Publications

Reprints of many of the following papers are available upon request to Hideaki Shiraishi.
  1. Shiraishi, H., Sasase, M. and Nakashima, A. S. (2024). Helicoid morphology of Arthrospira platensis NIES-39 confers temperature compensation in the longitudinal movement velocity of its trichomes. Phycology, 4, 104–116. (full copy)
  2. 白石英秋 (2023). 光を利用したゲノム解読技術：光合成による有用物質生産の基盤．光アライアンス（日本工業出版）, 34(8), 30-34．
  3. Shiraishi, H. and Nishida, H. (2023). Complete genome sequence of the edible filamentous cyanobacterium Arthrospira platensis NIES-39 based on long-read sequencing. Microbiol. Resour. Announc. 12, e0113922 [PubMed] [Full copy]
  4. Shiraishi, H. and Toyoda, A. (2021). The use of a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide-based colorimetric assay in the viability analysis of the filamentous cyanobacterium Arthrospira platensis. Biosci. Biotechnol. Biochem, 85, 739-742. [PubMed]
  5. Tadama, S. and Shiraishi, H. (2017). Growth of the edible microalga Arthrospira platensis in relation to boron supply. Int. J. GEOMATE, 30, 90-95.
    [Full copy]
  6. Shiraishi, H. (2016). Cryopreservation of the edible alkalophilic cyanobacterium Arthrospira platensis. Biosci. Biotechnol. Biochem. 80, 2051-2057. [PubMed]
  7. Tadama, S. and Shiraishi, H. (2016). Growth of the edible alkalophilic alga Arthrospira platensis in relation to boron supply. In Hossain, Z. (ed), "Science, Engineering and Environment" (conference proceedings; The GEOMATE International Society, Tsu, Japan; ISBN 978-4-9905958-7-6 C3051). pp. 65-70.
  8. Shiraishi, H. (2015). Association of heterotrophic bacteria with aggregated Arthrospira platensis exopolysaccharides: implications in the induction of axenic cultures. Biosci. Biotechnol. Biochem., 79, 331-341. [PubMed]
  9. Shiraishi, H. and Tabuse, Y. (2013). The AplI restriction-modification system in an edible cyanobacterium, Arthrospira (Spirulina) platensis NIES-39, recognizes the nucleotide sequence 5’-CTGCAG-3’. Biosci. Biotechnol. Biochem., 77, 782-788.[PubMed][Free Full Text]
  10. Shiraishi, H. (2008). Hatching enzyme of Volvox: a possible implication in the evolution of multicellularity. J. Biochem. Tech. 1, 21-22.
  11. Fukada, K., Inoue, T. and Shiraishi, H. (2006). A post-translationally regulated protease, VheA, is involved in the liberation of juveniles from parental spheroids in Volvox carteri. Plant Cell, 18, 2554-2566. [PubMed]
  12. Aono, N., Inoue, T. and Shiraishi, H. (2005). Genes specifically expressed in sexually differentiated female spheroids of Volvox carteri. J. Biochem. (Tokyo), 138 (4), 375-382. [PubMed]
  13. Shiraishi, H. (2005). Roles of non-coding RNA in gene expression. J. Plant Res., 118 (Suppl.), 31.
  14. 白石英秋（2004）. Non-coding RNA: 遺伝子発現と進化. 蛋白質 核酸 酵素, 49, 2510-2520.
  15. Shiraishi, H. (2004). Two-dimensional fractionation of complex mixuture of oligonucleotides in microRNA size range. Nucleic Acids Res. Suppl. 48, 293-294.
  16. Yoshioka W, Ikawa Y, Jaeger L, Shiraishi H, Inoue T. (2004). Generation of a catalytic module on a self-folding RNA. RNA, 10,1900-1906.
  17. Ohuchi, S.J., Ikawa, Y., Shiraishi, H. and Inoue T. (2004). Artificial modules for enhancing rate constants of a group I intron ribozyme without a P4-P6 core element. J. Biol. Chem. 279, 540-546.
