Laboratory for Nonnatural Amino Acid Technology | RIKEN BDR

Laboratory for Nonnatural Amino Acid Technology

Team Leader

Kensaku SakamotoPh.D.

  • Location:Yokohama
  • E-mail:kensaku.sakamoto[at]riken.jpPlease replace [at] with @.

We create alternative biosystems by engineering the genetic code

Research Summary

What is Synthetic biology?
Proteins useful for life-science studies and medical applications can be synthesized in living cells programmed with the blueprint for the proteins. The cells engineered to utilize novel amino acids in proteins will facilitate the addition of artificial marks onto proteins, and also the synthesis of proteins linked to pharmaceuticals. These cells will help to realize new structures and functions of proteins. We also exploit this platform technology to provide unique, technical supports for drug discovery.

Collaborations with Structural Biology
Synthetic Biology should work together with Structural Biology, to develop novel proteins and enzymes based on structural knowledge. Not only for engineering, has such collaboration proved useful for elucidating structural basis for the functions of proteins, receptors, and enzymes.

Fig.1

Novel protein stabilization mechanism: Proteins can structurally be stabilized by incorporating non-natural amino acids (bromotyrosines in this case) into them. The left panel shows the tertiary structure of a stabilized enzyme, which was revealed by X-ray crystallography. The right panel shows the local structure around a bromotyrosine included in the whole structure at the left. This amino acids is snugly located between two lysine residues, thereby contributing to the enhanced stability of the enzyme. The other incorporated bromotyrosines also contribute to the stability in similar manners.

Research Theme

  • Engineering the genetic code in living cells
  • Developing novel proteins with non-natural amino acids
  • Technology development to engineer antibodies useful as biologics

Main Publications List

  • Yanagisawa T, Kuratani M, Seki E, et al.
    Structural Basis for Genetic-Code Expansion with Bulky Lysine Derivatives by an Engineered Pyrrolysyl-tRNA Synthetase.
    Cell chemical biology doi: 10.1016/j.chembiol.2019.03.008
  • Sakamoto K and Hayashi A.
    Synthetic tyrosine tRNA molecules with noncanonical secondary structures.
    International Journal of Molecular Sciences 20(1), 92 (2019) doi: 10.3390/ijms20010092
  • Teramoto H, Amano Y, Iraha F, et al.
    Genetic code expansion of the silkworm Bombyx mori to functionalize silk fiber.
    ACS Synthetic Biology 7, 801–806 (2018) doi: 10.1021/acssynbio.7b00437
  • Ohtake K, Mukai T, Iraha F, et al.
    Engineering an automaturing transglutaminase with enhanced thermostability by genetic code expansion with two codon reassignments.
    ACS Synthetic Biology 7, 2170–2176 (2018) doi: 10.1021/acssynbio.8b00157
  • Handoko L, Kaczkowski B, Hon C-C, et al.
    JQ1 affects BRD2-dependent and independent transcription regulation without disrupting H4-hyperacetylated chromatin states.
    Epigenetics 13, 410–431 (2018) doi.org/10.1080/15592294.2018.1469891
  • Takahashi M, and Sakamoto K.
    Engineering of Escherichia coli β-lactamase TEM-1 variants showing higher activity under acidic conditions than at the neutral pH.
    Biochemical and Biophysical Research Communications 505, 333–337 (2018) doi.org/10.1016/j.bbrc.2018.09.096
  • Yamaguchi A, Iraha F, Ohtake K, and Sakamoto, K.
    Pyrrolysyl-tRNA synthetase with a unique architecture enhances the availability of lysine derivatives in synthetic genetic codes.
    Molecules 23, 2460 (2018) doi.org/10.3390/molecules23102460
  • Osamura T, Okuda M, Yamaguchi A, et al.
    Variants of the industrially relevant protease KP-43 with suppressed activity under alkaline conditions developed using expanded genetic codes.
    Biochemistry and Biophysics Reports 17, 93–96 (2018) doi: 10.1016/j.bbrep.2018.12.001
  • Yamaguchi A, Matsuda T, Ohtake K, et al.
    Incorporation of a doubly functionalized synthetic amino acid into proteins for creating chemical and light-induced conjugates.
    Bioconjugate Chemistry 27, 198-206 (2015) doi.org/10.1021/acs.bioconjchem.5b00602
  • Mukai T, Yamaguchi A, Ohtake K, et al.
    Reassignment of a rare sense codon to a non-canonical amino acid in Escherichia coli.
    Nucleic Acids Research 43, 8111-8122 (2015) doi.org/10.1093/nar/gkv787
  • Mukai T, Hoshi H, Ohtake K, et al.
    Highly reproductive Escherichia coli cells with no specific assignment to the UAG codon.
    Scientific Reports 5: 9699 (2015) doi: 10.1038/srep09699

All Publications

Member

Kensaku SakamotoTeam Leader kensaku.sakamoto[at]riken.jp
Motoaki WakiyamaDeputy Team Leader motoaki.wakiyama[at]riken.jp
Akira WadaSenior Research Scientist awada[at]riken.jp
Akiko Matsumoto (Hayashi)Senior Technical Scientist akiko.matsumoto[at]riken.jp
Kazumasa OhtakeResearch Scientist kazumasa.ohtake[at]riken.jp
Mihoko TakahashiTechnical Scientist mihoko.takahashi[at]riken.jp

*:concurrent / Please replace [at] with @.