- Fujishima, Kosuke
- Research Scientist
Main Publication List and Awards
26. Fujishima K., Wang, K. M., Palmer, J. A., Abe, N., Nakahigashi, K., Endy, D., and Rothschild, L. J. (2018). Reconstruction of cysteine biosynthesis using engineered cysteine-free enzymes. Sci Rep, 8(1), 1776.
25. Froese T., Campos IJ., Fujishima K., Kiga, D., and Virgo N. (2018). Horizontal transfer of code fragments between protocells can explain the origins of the genetic code without vertical descent. Sci Rep, 8(1), 457.
24. Kaneta A., Fujishima, K., Morikazu, W., Hori, H., and Hirata, A. (2018). The RNA-splicing endonuclease from the euryarchaeaon Methanopyrus kandleri is a heterotetramer with constrained substrate specificity. Nucleic Acids Res, 46(4) 1958-1972.
23. Kitadai, N., Kameya, M., and Fujishima K. (2017). Origin of the Reductive Tricarboxylic Acid (rTCA) Cycle-Type CO2 Fixation: A Perspective. Life, 7(4), 39.
22. Matsubara T, Fujishima K, Saltikov CW, Nakamura S, 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)
21.Paulino-Lima IG, Fujishima K, Navarrete JU, Galante D, Rodrigues F, Azua-Bustos A, Rothschild LJ. Extremely high UV-C radiation resistant microorganisms from desert environments with different manganese concentrations. J Photochem Photobiol B, 163:327-36. (2016)
20. Holm Hansen AC, Paulino-Lima IG, Fujishima K, Rothschild LJ, 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)
19. Fujishima K., Venter C., Wang K., Ferreira R. and Rothschild L. An overhang-based exon shuffling method for creating a customized random DNA library. Sci Rep, 5: 9740. (2015)
18. Ikeda KT, Hirose Y, Hiraoka K, Noro E, Fujishima K, Tomita M, Kanai A. Identification, expression, and molecular evolution of microRNAs in the "living fossil" Triops cancriformis (tadpole shrimp). RNA, 21(2):230-242. (2015)
17. Fujishima K and Kanai A. tRNA gene diversity in the three domains of life. Front Genet, (5):142. (2014)
16. Fujishima K and Kanai A. Split Gene. Brenner’s Encyclopedia of Genetics, 2nd edition, 543-544. (2013)
15. Hirata A, Fujishima K, Yamagami R, Kawamura T, Banfield JF, Kanai A, 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)
14. 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)
13. 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)
12. 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)
11. 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)
10. 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)
9. 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).
8. 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).
7. 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).
6. 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).
5. 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).
4. 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).
3. 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).
2. 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).
1. 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).
Honors and Awards
2016 WIRED Audi INNOVATION AWARD2016
2016 Best Measurement project (Team advisor of Stanford-Brown), International Genetically Engineered Machine Competition (iGEM)
2015 NASA Science Innovation Funding award (FY2016)
2015 Best Manufacturing project (Team advisor of Stanford-Brown), International Genetically Engineered Machine Competition (iGEM)
2014 NASA Center Innovation Funding award (FY2015)
2012 Best Poster Presentation, Gordon Research Seminar (GRS): Origin of Life, USA
2011 28th Inoue Research Award for Young Scientist, Inoue Foundation for Science, Japan
2010 Best Oral Presenter Award, 3rd AYRCOB 2010, Taiwan
2009 Nature Reviews Molecular Cell Biology Award, RNA 2009 Meeting, USA
The origin of life remains one of the fundamental questions in modern biology. The mystery lies in how the transition was made from the prebiotic world of inanimate chemicals to the Central Dogma-based biological system. At the heart of the issue is how RNA chain and polypeptides arose from the chemical disequilibria, interacted, and ultimately led to a functioning biological system. I had been working on transfer RNA, known as the molecular fossil that decodes genetic information on a nucleotide chain to an amino acid. In other words, tRNA is a molecule that bridges the gap between the generally accepted RNA world (RNA based biological system) and modern biology. Most attempts to understand the origin of life so far focus on RNA and hardly any work has been done on synthesizing abiotically produced short peptides that are likely existed earlier than chain of nucleotides on early Earth, let alone extraterrestrial environments. Hence, my research is centered on testing the ‘peptide-first hypothesis’ by synthesizing a large pool of de novo peptides and proteins in an in vitro system to understand their function, evolution and heredity prior to the emergence of genetic system. These challenging researches will became part of a role model for the emerging field of “Synthetic Astrobiology”.