  18. Atsumi, S., Ikawa, Y., Shiraishi, H. and Inoue, T. (2003). Selections for constituting new RNA-protein interactions in catalytic RNP. Nucleic Acids. Res. 31, 661-669.
  19. Aono, N., Shimizu, T., Inoue, T. and Shiraishi, H. (2002). Palindromic repetitive elements in the mitochondrial genome of Volvox. FEBS Letters, 521, 95-99. [PubMed]
  20. Shimizu, T., Inoue, T. and Shiraishi, H. (2002). Cloning and characterization of novel extensin-like cDNAs that are expressed during late somatic phase in the green alga Volvox carteri. Gene, 284, 179-187. [PubMed]
  21. Ohki, Y., Ikawa, Y., Shiraishi, H. and Inoue, T. (2002). Role of a conserved J8/7 X P4 base-triple in the Tetrahymena ribozyme. J. Biochem. (Tokyo), 132, 713-718.
  22. Ohuchi, S. J., Ikawa, Y., Shiraishi, H. and Inoue, T. (2002). Modular engineering of a group I intron ribozyme. Nucleic Acids Res., 30, 3473-3480.
  23. Ikawa, Y., Fukada, K., Watanabe, S., Shiraishi H. and Inoue T. (2002). Design, construction and analysis of a novel class of self-folding RNA. Structure, 10, 527-534.
  24. Oe, Y., Ikawa, Y., Shiraishi, H. and Inoue, T. (2002). The relationship between the self-splicing activity and the solidity of the master domain of the Tetrahymena group I ribozyme. Biochem. Biophys. Res. Commun., 291, 1225-1231.
  25. Shimizu, T., Inoue, T. and Shiraishi, H. (2001). A senescence-associated S-like RNase in the multicellular green alga Volvox carteri. Gene, 274, 227-235. [PubMed]
  26. Ohki, Y.,Ikawa, Y., Shiraishi, H. and Inoue, T. (2001). A deteriorated triple-helical scaffold accelerates formation of the Tetrahymena ribozyme active-structure, FEBS Lettes, 493, 95-100.
  27. Ikawa, Y., Yoshioka, W., Ohki, Y., Shiraishi, H. and Inoue, T. (2001). Self-splicing of the Tetrahymena group I ribozyme without conserved base-triples. Genes to Cells, 6, 411-20.
  28. Oe, Y., Ikawa, Y., Shiraishi, H. and Inoue, T. (2001). Conserved base-pairings between C266-A268 and U307-G309 in the P7 of the Tetrahymena ribozyme is nonessential for the in vitro self-splicing reaction. Biochem Biophys Res Commun. 284, 948-54.
  29. Ikawa, Y., Nohmi, K., Atsumi, S., Shiraishi, H. and Inoue, T. (2001). A comparative study on two GNRA-tetraloop receptors: 11-nt and IC3 motifs. J. Biochem. (Tokyo), 130, 251-255.
  30. Atsumi, S., Ikawa, Y., Shiraishi, H. and Inoue, T. (2001). Design and development of a catalytic ribonucleoprotein. EMBO J. 20, 5453-5460.
  31. Ohuchi, SJ., Ikawa, Y., Shiraishi, H. & Inoue, T. (2001) . A simulated molecular evolution from minimal catalytic domain of a group I ribozyme. Nucleic Acids Res.,Supplment, 1. 125-126.
  32. Ikawa, Y., Shiraishi H. and Inoue, T. (2000). Characterization of P8 and J8/7 elements in the conserved core of the Tetrahymena group I intron ribozyme. Biochem Biophys Res Commun. 267, 85-90.
  33. Naito, Y., Shiraishi, H. and Inoue, T. (2000). Requirements for alternative forms of the activator domain, P5abc, in the Tetrahymena ribozyme. FEBS Letters. 466, 273-278.
  34. Ikawa, Y., Shiraishi, H. and Inoue, T. (2000). A small structural element, Pc-J5/5a, plays dual roles in a group IC1 intron RNA. Biochem. Biophys. Res. Comm. 274, 259-265.
