Shin ichi Yokobori

Summary

Affiliation: Tokyo University of Pharmacy and Life Science
Country: Japan

Publications

  1. pmc Life without tRNAArg-adenosine deaminase TadA: evolutionary consequences of decoding the four CGN codons as arginine in Mycoplasmas and other Mollicutes
    Shin ichi Yokobori
    Laboratory of Extremophiles, Department of Applied Life Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432 1 Horinouchi, Hachioji, Tokyo 192 0392, Japan
    Nucleic Acids Res 41:6531-43. 2013
  2. pmc Complete DNA sequence of the mitochondrial genome of the ascidian Halocynthia roretzi (Chordata, Urochordata)
    S i Yokobori
    Department of Molecular Biology, School of Life Science, Tokyo University of Pharmacy and Life Science, Horinouchi, Hachioji, Tokyo 192 0392, Japan
    Genetics 153:1851-62. 1999
  3. ncbi request reprint Mitochondrial genome of Ciona savignyi (Urochordata, Ascidiacea, Enterogona): comparison of gene arrangement and tRNA genes with Halocynthia roretzi mitochondrial genome
    Shin ichi Yokobori
    Department of Molecular Biology, School of Life Science, Tokyo University of Pharmacy and Life Science, 1432 1, Horinouchi, Hachioji, Tokyo 192 0392, Japan
    J Mol Evol 57:574-87. 2003
  4. ncbi request reprint Long-term conservation of six duplicated structural genes in cephalopod mitochondrial genomes
    Shin ichi Yokobori
    Laboratory for Cellular Biochemistry, Department of Molecular Biology, School of Life Science, Tokyo University of Pharmacy and Life Science, Tokyo, Japan
    Mol Biol Evol 21:2034-46. 2004
  5. ncbi request reprint Complete nucleotide sequence of the mitochondrial genome of Doliolum nationalis with implications for evolution of urochordates
    Shin ichi Yokobori
    Department of Molecular Biology, School of Life Science, Tokyo University of Pharmacy and Life Science, Hachioji, Tokyo 192 0392, Japan
    Mol Phylogenet Evol 34:273-83. 2005
  6. doi request reprint Complete nucleotide sequences of mitochondrial genomes of two solitary entoprocts, Loxocorone allax and Loxosomella aloxiata: implications for lophotrochozoan phylogeny
    Shin ichi Yokobori
    Laboratory for Cellular Biochemistry, Department of Molecular Biology, School of Life Science, Tokyo University of Pharmacy and Life Sciences, 1432 1 Horinouchi, Hachioji, Tokyo 192 0392, Japan
    Mol Phylogenet Evol 47:612-28. 2008
  7. ncbi request reprint Mitochondrial genome structure and evolution in the living fossil vampire squid, Vampyroteuthis infernalis, and extant cephalopods
    Shin ichi Yokobori
    Laboratory of Cellular Biochemistry, Department of Molecular Biology, School of Life Science, Tokyo University of Pharmacy and Life Sciences, 1432 1 Horinouchi, Hachioji, Tokyo 192 0392, Japan
    Mol Phylogenet Evol 44:898-910. 2007
  8. pmc Gain and loss of an intron in a protein-coding gene in Archaea: the case of an archaeal RNA pseudouridine synthase gene
    Shin ichi Yokobori
    Department of Molecular Biology, School of Life Science, Tokyo University of Pharmacy and Life Science, Horinouchi, Hachioji, Tokyo 192 0392, Japan
    BMC Evol Biol 9:198. 2009
  9. doi request reprint Deinococcus aetherius sp. nov., isolated from the stratosphere
    Yinjie Yang
    Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, Hachioji, Tokyo 192 0392, Japan
    Int J Syst Evol Microbiol 60:776-9. 2010
  10. doi request reprint A bacterial elongation factor G homologue exclusively functions in ribosome recycling in the spirochaete Borrelia burgdorferi
    Takuma Suematsu
    Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
    Mol Microbiol 75:1445-54. 2010

