研究実績

  • 研究概要 / Research Interest

生命の起源に関する諸問題の中でも大きな謎の一つが、どのようにして生命が機能性のポリマーを利用するようになったかという点である。タンパク質とRNAというアミノ酸と核酸ベースの高分子がエネルギーの非平衡状態の中でどのような化学進化の過程で作られ、維持されるようになったのか、またそれらの機能、進化、遺伝性を理解することが重要である。過去には翻訳系に関わるアミノ酸のキャリアであるtRNA分子の進化に着目した研究を行ってきたが、現在は主に宇宙生物学における「生命の起源」問題を中心に扱っている。特に合成生物学的な手法を用いて、過去にありえた分子を試験管内で合成し、ハイスループットにその機能と進化実験を行っている。また地球化学の研究者達とともに、原始地球を想定した環境や氷衛星などの地球外環境において生命につながるような化学進化が進むのかを様々な分析法を用いて調べている。長期的な目標として生命システムに至るより普遍的で確からしいシナリオを描くことを目指している。

One of the great mysteries among the questions concerning the origin of life is how life came to utilize functional polymers. It is important to understand how amino acid-based and nucleic acid-based macromolecules, proteins and RNAs, were created and maintained through chemical evolution in a non-equilibrium system, as well as their functionality, evolvability, and heredity. Currently, we are using various synthetic biology and analytical chemistry methods to reconstruct and analyze the properties of primitive proteins, RNAs and their precursors through in vitro evolution experiments. We are also working with geochemists to experimentally investigate in which primitive terrestrial and extraterrestrial environments are favorable for producing active functional polymers. Our long-term goal is to develop a more universal and plausible scenario for the emergence of life-like systems.


Projects

  • 合成生物学を用いたde novo及び原始的タンパク質の合成と機能解析
  • 地球及び他天体環境における化学進化実験
  • 地球外生命探査に向けた超高速衝突実験と有機物分析
  • 極限環境微生物の分離同定と耐性能の評価
  • CO2固定酵素のスクリーニングと機能強化
  • 初期の翻訳系の再構築に向けた関連分子の解析
  • Synthesis and functional analysis of de novo and proteins using synthetic biology
  • Chemical evolution experiments on Earth and other extraterrestrial environments
  • Understanding the function of RNA and proteins in the primodial stages of translation machienary
  • Hypervelocity impact experiments and analysis of organic matters for future biosignature detection platform
  • Isolation and identification of microorganisms in extreme environments
  • Screening and engineering of CO2-fixing enzymes

発表論文 / Publication

Google scholar: https://scholar.google.com/citations?user=uTg9qxEAAAAJ&hl=ja

Researchgate: https://www.researchgate.net/profile/Kosuke_Fujishima

Vyacheslav Tretyachenko, Jiri Vymetal, Tereza Neuwirthova, Jiri Vondrasek, Kosuke Fujishima, Klara Hlouchova Structured proteins are abundant in unevolved sequence space. bioRxiv, submitted

Valerio G Giacobelli, Kosuke Fujishima, Martin Lepšík, Vyacheslav Tretyachenko, Tereza Kadavá, Lucie Bednárová, Petr Novák, Klára Hlouchová. In vitro evolution reveals primordial RNA-protein interaction mediated by metal cations. bioRxiv, submitted

Galinanes Reyes SL, Kuruma Y, Fujimi M, Yamazaki M, Eto S, Nishikawa S, Tamaki S, Kobayashi A, Mizuuchi R, Rothschild LJ, Ditzler M, Fujishima K. PURE mRNA display and cDNA display provide rapid detection of consensus binding motif via high-throughput sequencing. Biotechnol Bioeng, 118(4):1736-1749. (2021)

Tretyachenko V, Voráček V, Souček R, Fujishima K, Hlouchová K. CoLiDe: Combinatorial Library Design tool for probing protein sequence space. Bioinformatics, Sep 21:btaa804. (2020)

Jia TZ, 藤島 皓介, 丹羽 達也, 液-液相分離と生命の起源. 生物工学会誌 第98巻 第5号 228–254(2020)

Wang P, Fujishima K, Berhanu S, Kuruma Y, Jia T, Khusnutdinova AN, Yakunin AF, and McGlynn SE. A bi-functional polyphosphate kinase driving NTP regeneration and reconstituted cell-free protein synthesis. ACS Synbio, 9 (1), 36-42. (2020)