  35. Ikawa ,Y., Naito, D., Shiraishi, H. and Inoue, T. (2000). Structure-function relationships of two closely related group IC3 intron ribozymes from Azoarcus and Synechococcus pre-tRNA. Nucleic Acids Res. 28, 3267-3277.
  36. Ikawa, Y., Shiraishi, H. and Inoue, T. (2000). Minimal catalytic domain of a group I self-splicing intron RNA. Nature struct. biol., 7, 1032-1035.
  37. Oe, Y., Ikawa,Y., Shiraishi, H. and Inoue, T. (2000). Analysis of the P7 region within the catalytic core of the Tetrahymena ribozyme by employing in vitro selection. Nucleic Acids Symp. Series, 44, 197-198.
  38. Ikawa, Y., Shiraishi, H. and Inoue, T. (1999). Trans-activation of the Tetrahymena group I intron ribozyme via a non-native RNA-RNA interaction. Nucleic Acids Res. 27, 1650-1655.
  39. Ikawa, Y., Naito, D., Aono, N., Shiraishi, H. and Inoue, T. (1999). A conserved motif in group IC3 introns is a new class of GNRA receptor. Nucleic Acids Res. 27, 1859-1865.
  40. Naito, Y., Shiraishi, H. and Inoue, T. (1998). P5abc of the Tetrahymena ribozyme consists of three functional independent elements. RNA, 4 , 837-846.
  41. Ikawa, Y., Shiraishi, H. and Inoue, T. (1998). Trans-activation of the Tetrahymena group I intron ribozyme by its P2-2.1 domains. J. Biochem. (Tokyo), 123, 528-533.
  42. Ikawa, Y, Ohta, H., Shiraishi, H. and Inoue, T. (1997). Long-range interaction between the P2.1 and P9.1 peripheral domains of the Tetrahymena ribozyme. Nucleic Acids Res. 25, 1761-1765.
  43. Ikawa, Y., Shiraishi, H. and Inoue, T. (1997). Identification of the nucleotides in the A-rich bulge of the Tetrahymena ribozyme responsible for an efficient self-splicing reaction. J. Biochem. (Tokyo), 122, 878-882.
  44. Ikawa, Y., Shiraishi, H. and Inoue, T. (1996). Characterization of the newly constructed domains that replace P5abc within the Tetrahymena ribozyme. FEBS Letters 394, 5-8.
  45. Shiraishi, H. and Shimura, Y. (1996). Genetic analysis of the structure and function of RNase P from E. coli. Mol. Biol. Rep. 22, 111-114.
  46. Ikawa, Y, Naito, Y., Shiraishi, H. and Inoue, T. (1996). Structure, function and molecular evolution of group I intron ribozyme. Nucleic Acids Symp. Series, 35, 195-196.
  47. Ikawa, Y., Shiraishi, H. and Inoue, T. (1995). The Tetrahymena ribozyme tolerates diverse activator-domains that replace P5abc. In Go, M. and Schimmel, P. (eds), "Tracing Biological Evolution in Protein and Gene Structures" pp.115-123 (Elsevier, Amsterdam) .
  48. Okamoto, H., Yano, A., Shiraishi, H., Okada, K. and Shimura, Y. (1994). Genetic complementation of apetala3 mutant with an Arabidopsis thaliana gene homologous to DEFICIENCE of Antirrhinum majus. Plant Mol. Biol. 26, 465-472.
  49. Itoh, T., Shiraishi, H., Okada, K. and Shimura, Y. (1994). Two amidophosphoribosyl-transferase genes of Arabidopsis thaliana expressed in different organs. Plant Mol. Biol. 26, 529-533.
  50. Kinoshita, T., Hara-Nishimura, I., Siraishi, H., Okada, K., Shimura, Y. and Nishimura, M. (1994). Nucleotide sequences of a transmembrane protein (TMP-C) cDNA in Arabidopsis thaliana. Plant Physiol. 105, 1441-1442.
