Publications

Original papers

  1. Seo K, Okada K, Ichihashi N.*
    Mutagenic effect of ultraviolet radiation and trimethyl psoralen in Mycoplasma towards minimal genome.
    Genes Genet Syst. 99, 24-00061 (2024)
  2. Sugii, S.+, Hagino, K.+, Mizuuchi, R., Ichihashi, N.* (+ equally contributed)
    Cell-Free Expression of RuBisCO for ATP Production in the Synthetic Cells
    Synthetic Biology 8, ysad016 (2023) PDF
  3. Ueda, K., Mizuuchi, R.*, Ichihashi, N.*
    Emergence of linkage between cooperative RNA replicators encoding replication and metabolic enzymes through experimental evolution
    PLOS Genetics 19, e1010471 (2023) PDF
  4. Mizuuchi, R.*, Ichihashi, N.
    Minimal RNA self-reproduction discovered from a random pool of oligomers
    Chemical Science, 14, 7656-7664 (2023)
  5. Seo, K., Ichihashi, N.*
    Investigation of Compatibility between DNA Replication, Transcription, and Translation for in Vitro Central Dogma
    ACS Synthetic Biology, 12, 1813–1822 (2023)
  6. Hagino, K., Ichihashi, N.*
    In vitro transcription/translation-coupled DNA replication through partial regeneration of 20 aminoacyl-tRNA synthetases
    ACS Synthetic Biology, 12, 1252–1263 (2023) Full text
  7. Kamiura, R., Mizuuchi, R., Ichihashi, N.*
    Plausible pathway for a host-parasite molecular replication network to increase its complexity through Darwinian evolution
    Plos Computational Biology, 18, e1010709 (2022) PDF
  8. Ohta, K., Shimizu, T., Oshima, T., Ichihashi, N.*
    Genetic analysis of Bacillus subtilis stable L-forms obtained via long-term cultivation
    The Journal of General and Applied Microbiology, 69, 45-52 (2023) PDF
  9. Maeda, Y., Mizuuchi, R., Shigenobu, S., Shibai, A., Kotani, H., Furusawa, C., Ichihashi, N.*
    Experimental evidence for the correlation between RNA structural fluctuations and the frequency of beneficial mutations
    RNA, 28, 1659-1667 (2022)
  10. Miyachi, R., Shimizu, Y., Ichihashi, N.*
    Transfer RNA Synthesis-Coupled Translation and DNA Replication in a Reconstituted Transcription/Translation System
    ACS Synthetic Biology, 11, 2791–2799 (2022) Full text
  11. Mizuuchi, R.*, Furubayashi, T., Ichihashi, N.* (*co-corresponding)
    Evolutionary transition from a single RNA replicator to a multiple replicator network
    Nature Communications, 13, 1460 (2022) PDF
  12. Yukawa, K., Mizuuchi, R., Ichihashi, N.*
    Relaxed Substrate Specificity in Qβ Replicase through Long-Term In Vitro Evolution
    Life, 12(1), 32 (2021) PDF
  13. Okauchi, H., Ichihashi, N.*
    Continuous cell-free replication and evolution of artificial genomic DNA in a compartmentalized gene expression system
    ACS Synthetic Biology, 10, 3507–3517 (2021)
  14. Tsuji, G.*, Sunami, T., Oki, M., Ichihashi, N.
    Exchange of Proteins in Liposomes through Streptolysin O Pores.
    ChemBioChem 22, 1966-1973 (2021)
  15. Mizuuchi, R.*, Ichihashi, N.
    Translation-coupled RNA replication and parasitic replicators in membrane-free compartments
    Chemical communications, 56, 13453-13456 (2020)
  16. Furubayashi, T., Ueda, K., Bansho, Y., Motooka, D., Nakamura, S., Mizuuchi, R., Ichihashi, N.*
    Emergence and diversification of a host-parasite RNA ecosystem through Darwinian evolution
    eLIFE 9:e56038 (2020) PDF
  17. Okauchi, H., Sakatani,Y., Ohtsuka, K., Ichihashi, N.*
    Minimization of elements for isothermal DNA replication by an evolutionary approach
    ACS Synthetic Biology 9, 1771?1780 (2020)
  18. Mizuuchi, R., Usui, K., Ichihashi, N.*
    Structural transition of replicable RNAs during in vitro evolution with Qβ replicase
    RNA 26, 83-90 (2020).