Collaborators

Detail Information

Publications27

  1. pmc Life without tRNAArg-adenosine deaminase TadA: evolutionary consequences of decoding the four CGN codons as arginine in Mycoplasmas and other Mollicutes
    Shin ichi Yokobori
    Laboratory of Extremophiles, Department of Applied Life Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432 1 Horinouchi, Hachioji, Tokyo 192 0392, Japan
    Nucleic Acids Res 41:6531-43. 2013
    ..The key point of our model is that the A-to-I deamination activity had to be controlled before the loss of the tadA gene, allowing the stepwise evolution of Mollicutes toward an alternative decoding strategy. ..
  2. pmc Complete DNA sequence of the mitochondrial genome of the ascidian Halocynthia roretzi (Chordata, Urochordata)
    S i Yokobori
    Department of Molecular Biology, School of Life Science, Tokyo University of Pharmacy and Life Science, Horinouchi, Hachioji, Tokyo 192 0392, Japan
    Genetics 153:1851-62. 1999
    ..The amino acid sequences of Halocynthia mt-proteins deduced from their gene sequences are quite different from those in other metazoans, indicating that the substitution rate in Halocynthia mt-protein genes is also accelerated...
  3. ncbi request reprint Mitochondrial genome of Ciona savignyi (Urochordata, Ascidiacea, Enterogona): comparison of gene arrangement and tRNA genes with Halocynthia roretzi mitochondrial genome
    Shin ichi Yokobori
    Department of Molecular Biology, School of Life Science, Tokyo University of Pharmacy and Life Science, 1432 1, Horinouchi, Hachioji, Tokyo 192 0392, Japan
    J Mol Evol 57:574-87. 2003
    ..Only three gene boundaries are shared between the Halocynthia and the Ciona mt genomes. Molecular phylogenetic analyses based on amino acid sequences of mt protein genes failed to demonstrate the monophyly of the chordates...
  4. ncbi request reprint Long-term conservation of six duplicated structural genes in cephalopod mitochondrial genomes
    Shin ichi Yokobori
    Laboratory for Cellular Biochemistry, Department of Molecular Biology, School of Life Science, Tokyo University of Pharmacy and Life Science, Tokyo, Japan
    Mol Biol Evol 21:2034-46. 2004
    ..Molecular phylogenetic analyses of mt protein genes are suggestive, although not statistically significantly so, of a monophyletic relationship between W. scintillans and T. pacificus...
  5. ncbi request reprint Complete nucleotide sequence of the mitochondrial genome of Doliolum nationalis with implications for evolution of urochordates
    Shin ichi Yokobori
    Department of Molecular Biology, School of Life Science, Tokyo University of Pharmacy and Life Science, Hachioji, Tokyo 192 0392, Japan
    Mol Phylogenet Evol 34:273-83. 2005
    ..Given the paraphyletic nature of ascidians, it seems likely that the common ancestor of ascidians and thaliaceans was sessile, as are the present-day ascidians, and that the thaliaceans subsequently evolved a pelagic lifestyle...
  6. doi request reprint Complete nucleotide sequences of mitochondrial genomes of two solitary entoprocts, Loxocorone allax and Loxosomella aloxiata: implications for lophotrochozoan phylogeny
    Shin ichi Yokobori
    Laboratory for Cellular Biochemistry, Department of Molecular Biology, School of Life Science, Tokyo University of Pharmacy and Life Sciences, 1432 1 Horinouchi, Hachioji, Tokyo 192 0392, Japan
    Mol Phylogenet Evol 47:612-28. 2008
    ..Molecular phylogenetic analyses based on the sequences of mt protein-coding genes suggested a possible close relationship between Entoprocta and Phoronida, and a close relationship among Brachiopoda, Annelida, and Echiura...
  7. ncbi request reprint Mitochondrial genome structure and evolution in the living fossil vampire squid, Vampyroteuthis infernalis, and extant cephalopods
    Shin ichi Yokobori
    Laboratory of Cellular Biochemistry, Department of Molecular Biology, School of Life Science, Tokyo University of Pharmacy and Life Sciences, 1432 1 Horinouchi, Hachioji, Tokyo 192 0392, Japan
    Mol Phylogenet Evol 44:898-910. 2007
    ..Therefore, it is reasonable to recognize three major groups in Coleoidea--Vampyromorpha, Octopoda, and Decapodiformes...
  8. pmc Gain and loss of an intron in a protein-coding gene in Archaea: the case of an archaeal RNA pseudouridine synthase gene
    Shin ichi Yokobori
    Department of Molecular Biology, School of Life Science, Tokyo University of Pharmacy and Life Science, Horinouchi, Hachioji, Tokyo 192 0392, Japan
    BMC Evol Biol 9:198. 2009