  51. Shiraishi, H., Okada, K. and Shimura, Y. (1993). Nucleotide sequences recognized by the AGAMOUS MADS domain of Arabidopsis thaliana in vitro. Plant J., 4, 385-398. [Pubmed]
  52. Nishida, I., Tasaka, Y., Shiraishi, H. and Murata., N. (1993). The gene and the RNA for the precursor to the plastid-located glycerol-3-phosphate acyltransferase of Arabidopsis haliana. Plant. Mol. Biol., 21, 267-277.
  53. Sakamoto, K., Shiraishi, H., Okada, K. and Shimura, Y. (1993). Proteins induced by physical stimuli in root-tips of Arabidopsis thaliana seedlings. Plant Cell Physiol., 34, 297-304.
  54. Akama, K., Shiraishi, H., Ohta, S., Nakamura, K., Okada, K. and Shimura, Y. (1992). Efficient transformation using hypocotyl explants of Arabidopsis thaliana: comparison of the efficiencies with various organs, plant ecotypes and Agrobacterium strains. Plant Cell Reports, 7, 7-12.
  55. Kawata, T., Imada, T., Shiraishi, H., Okada, K. Shimura, Y. and Iwabuchi, M. (1992). A cDNA clone encoding HBP1-b homologue in Arabidopsis thaliana. Nucleic Acids Res. 20, 1141.
  56. 白石英秋．花の器官発生を制御する遺伝子．細胞（ニュー・サイエンス社）, 24, 160-164 (1992)
  57. 白石英秋．花の器官形成の遺伝的制御．Plant Science Tomorrow No.6 (Plant Science Tomorrow 刊行会, pp. 6-7 (1992).
  58. 白石英秋, 岡田清孝, 志村令郎．アラビドプシスとその変異体．植物バイオテクノロジーII（山田康之, 岡田吉美 編, 現代化学増刊 20, 東京化学同人）, pp. 181-187 (1991).
  59. Nishida, I., Tasaka, Y., Shiraishi, H., Okada, K., Shimura, Y., Beppu, T. and Murata, N. (1990). The genomic gene and cDNA for the plastidial glycerol-3-phosphate acyltransferase of Arabidopsis. In Quinn,P.J., Harwood,J.L. (eds) Plant Lipid Biochemistry, Structure and Utilization (Portland Press, London), pp. 462-464.
  60. Shiraishi, H. and Shimura, Y. (1990). Random introduction of localized single nucleotide substitutions into cloned DNA. DNA and Protein Engineering Techniques, 2, 43-45.
  61. Shimura, Y. and Shiraishi, H. (1990). Genetics of transfer RNA processing in Escherichia coli. Methods Enzymol. 181, 395-400.
  62. Okada, K.,Komaki, M. M.,Shiraishi, H.,Shimura, Y. (1989). Mutational Analyses of Flower Development of Arabidopsis thaliana. J. Cell Biochem. suppl. 285.
  63. Shiraishi, H. and Shimura, Y. (1988). Functional domains of the RNA component of ribonuclease P revealed by chemical probing of mutant RNAs. EMBO J. 7, 3817-3821.
  64. Shiraishi, H. and Shimura, Y. (1988). A rapid and efficient method for targeted random mutagenesis. Gene, 64, 313-319.
  65. Shiraishi, H. and Shimura, Y. (1988). Higher-order structures and functional domains of the RNA component of ribonuclease P from Eschericha coli. Nucleic Acids Symposium Series 20, 139.
  66. 白石英秋，志村令郎．tRNAの生合成およびプロセシング．細胞工学（秀潤社）, 5, 238-249 (1986)．
  67. Shiraishi, H. and Shimura, Y. (1986). Mutations affecting two distinct functions of the RNA component of RNase P. EMBO J. 5, 3673-3679.
  68. Shimura, Y., Shiraishi, H. and Sakamoto, H. (1986). Aspects of RNA catalysis in RNA processing. Adv. Biophys. 21, 239-254.

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