  19. Sakatani,Y., Mizuuchi, R., Ichihashi, N.*
    In vitro evolution of phi29 DNA polymerases through compartmentalized gene expression and rolling-circle replication
    Protein Engineering Design and Selection, 32, 481?487 (2019)
  20. Ohta, K., Ichihashi, N.*
    Liposome fragment-mediated introduction of multiple plasmids into Bacillus subtilis
    Biochemistry and Biophysics Reports, 18, 100646 (2019).
  21. Kamiura, R., Matsuda, F., Ichihashi, N.*
    Survival of membrane-damaged Escherichia coli in a cytosol-mimicking solution
    J Biosci Bioeng, 128, 558-563 (2019).
  22. Ueda, K., Mizuuchi, R., Matsuda, F., Ichihashi, N.*
    A fusion method to develop an expanded artificial genomic RNA replicable by Qβ replicase
    Chembiochem, 20, 2331-2335 (2019).
  23. Sakatani, Y., Yomo, T., Ichihashi, N.
    Self-replication of circular DNA by a self-encoded DNA polymerase through rolling-circle replication and recombination.
    Sci Rep 8, 13089 (2018) PDF
  24. Mizuuchi, R. and Ichihashi, N.
    Sustainable replication and coevolution of cooperative RNAs in an artificial cell-like system.
    Nat Ecol Evol. 2 (10), 1654-1660 (2018) PDF
  25. Yoshiyama, T., Ichii, T., Yomo, T., Ichihashi, N.
    Automated in vitro evolution of a translation-coupled RNA replication system in a droplet flow reactor.
    Sci Rep 8, 11867. (2018) PDF
  26. Tsuji, G., Sunami, T., Ichihashi, N.
    Production of giant unilamellar vesicles by the water-in-oil emulsion-transfer method without high internal concentrations of sugars.
    J Biosci Bioeng. 126(4):540-545 (2018) PDF
  27. Furubayashi, T., Ichihashi, N.
    Sustainability of a compartmentalized host-parasite replicator system
    Life, 8(1), 3; doi: 10.3390/life8010003 (2018) PDF
  28. Murase, Y., Nakanishi, H., Tsuji, G., Sunami, S., Ichihashi, N.
    In vitro evolution of unmodified 16S rRNA for simple ribosome reconstitution
    ACS Synthetic Biology, 7, 576-583 (2018) PDF
  29. Tsuji, S., Ichihashi, N.
    Translation activity of chimeric ribosomes composed of Escherichia coli and Bacillus subtilis or Geobacillus stearothermophilus subunits
    Biochem Biophys Rep, 10, 325-328 (2017) PDF
  30. Yumura, M., Yamamoto, N., Yokoyama, K., Mori, H., Yomo, T., Ichihashi, N.
    Combinatorial selection for replicable RNA by Qβ replicase while maintaining encoded gene function
    Plos ONE, 12(3): e0174130 (2017) PDF
  31. Aita, T., Ichihashi, N., Yomo, T.
    Inference of fitness values and putative appearance time points for evolvable self-replicating molecules from time series of occurrence frequencies in an evolution reactor.
    J Theoretical Biol, 401, 38-42 (2016)
  32. Sunami, T., Ichihashi, N., Nishikawa, T., Kazuta, Y., Yomo, T.
    Effect of Liposome Size on Internal RNA Replication Coupled with Replicase Translation.
    ChemBioChem, 17, 1282-1289 (2016)
  33. Mizuuchi, R., Ichihashi, N.*, Yomo, T. (*corresponding)
    Adaptation and diversification of an RNA replication system under initiation- or termination-impaired translational conditions.
    ChemBioChem, 17, 1229-1232 (2016) PDF
  34. Bansho, Y., Furubayashi, T., Ichihashi, N.*, Yomo, T.* (*co-corresponding)
    Host-parasite oscillation dynamics and evolution in a compartmentalized RNA replication system.
    PNAS,113(5),4045-4050.(2016) PDF
  35. Furubayashi T, Nakano T, Eckford A, Okaie Y, Yomo T.(2016) Packet Fragmentation and Reassembly in Molecular Communication. IEEE Transactions on NanoBioscience ,(99),1-5.
  36. Taro Furubayashi, Tadashi Nakano, Andrew Eckford, Norikazu Ichihashi, Tetsuya Yomo.(2015) Packet Replication and Noise in Reliable End-to-end Molecular Communication. 9th EAI International Conference on Bio-inspired Information and Communications Technologies,1-2.