    ..However, the exact timing of the intron insertion was not determined and verification of the putative secondary loss of the intron in some lineages was not performed...
  9. doi request reprint Deinococcus aetherius sp. nov., isolated from the stratosphere
    Yinjie Yang
    Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, Hachioji, Tokyo 192 0392, Japan
    Int J Syst Evol Microbiol 60:776-9. 2010
    ..Therefore, we propose a new species of the genus Deinococcus, Deinococcus aetherius sp. nov. (type strain, ST0316(T) =JCM 11751(T) =DSM 21230(T))...
  10. doi request reprint A bacterial elongation factor G homologue exclusively functions in ribosome recycling in the spirochaete Borrelia burgdorferi
    Takuma Suematsu
    Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
    Mol Microbiol 75:1445-54. 2010
    ..These results indicate that two B. burgdorferi EF-G paralogues are close relatives to mitochondrial EF-G paralogues rather than the conventional bacterial EF-G, in both their phylogenetic and biochemical features...
  11. ncbi request reprint Extremely thermophilic translation system in the common ancestor commonote: ancestral mutants of Glycyl-tRNA synthetase from the extreme thermophile Thermus thermophilus
    Hideaki Shimizu
    Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, 1432 1 Horinouchi, Hachioji, Tokyo 192 0392, Japan
    J Mol Biol 369:1060-9. 2007
    ..Six mutants showed higher thermostability than wild-type enzyme and seven mutants showed higher activity than wild-type enzyme at 70 degrees C, suggesting an extremely thermophilic translation system in the common ancestor Commonote...
  12. pmc Experimental evidence for the thermophilicity of ancestral life
    Satoshi Akanuma
    Department of Applied Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432 1 Horinouchi, Hachioji, Tokyo 192 0392, Japan
    Proc Natl Acad Sci U S A 110:11067-72. 2013
    ....
  13. ncbi request reprint [Evolution of genome structure and genetic code of metazoan mitochondria]
    Shin ichi Yokobori
    Laboratory for Cellular Biochemistry, Department of Molecular Biology, School of Life Science, Tokyo University of Pharmacy and Life Science
    Nihon Rinsho 60:17-23. 2002
  14. ncbi request reprint Structural analysis of the plasmid pTA1 isolated from the thermoacidophilic archaeon Thermoplasma acidophilum
    Kan Yamashiro
    Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, 1432 1 Horinouchi, Hachioji, Tokyo 192 0392, Japan
    Extremophiles 10:327-35. 2006
    ..The phylogenetic analysis suggested that plasmid pTA1 is possibly originated from the chromosomal DNA of Thermoplasma...
  15. ncbi request reprint Thermostability of ancestral mutants of Caldococcus noboribetus isocitrate dehydrogenase
    Hisako Iwabata
    Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, 1432 1 Horinouchi, Hachioji, Tokyo 192 0392, Japan
    FEMS Microbiol Lett 243:393-8. 2005
    ..The results are compatible with the hyperthermophilic universal ancestor (commonote) hypothesis. Incorporation of ancestral residues into a modern-day protein sequence can be used to improve protein thermostability...
  16. doi request reprint Deinococcus aerius sp. nov., isolated from the high atmosphere
    Yinjie Yang
    Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, Hachioji, Tokyo 192 0392, Japan
    Int J Syst Evol Microbiol 59:1862-6. 2009
    ..Therefore, a novel species of the genus Deinococcus, Deinococcus aerius sp. nov. (type strain, TR0125T=JCM 11750T=DSM 21212T), is proposed to accommodate this isolate...
  17. ncbi request reprint Multiple origins of the ascidian-Prochloron symbiosis: molecular phylogeny of photosymbiotic and non-symbiotic colonial ascidians inferred from 18S rDNA sequences
    Shin ichi Yokobori
    Laboratory for Cellular Biochemistry, Department of Molecular Biology, School of Life Science, Tokyo University of Pharmacy and Life Science, Tokyo 192 0392, Japan
    Mol Phylogenet Evol 40:8-19. 2006
    ..The results strongly support the hypothesis that establishment of the ascidian-Prochloron symbiosis occurred independently in the Didemnidae lineage at least once in each of the genera that possess symbiotic species...
  18. pmc Birth of Archaeal Cells: Molecular Phylogenetic Analyses of G1P Dehydrogenase, G3P Dehydrogenases, and Glycerol Kinase Suggest Derived Features of Archaeal Membranes Having G1P Polar Lipids
    Shin ichi Yokobori
    Laboratory of Extremophiles, Department of Applied Life Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432 1 Horinouchi, Hachioji, Tokyo 192 0392, Japan
    Archaea 2016:1802675. 2016