Takahagi W, Seo K, Shibuya T, Takano Y, Fujishima K, Saitoh M, Shimamura S, Matsui Y, Tomita M and Takai K. Peptide synthesis under the alkaline hydrothermal conditions on Enceladus. ACS Earth Space Chem, 3, 11, 2559-2568. (2019)

Urbina J, Patil A, Fujishima K, Paulino-Lima IG, Saltikov C, Rothschild LJ. A new approach to biomining: Bioengineering surfaces for metal recovery from aqueous solutions. Sci Rep. 9(1), 16422. (2019)

Fujishima, K., Dziomba, S, Yano H, Kebe SI, Guerrouache M, Carbonnier B, and Rothschild, LJ. The non-destructive separation of diverse astrobiologically relevant organic molecules by customizable capillary zone electrophoresis and monolithic capillary electrochromatography. Int J Astrobiol, 18, 6, 562-574. (2019)

Vecchioni S, Capece MC, Toomey E, Nguyen L, Ray A, Greenberg A, Fujishima K, Urbina J, Paulino-Lima IG, Pinheiro V, Shih J, Wessel G, Wind SJ, Rothschild LJ. Construction and characterization of metal ion-containing DNA nanowires for synthetic biology and nanotechnology. Sci Rep, 9(1), 6942. (2019)

Fujishima, K., Wang, K. M., Palmer, J. A., Abe, N., Nakahigashi, K., Endy, D., and Rothschild, L. J. Reconstruction of cysteine biosynthesis using engineered cysteine-free enzymes. Sci Rep, 8(1), 1776. (2018)

Kaneta A, Fujishima K, Morikazu W, Hori H, Hirata A. The RNA-splicing endonuclease from the euryarchaeaon Methanopyrus kandleri is a heterotetramer with constrained substrate specificity. Nucleic Acids Res. 46(4):1958-1972. (2018)

Froese, T., Campos, J. I., Fujishima, K., Kiga, D., and Virgo, N. Horizontal transfer of code fragments between protocells can explain the origins of the genetic code without vertical descent. Sci Rep, 8(1), 457. (2018)

Kitadai N., Kameya M. and Fujishima K. Origin of the Reductive Tricarboxylic Acid (rTCA) Cycle-Type CO2 Fixation: A Perspective. Life, 7(4), 39. (2017)

Matsubara T., Fujishima K, Saltikov CW., Nakamura S. and Rothschild LJ. Earth analogs for past and future life on Mars: Isolation of perchlorate resistant halophiles from Big Soda Lake. Int J Astrobiology, 1-11. (2016)

Paulino-Lima IG., Fujishima K., Navarrete JU, Galante D, Rodrigues F, Azua-Bustos A. and Rothschild LJ. Extremely high UV-C radiation resistant microorganisms from desert environments with different manganese concentrations. J Photochem Photobiol B, 163:327-36. (2016)

Holm Hansen AC., Paulino-Lima IG., Fujishima K., Rothschild LJ. and Jensen PR. Draft Genome Sequence of Hymenobacter sp. Strain AT01-02, Isolated from a Surface Soil Sample in the Atacama Desert, Chile. Genome Announc, 4(1) e01701-15. (2016)

Fujishima K., Venter C., Wang K., Ferreira R, and Rothschild LJ. An overhang-based exon shuffling method for creating a customized random DNA library. Sci Rep, 5: 9740. (2015)

Ikeda KT., Hirose Y., Hiraoka K, Noro E., Fujishima K., Tomita M. and Kanai A. Identification, expression, and molecular evolution of microRNAs in the "living fossil" Triops cancriformis (tadpole shrimp). RNA, 21(2):230-242. (2015)

Hirata A, Fujishima K, Yamagami R, Kawamura T, Banfield JF, Kanai A. and Hori H. X-ray structure of the fourth type of archaeal tRNA splicing endonuclease: insights into the evolution of a novel three-unit composition and a unique loop involved in broad substrate specificity Nucleic Acids Res, 40(20):10554-66. (2012)

Sugahara J., Fujishima K., Nunoura T., Takaki Y., Takami H., Takai K., Tomita M. and Kanai A. Genomic Heterogeneity in a Natural Archaeal Population Suggests a Model of tRNA Gene Disruption. PLoS ONE, 7(3):e32504. (2012)

