu Univ., 46, 1, 243-250, 46, 243-250, 2001.01. |
| 24. |
Ohnuma T., M. Yagi, T. Yamagami, T. Taira, Y. Aso, and M. Ishiguro,, Molecular cloning, functional expression, and mutagenesis of cDNA encoding rye seed chitinase-c, Biosci. Biotechnol. Biochem., 66, 2, 277-284, 66, 277-284, 2002.01. |
| 25. |
Taira T., T. Ohnuma, T. Yamagami, Y. Aso, M. Ishiguro, and M. Ishihara, Antifungal activity of rye seed chitinases: Different binding manner of class I and class II chitinases to the fungal cell walls, Biosci. Biotechnol. Biochem., 66, 5, 970-977, 66, 970-977, 2002.01. |
| 26. |
Suzukawa K., T. Yamagami, T. Ohnuma, H. Hirakawa, S. Kuhara, Y, Aso, and M. Ishiguro, Mutational analysis of amino acid residues involved in catalytic activity of a family 18 chitinase from tulip bulbs, Biosci. Biotechnol. Biochem., 67, 2, 341-346, 67, 341-346, 2003.01. |
| 27. |
Ohnuma T., M. Yagi, T. Taira, T. Yamagami, and M. Ishiguro,, Efficient production of recombinant plant chitinase with Novagen's E. coli Origami(DE3) strain, inNovations, 17, 12-13, 2003.01. |
| 28. |
Yamagami T., A. Tsuchisaka, K. Yamada, W. F. Haddon, L. A. Harden, and A. Theologis, Biochemical diversity among the 1-amino-cyclopropane-1-carboxylic acid synthase isozymes encoded by Arabidopsis gene family, J. Biol. Chem., 278, 49102-49112, 2003.12. |
| 29. |
Ohnuma., T., Taira, T., Yamagami, T., and Ishiguro, M., Molecular cloning, functional expression, and mutagenesis of cDNA encoding class I chitinase from rye (Secale cereale), Biosci. Biotech. Biochem., 68, 3, 324-332, 2004.03. |
| 30. |
Matsunaga, F., Takemura, K., Akita, M., Adachi, A., Yamagami, T., and Ishino, Y., Localized melting of duplex DNA by Cdc6/Orc1 at the DNA replication origin in the hyperthermophilic archaeon Pyrococcus furiosus, Extremophiles, 14, 21-31, 2009.01. |
| 31. |
Matsukawa, H., Yamagami, T.,Kawarabayasi, Y., Miyashita, Y., Takahashi, M., and Ishino, Y., A useful strategy to construct DNA polymerases with different properties by using genetic resources from environmental DNA, Genes Genet. Syst., 84, 3-13, 2009.11. |
| 32. |
Akita, M., Adachi, A, Takemura, K., Yamagami, T., Matsunaga, F., and Ishino, Y. , Cdc6/Orc1 from Pyrococcus furiosus may act as the origin recognition protein and Mcm helicase recruiter, Genes Cells , 15, 537-552, 2010.11. |
| 33. |
Yang, Y., Ishino, S., Yamagami, T., Kumamaru, T., Satoh, H., and Ishino, Y., The OsGEN-L protein from Oryza sativa possesses Holliday junction resolvase activity as well as 5'-flap endonuclease activity, J. Biochem. , 151, 317-327, 2012.11. |
| 34. |
Kuba, Y., Ishino, S., Yamagami, T., Tokuhara, M., Kanai, T., Fujikane, R.,Daiyasu., Atomi, H., Ishino, Y., Comparative analyses of the two PCNAs from the hyperthermophilic archaeon, Thermococcus kodakarensis, Genes Cells, 17, 923-937, 2012.11. |
| 35. |
Yamagami, T., Ishino, S., Kawarabayasi, Y., and Ishino, Y., Mutant Taq DNA polymerases with improved elongation ability as a useful reagent for genetic engineering., Front Microbiol. , 5:461, 2014.09. |
| 36. |