    ....
  19. doi request reprint Robustness of predictions of extremely thermally stable proteins in ancient organisms
    Satoshi Akanuma
    Department of Applied Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, 192 0392, Japan
    Evolution 69:2954-62. 2015
    ..The newly reconstructed ancestral proteins are still thermally stable, further supporting the hypothesis that the ancient organisms contained thermally stable proteins and therefore that they were thermophilic. ..
  20. doi request reprint Arabidopsis thaliana mitochondrial EF-G1 functions in two different translation steps
    Takuma Suematsu
    Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 0033, and Department of Applied Life Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432 1 Horinouchi, Hachioji shi, Tokyo 192 0392, Japan
    J Biochem 155:107-14. 2014
    ..Here, we propose that the functional division is not necessarily conserved among mitochondriate eukaryotes and also that EF-G1mt in organisms lacking EF-G2mt functions in two steps, similar to conventional bacterial EF-G. ..
  21. doi request reprint The possible interplanetary transfer of microbes: assessing the viability of Deinococcus spp. under the ISS Environmental conditions for performing exposure experiments of microbes in the Tanpopo mission
    Yuko Kawaguchi
    Laboratory for Extremophiles, Department of Applied Molecular Biology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432 1 Horinouchi, Hachioji, Tokyo, 192 0392, Japan
    Orig Life Evol Biosph 43:411-28. 2013
    ..We concluded that aggregated deinococcal cells will survive the yearlong exposure experiments. We propose that microbial cells can aggregate as an ark for the interplanetary transfer of microbes, and we named it 'massapanspermia'...
  22. ncbi request reprint Designing thermostable proteins: ancestral mutants of 3-isopropylmalate dehydrogenase designed by using a phylogenetic tree
    Keiko Watanabe
    Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, 1432 1 Horinouchi, Hachioji, Tokyo 192 0392, Japan
    J Mol Biol 355:664-74. 2006
    ..The results suggest also that this method could be an efficient way of designing mutant enzymes with higher thermostability based only on the primary structure and a phylogenetic tree...
  23. pmc An actin homolog of the archaeon Thermoplasma acidophilum that retains the ancient characteristics of eukaryotic actin
    Futoshi Hara
    Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, Hachioji, Tokyo 192 0392, Japan
    J Bacteriol 189:2039-45. 2007
    ..However, the low specificity of Ta0583 for nucleotide triphosphates indicates that Ta0583 is more primitive than eukaryotic actin. Taken together, our results suggest that Ta0583 retains the ancient characteristics of eukaryotic actin...
  24. doi request reprint Phylogeny-based design of a B-subunit of DNA gyrase and its ATPase domain using a small set of homologous amino acid sequences
    Satoshi Akanuma
    Department of Molecular Biology, Tokyo University of Pharmacy and Life Sciences, 1432 1 Horinouchi, Hachioji, Tokyo 192 0392, Japan
    J Mol Biol 412:212-25. 2011
    ....
  25. ncbi request reprint Quest for Ancestors of Eukaryal Cells Based on Phylogenetic Analyses of Aminoacyl-tRNA Synthetases
    Ryutaro Furukawa
    Laboratory of Extremophiles, Department of Applied Life Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432 1 Horinouchi, Hachioji, Tokyo, Japan
    J Mol Evol . 2016
    ..Based on our phylogenetic analyses, we proposed a model for the establishment of Eukarya...
  26. doi request reprint Ancestral amino acid substitution improves the thermal stability of recombinant lignin-peroxidase from white-rot fungi, Phanerochaete chrysosporium strain UAMH 3641
    Yasuyuki Semba
    Department of Applied Biology, Faculty of Life Science, Tokyo University of Pharmacy and Life Sciences, 1432 1, Horinouchi, Hachioji, Tokyo 192 0392, Japan
    Protein Eng Des Sel 28:221-30. 2015
    ..Several of these ancestral mutants showed higher thermal stabilities and increased specific activities and/or kcat/KM than those of wild-type LiP. ..
  27. doi request reprint Fluorescence imaging of microbe-containing particles shot from a two-stage Light-gas gun into an aerogel
    Yuko Kawaguchi
    Department of Applied Life Sciences School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Horinouchi, Hachioji, Tokyo, 192 0392, Japan
    Orig Life Evol Biosph 44:43-60. 2014
    ..The developed methods are suitable to determine if microbes exist at the International Space Station altitude. ..