  37. Taro Furubayashi, Tadashi Nakano, Andrew Eckford, Tetsuya Yomo.(2015) Reliable End-to-end Molecular Communication with Packet Replication and Retransmission. 2015 IEEE Global Communications Conference (GLOBECOM),1-6.
  38. Tomita K, Ichihashi N, Yomo T.(2015) Replication of partial double-stranded RNAs by Qβ replicase. Biochem Biophys Res Commun,467(2),293-296.
  39. Yoshiyama T, Motohashi C, Ichihashi N, Ichii T, Yomo T.(2015) Maintenance of a translation-coupled RNA replication in dynamic micro-sized compartments under continuous stirring and flow. Chemical Engineering Journa,283(14015),896-902.
  40. Ichihashi N, Aita T, Motooka D, Nakamura S, Yomo T.(2015) Periodic pattern of genetic and fitness diversity during evolution of an artificial cell-like system. Molecular Biology and Evolution,32(12),3205-3214.
  41. Takako Awai, Norikazu Ichihashi,Tetsuya Yomo.(2015) Activities of 20 aminoacyl-tRNA synthetases expressed in a reconstituted translation system in Escherichia coli. Biochemistry and Biophysics Reports,3,140-143.
  42. Usui, K.*, Ichihashi, N.*, Yomo, T. (*equally contributed) (2015) A design principle for a single-stranded RNA genome that replicates with less double-strand formation. Nucleic Acids Research,43(16),8033-8043.
  43. Sakatani Y, Ichihashi N, Kazuta Y, Yomo T.(2015) A transcription and translation-coupled DNA replication system using rolling-circle replication. Scientific Reports,5,(10404),10.1038/srep10404,1-9.
  44. Kotaro Nishiyama, Norikazu Ichihashi, Yasuaki Kazuta, Tetsuya Yomo.(2015) Development of a reporter peptide that catalytically produces a fluorescent signal through α-complementation. Protein Science,24,(5),599-603.
  45. Ichihashi N, Kobori S, Yomo T.(2015) Simple identification of two causes of noise in an aptazyme system by monitoring cell-free transcription. Methods in Enzymology,550,93-107.
  46. Uno K, Sunami T, Ichihashi N, Kazuta Y, Matsuura T, Yomo T.(2014) The Evolutionary Enhancement of Genotype-Phenotype Linkages in the Presence of Multiple Copies of Genetic Material. Chembiochem,15(15),2281?2288.
  47. Ryo Mizuuchi,Norikazu Ichihashi,Kimihito Usui,Yasuaki Kazuta,and Tetsuya Yomo.(2014) Adaptive Evolution of an Artificial RNA Genome to a Reduced Ribosome . ACS Synthetic Biology,4(3),292-298.
  48. Yasuaki Kazuta,Tomoaki Matsuura,Norikazu Ichihashi,Tetsuya Yomo.(2014) Synthesis of milligram quantities of proteins using a reconstituted in vitro protein synthesis system. Journal of Bioscience and Bioengineering,118(5),554?557.
  49. Kimihito Usui, Norikazu Ichihashi, Yasuaki Kazuta, Tomoaki Matsuura, Tetsuya Yomo.(2014) Effects of ribosomes on the kinetics of Qb replication. FEBS Letters.,588(1),117-123.
  50. Takuyo Aita, Norikazu Ichihashia, Tetsuya Yomo. (2013) Probabilistic model based error correction in a set of various mutant sequences analyzed by next-generation sequencing. Computational Biology and Chemistry.,2013(47),221-230.
  51. Norikazu Ichihashi, Kimihito Usui, Yasuaki Kazuta, Takeshi Sunami, Tomoaki Matsuura, Tetsuya Yomo. (2013) Darwinian evolution in a translation-coupled RNA replication system within a cell-like compartment. Nature Communications.,4(2494),1-7.
  52. Kimihito Usui, Norikazu Ichihashi, Yasuaki Kazuta, Tomoaki Matsuura, Tetsuya Yomo.(2013) Kinetic model of double-stranded RNA formation during long RNA replication by Qβ replicase. FEBS Letters.,2013(587),2565-2571.
  53. Shungo Kobori, Norikazu Ichihashi, Yasuaki Kazuta, Tetsuya Yomo.(2013) A controllable gene expression system in liposomes that includes a positive feedback loop. Mol. BioSyst.,9(6),1282-1285.