Ishino, S., Yamagami, T., Kitamura, M., Kodera, N., Mori, T., Sugiyama, S., Ando, T., Goda, N., Tenno, T,, Hiroaki, H., and Ishino, Y, Multiple interactions of the intrinsically disordered region between the helicase and the nuclease domains of the archaeal Hef protein, J. Biol. Chem., 289, 21627-21636, 2014.11. |
| 37. |
Yamagami, T., Matsukawa, H., Tsunekawa, S., Kawarabayasi, Y., Ishino, S., and Ishino, Y. , A longer finger-subdomain of family A DNA polymerases found by metagenomic analysis strengthens DNA binding and primer extension abilities., Gene, 10.1016, 576: 690-695, 2015.10. |
| 38. |
Shiraishi, M., Ishino, S., Yamagami, T., Egashira, Y., Kiyonari, S., and Ishino, Y., A novel endonuclease that may be responsible for damaged DNA base repair in Pyrococcus furious, Nucleic Acids Res. , 43, 2858-2863, 2015.11. |
| 39. |
Ishino, S, Makita, N, Shiraishi, M, Yamagami, T, and Ishino, Y. , EndoQ and EndoV work individually for damaged DNA base repair in Pyrococcus furious, Biochimie, 118, 264-269, 2015.11. |
| 40. |
Ishino, S., Nishi, Y., Oda, S., Uemori, T., Sagara, T., Takatsu, N., Yamagami, T., Shirai, T., and Ishino, Y. , Identification of a mismatch-specific endonuclease in hyperthermophilic Archaea, Nucleic Acids Res. , 44, 2977-2986, 2016.11. |
| 41. |
Shiraishi, M., Ishino, S., Yoshida, K., Yamagami, T., Cann, I., and Ishino, Y., PCNA is involved in the EndoQ-mediated DNA repair process in Thermococcales, Sci. Rep., 6, 25532, 2016.11. |
| 42. |
Oyama, T., Ishino, S., Shirai, T., Yamagami, T., Nagata, M., Ogino, H., Kusunoki, M., and Ishino, Y., Atomic structure of an archaeal GAN suggests its dual roles as an exonuclease in DNA repair and a CMG component in DNA replication, Nucleic Acids, Res, 44, 9509-9517, 2016.11. |
| 43. |
Nagata, M., Ishino, S., Yamagami, T., Ogino, H., Simons, J-R., Kanai, T., Atomi, H., and Ishino, Y., The Cdc45/RecJ-like protein forms a complex with GINS and MCM, and is important for DNA replication in Thermococcus kodakarensis, Nucleic Acids Res. , 45, 10693-10705, 2017.11. |
| 44. |
Nagata, M., Ishino, S., Yamagami, T., Simons, J-R., Kanai, T., Atomi, H., and Ishino, Y., Possible function of the second RecJ-like protein in stalled replication fork repair by interacting with Hef, Sci Rep., 7, 16949, 2017.11. |
| 45. |
Daimon, K., Ishino, S., Imai, N., Nagumo, S., Yamagami, T., Matsukawa, H. and Ishino, Y., Two Family B DNA Polymerases From Aeropyrum pernix, Based on Revised Translational Frames, Frontiers in Molecular Biosciences, 5, 3389, 2018.11. |
| 46. |
Takashima, N., Ishino, S., Oki, K., Takafuji, M., Yamagami, T., Matsuo, R., Mayanagi, K., and Ishino, Y., Elucidating functions of DP1 and DP2 subunits from the Thermococcus kodakarensis family D DNA polymerase, Extremophiles, 23, 161-172, 2018.11. |
| 47. |
Nagata, M., Ishino, S., Yamagami, T., and Ishino, Y. , Replication protein A complex in Thermococcus kodakarensis interacts with DNA polymerases and helps their effective strand synthesis, Biosci. Biotechnol. Biochem., 83, 695-704, 2018.11. |
| 48. |
Mayanagi, K., Oki, K., Miyazaki, N., Ishino, S., Yamagami, T., Morikawa, K., Iwasaki, K., Kohda, D., Shirai, T., and Ishino, Y, Two conformations of DNA polymerase D-PCNA-DNA, an archaeal replisome complex, revealed by cryo-electron microscopy, BMC Biol., 2020.11. |