Hamashima K., Fujishima K., Masuda T., Sugahara J., Tomita M. and Kanai A. Nematode-specific tRNAs that decode an alternative genetic code for leucine. Nucleic Acids Res, 40(8):3653-62 (2011)

Murakami S., Fujishima K., Tomita M. and Kanai A. Metatranscriptomic analysis of microbes in an ocean-front deep subsurface hot spring reveals novel small RNAs and type-specific tRNA degradation. Appl Environ Microbiol, 78(4):1015-1022 (2011)

Fujishima K., Sugahara J., Miller CS., Baker BJ., Di Giulio M., Takesue K., Sato A., Tomita M., Banfield JF. and Kanai A. A novel three-unit tRNA splicing endonuclease found in ultrasmall Archaea possesses broad substrate specificity. Nucleic Acids Res, 39(22):9695-704 (2011)

Fujishima K., Sugahara J., Tomita M. and Kanai A. Large-scale tRNA intron transposition in the archaeal order Thermoproteales represents a novel mechanism of intron gain. Mol Biol Evol, 27(10):2233-43 (2010)

Takane K., Fujishima K., Watanabe Y., Sato A., Saito N., Tomita M. and Kanai A. Computational prediction and experimental validation of evolutionarily conserved microRNA target genes in bilaterian animals. BMC Genomics, 11(1):101 (2010)

Kitamura S., Fujishima K., Sato A., Tsuchiya D., Tomita M. and Kanai A. Characterization of RNase HII substrate recognition using RNase HII-Argonaute chimeric enzymes from Pyrococcus furiosus. _Biochem J, 426(3):337-44 (2010)

Fujishima K., Sugahara J., Kikuta K., Hirano R., Sato A., Tomita M. and Kanai A. Tri-split tRNA is a transfer RNA made from three transcripts that provides insight into the evolution of fragmented tRNAs in archaea. Proc Natl Acad Sci U S A, 106(8):2683-7 (2009).

Sugahara J., Fujishima K., Morita K., Tomita M. and Kanai A. Disrupted tRNA gene diversity and possible evolutionary scenarios. J Mol Evol, 69(5):497-504 (2009)

Fujishima K., Sugahara J., Tomita M. and Kanai A. Sequence Evidence in the Archaeal Genomes that tRNAs Emerged Through the Combination of Ancestral Genes as 5' and 3' tRNA Halves. PLoS ONE, 25(12):2709-16 (2008)

Sugahara J., Kikuta K., Fujishima K., Yachie N., Tomita M. and Kanai A. Comprehensive analysis of archaeal tRNA genes reveals rapid increase of tRNA introns in the order thermoproteales. Mol Biol Evol, 25(12):2709-16 (2008)

Fujishima K., Komasa M., Kitamura S., Tomita M. and Kanai A. Comparison and characterization of proteomes in the three domains of life using 2D correlation analysis. Progress of Theoretical Physics Supplement, 173:206-18 (2008)

Fujishima K., Komasa M., Kitamura S., Suzuki H., Tomita M. and Kanai A. Proteome-wide prediction of novel DNA/RNA-binding proteins using amino acid composition and periodicity in the hyperthermophilic archaeon Pyrococcus furiosus. DNA Res, 14(3):91-102 (2007)

Review

Fujishima K and Kanai A. tRNA gene diversity in the three domains of life. Front Genet, (5):142. (2014)

Fujishima K and Kanai A. Split Gene. Brenner’s Encyclopedia of Genetics, 2nd edition, 543-544. (2013)

Book

連載:新分野創造「シンセティック・アストロバイオロジー」 細胞工学,学研メディカル秀潤社

第1回「アストロバイオ×合成生物学」 Vol.34 No.2 (2015)

第2回「火星移住と合成生物学(前編)」Vol.34 No.4 (2015)

第3回「火星移住と合成生物学(後編)」Vol.34 No.7 (2015)

第4回「第二の生命と合成生物学(前編)」Vol.34 No.12 (2015)

第5回「第二の生命と合成生物学(後編)」Vol.35 No.1 (2016)

第6回「生命の起源と合成生物学」Vol.35 No.3 (2016)

おもろいバイオロジー第8回 拝啓,未来のアストロバイオロジストへ 細胞工学 Vol.32 No.12 (2013),学研メディカル秀潤社

Fujishima K, Sugahara J, Kanai A. 三つの遺伝子に断片化したtRNAの発見. 生化学 Vol.82(7):606-12 (2010), 日本生化学会