  54. Kotaro Nishiyama, Norikazu Ichihashi, Tomoaki Matsuura, Yasuaki Kazuta, Tetsuya Yomo.(2012) α-Complementation in an artificial genome replication system in liposomes. Chembiochem. ,2012(13),2701-2706.
  55. Takehiro Nishikawa, Takeshi Sunami, TomoakiMatsuura, Tetsuya Yomo.(2012) Directed Evolution of Proteins through In Vitro Protein Synthesis in Liposomes. Journal of Nucleic Acids.,2012,1-11.
  56. Tomoaki Matsuura, Kazufumi Hosoda, Yasuaki Kazuta, Norikazu Ichihashi, Hiroaki Suzuki, Tetsuya Yomo.(2012) Effects of Compartment Size on the Kinetics of Intracompartmental Multimeric Protein Synthesis. ACS Synth. Biol.,2012(1),1431-1437.
  57. Shungo Kobori, Norikazu Ichihashi, Yasuaki Kazuta, Tomoaki Matsuura, Tetsuya Yomo.(2012) Kinetic analysis of aptazyme-regulated gene expression in a cell-free translation system:modeling of ligand-dependent and -independent expression. RNA.,18(8),1458-1465.
  58. Yohsuke Bansho, Norikazu Ichihashi, Yasuaki Kazuta, Tomoaki Matsuura, Hiroaki Suzuki, Tetsuya Yomo.(2012) Importance of parasite RNA species repression for prolonged translation-coupled RNA self-replication. Chemistry and Biology.,19(4),478-487.
  59. Takehiro Nishikawa, Takeshi Sunami, Tomoaki Matsuura, Norikazu Ichihashi, Tetsuya Yomo.(2012) Construction of Gene Screening System Using Giant Unilamellar Liposomes and Fluorescence Activated Cell Sorter. analytical chemistry 2012.,84,5017-5024.
  60. Tomoaki Matsuura, Kazufumi Hosoda, Norikazu Ichihashi, Yasuaki Kazuta, Tetsuya Yomo.(2011) Kinetic Analysis of -Galactosidase and -Glucuronidase Tetramerization Coupled with Protein Translation. Journal of Biological Chemistry.,286(25),22028-22034.
  61. Norikazu Ichihashi, Tomoaki Matsuura, Kazufumi Hosoda and Tetsuya Yomo.(2010) Identification of two forms of Qβ replicase with different thermal stabilities but identical RNA replication activity. The Journal of Biological Chemistry.,285(48), 37210-37217.
  62. Hiroya Urabe, Norikazu Ichihashi, Tomoaki Matsuura, Kazufumi Hosoda, Yasuaki Kazuta, Hiroshi Kita, Tetsuya Yomo.(2010) Compartmentalization in a water-in-oil emulsion repressed the spontaneous amplification of RNA by Qbeta replicase. Biochemistry, 49(9), 1809-1813.
  63. Kurokawa, K., Mizumura, H., Takaki, T., Ishii, Y., Ichihashi, N., Bok Luel Lee, Sekimizu, K. Rapid Exchange of Bound ADP on the Staphylococcus aureus Replication Initiation protein DnaA. Journal of Biological Chemistry, 284, 34201-10, (2009)
  64. Ichihashi, N., Matsuura, T., Kita, H., Hosoda, K., Sunami, T., Tsukada, K., and Yomo, T. (2008) Importance of translation-replication balance for efficient replication by the self-encoded replicase ChemBioChem, 9 (18),3023-3028.
  65. Kita, H., Matsuura, T., Sunami, T., Hosoda, K., Ichihashi, N., Tsukada, K., Urabe, I., and Yomo T. (2008) Replication of genetic information with self-encoded replicase in liposomes. ChemBioChem, 9 (15),2403-2410.
  66. Hosoda, K., Matsuura, T., Kita, H., Ichihashi, N., Tsukada, K., Urabe, I., and Yomo, T. (2008) A novel sequence-specific RNA quantification method using nicking endonuclease,dual-labeled fluorescent DNA probe, and conformation-interchangeable oligo-DNA. RNA,14,584-592.
  67. Hosoda, K., Matsuura, T., Kita, H., Ichihashi, N., Tsukada, K.,and Yomo, T. (2007) Kinetic analysis of the entire RNA amplification process by Qβreplicase.J. Biol. Chem., 282 (21),15516-15527.
  68. Murai, N., Kurokawa, K., Ichihashi, N., Matsuo, M., Sekimizu, K. Isolation of a temperature-sensitive dnaA mutant of Staphylococcus aureus. FEMS microbiology letters, 254, 19-26, (2006)
  69. Oku, Y., Kurokawa, K., Ichihashi, N., Sekimizu, K. Characterization of the Staphylococcus aureus mprF gene, involved in lysinylation of phosphatidylglycerol Microbiology 150, 45-51, (2004)
  70. Ichihashi, N., Kurokawa, K., Matsuo, M., Kaito, C., Sekimizu, K. Inhibitory effects of basic or neutral phospholipid on acidic phospholipid-mediated dissociation of adenine nucleotide bound to DnaA protein, the initiator of chromosomal DNA replication. Journal of Biological Chemistry, 278, 28778-28786, (2003)

    71. Reviews

  71. Seo, K., Hagino, K., *Ichihashi, N.
    Progresses in Cell-Free In Vitro Evolution.
    Advances in Biochemical Engineering/Biotechnology, Springer, Berlin, Heidelberg.
    https://doi.org/10.1007/10_2023_219 (2023)
  72. Yukawa, K., Mizuuchi, R., *Ichihashi, N.
    How prebiotic complexity increases through Darwinian evolution.
    Curr Opin Syst Biol, 34, 100456 (2023) PDF
  73. Furubayashi, T., Ichihashi, N.
    How evolution builds up complexity?: In vitro evolution approaches to witness complexification in artificial molecular replication systems
    Biophysics and Physicobiology, 19, e190005 (2022)
  74. Ichihashi, N.; Stano, P. 　
    Trends and Outlooks in Synthetic Biology; A Special Issue for Celebrating 10 Years of Life and Its Landmarks. 　
    Life 12, 181 (2022)
  75. Mizuuchi, R.*, Ichihashi, N.*
    Primitive Compartmentalization for the Sustainable Replication of Genetic Molecules.
    Life 11, 191(2021).
  76. 市橋伯一
    リボソームのin vitro進化技術の開発
    生物工学　2019年8月号 97巻　481-484(2019).
  77. Ichihashi, N.*
    What can we learn from the construction of in vitro replication systems?
    Ann N Y Acad Sci, 1447, 144-156 (2019).
  78. 市橋伯一 進化する人工細胞の構築と生命の起源 人工細胞の創製とその応用 　植田 充美 (監修), 第3章2節 シーエムシー出版 (2017)
  79. Ichihashi, N., and Yomo, T.
    Constructive approaches for understanding the origin of self-replication and evolution
    Life, 6(3), 26 (2016) PDF
  80. 市橋伯一、四方哲也　　 人工細胞モデルとダーウィン進化 生物工学　2015年　第10号　第93巻　7－10
  81. 市橋伯一　　 生命は如何に進化しうるのか‐合成生物学的アプローチ Journal of Japanese Society for Extremophiles 13, 59-62 (2014)
  82. Ichihashi N, Yomo T Positive roles of compartmentalization in internal reactions. Curr Opin Chem Biol. 22C 12-17 (2014)
  83. 市橋伯一、四方哲也　　 人工細胞のデザインと構築 高分子　2014年6月号 63巻　376-378
  84. 角南武志、市橋伯一、松浦友亮、鈴木宏明、四方哲也 リポソーム内で自己複製システムを創る 実験医学増刊 2011年29, 152-159,
  85. Ichihashi, N., Matsuura, T., Kita, H., Sunami, T., Suzuki, H., Yomo, T. Constructing partial models of cells. Cold Spring Harbor Perspective in Biology 2, a004945, 2010.
  86. 市橋伯一、四方哲也 人工細胞：生命を深く理解するために 科学 80, 740-742, 2010年
  87. 市橋伯一 進化する自己複製システムの構築にむけて 生物物理 50, 128-129, 2010年
  88. Ichihashi, N., Matsuura, T., Kita, H., Sunami, T., Suzuki, H., Yomo, T. Constructive approaches for the origin of life. A captor in “Genesis - in the Beginning: Precursors of Life, Chemical Models and Early Biological Evolution.” J. Seckbach Ed., Springer, 2012
  89. Matsuura, T., Ichihashi, N., Sunami, T., Kita, H., Suzuki, H., Yomo, T. Evolvability and Self-Replication of Genetic Information in Liposomes A captor in “The Minimal Cell : The Biophysics of Cell Compartment and the Origin of Cell Functionality” Springer, 2010