Yuki Goto, Ph.D.

Associate Professor

CV



Education

2003:
B.Sc., Faculty of Engineering, Kyoto University
Thesis advisor: Prof. Isao Saito
2005:
M.Sc., Graduate School of Engineering, Kyoto University
Thesis advisor: Prof. Kazuhiko Nakatani
2008:
Ph.D., Graduate School of Engineering, The University of Tokyo
Thesis advisor: Prof. Hiroaki Suga

Professional career

2006-2008:
Research Fellow of the Japan Society for the Promotion of Science
2008-2009:
Postdoctoral research associate, University of Illinois at Urbana-Champaign (JSPS Postdoctoral Fellow for Research Abroad)
Advisor: Prof. Wilfred A. van der Donk
2009-2010:
Assistant professor, Research Center for Advanced Science and Technology, The University of Tokyo
2010-2016:
Assistant professor, Graduate School of Science, The University of Tokyo
2011-2015:
Investigator, PRESTO (Design and Control of Cellular Functions), Japan Science and Technology Agency
2016-present:
Associate professor, Graduate School of Science, The University of Tokyo

Contact Info

  • Room #2208, West wing, Chemistry Bildg.
    Department of Chemistry, Graduate School of Science, The University of Tokyo
  • E-mail… y-goto"at"chem.s.u-tokyo.ac.jp (change "at" to @)
  • TEL…+81-3-5841-4338
  • FAX…+81-3-5841-8372

Publication (Journal articles)

"New developments in RiPP discovery, enzymology and engineering."
M. Montalban-Lopez; T.A. Scott; S. Ramesh; I.R. Rahman; A.J. van Heel; J.H. Viel; V. Bandarian; E. Dittmann; O. Genilloud; Y. Goto; M.J. Grande Burgos; C. Hill; S. Kim; J. Koehnke; J.A. Latham; A.J. Link; B. Martinez; S.K. Nair; Y. Nicolet; S. Rebuffat; H.G. Sahl; D. Sareen; E.W. Schmidt; L. Schmitt; K. Severinov; R.D. Sussmuth; A.W. Truman; H. Wang; J.K. Weng, et al.
Nat Prod Rep, (2020) in press.
"Promiscuous Enzymes Cooperate at the Substrate Level En Route to Lactazole A."
A.A. Vinogradov; M. Shimomura; N. Kano; Y. Goto; H. Onaka; H. Suga
J. Am. Chem. Soc., 142, 13886-13897 (2020)
"A Macrocyclic Peptide Library with a Structurally Constrained Cyclopropane-containing Building Block Leads to Thiol-independent Inhibitors of Phosphoglycerate Mutase."
R. Okuma; T. Kuwahara; T. Yoshikane; M. Watanabe; P. Dranchak; J. Inglese; S. Shuto; Y. Goto; H. Suga
Chem. Asian J., 15, 2631-2636 (2020)
"Minimal lactazole scaffold for in vitro thiopeptide bioengineering."
A.A. Vinogradov; M. Shimomura; Y. Goto; T. Ozaki; S. Asamizu; Y. Sugai; H. Suga; H. Onaka
Nat. Commun., 11, 2272 (2020)
"Chemoenzymatic Posttranslational Modification Reactions for the Synthesis of Ψ[CH2NH]-Containing Peptides."
Y. Kato; T. Kuroda; Y. Huang; R. Ohta; Y. Goto; H. Suga
Angew. Chem. Int. Ed. Engl., 59, 684-688 (2020)
"In Vitro Biosynthesis of Peptides Containing Exotic Azoline Analogues."
Y. Goto; H. Suga
ChemBioChem, 21, 84-87 (2020)
"Exploring the Post-translational Enzymology of PaaA by mRNA Display."
S.R. Fleming; P.M. Himes; S.V. Ghodge; Y. Goto; H. Suga; A.A. Bowers
J. Am. Chem. Soc., 142, 5024-5028 (2020)
"Improved Stability of siRNA-Loaded Lipid Nanoparticles Prepared with a PEG-Monoacyl Fatty Acid Facilitates Ligand-Mediated siRNA Delivery."
Y. Sakurai; W. Mizumura; K. Ito; K. Iwasaki; T. Katoh; Y. Goto; H. Suga; H. Harashima
Mol. Pharm., 17, 1397-1404 (2020)
"Generation of non-standard macrocyclic peptides specifically binding TSC-22 homologous gene-1."
S.T.P. Tran; C.J. Hipolito; H. Suzuki; R. Xie; H.D. Kim Tuyen; P.T. Dijke; N. Terasaka; Y. Goto; H. Suga; M. Kato
Biochem. Biophys. Res. Commun., 516, 445-450 (2019)
"Ribosomal Synthesis of Backbone-Cyclic Peptides Compatible with In Vitro Display."
R. Takatsuji; K. Shinbara; T. Katoh; Y. Goto; T. Passioura; R. Yajima; Y. Komatsu; H. Suga
J. Am. Chem. Soc., 141, 2279-2287 (2019)
"Ribosomal Formation of Thioamide Bonds in Polypeptide Synthesis."
R. Maini; H. Kimura; R. Takatsuji; T. Katoh; Y. Goto; H. Suga
J. Am. Chem. Soc., 141, 20004-20008 (2019)
"Meeting Peptides in Kyoto."
S. Futaki; K. Matsuzaki; Y. Goto
Chembiochem, 20, 2015-2016 (2019)
"Flexizyme-Enabled Benchtop Biosynthesis of Thiopeptides."
S.R. Fleming; T.E. Bartges; A.A. Vinogradov; C.L. Kirkpatrick; Y. Goto; H. Suga; L.M. Hicks; A.A. Bowers
J. Am. Chem. Soc., 141, 758-762 (2019)
"Non-competitive cyclic peptides for targeting enzyme-substrate complexes."
T.E. McAllister; T.L. Yeh; M.I. Abboud; I.K.H. Leung; E.S. Hookway; O.N.F. King; B. Bhushan; S.T. Williams; R.J. Hopkinson; M. Munzel; N.D. Loik; R. Chowdhury; U. Oppermann; T.D.W. Claridge; Y. Goto; H. Suga; C.J. Schofield; A. Kawamura
Chem Sci, 9, 4569-4578 (2018)
"Engineering of RiPP pathways for the production of artificial peptides bearing various non-proteinogenic structures."
Y. Goto; H. Suga
Curr. Opin. Chem. Biol., 46, 82-90 (2018)
"Artificial In Vitro Biosynthesis Systems for the Development of Pseudo-Natural Products."
Y. Goto; H. Suga
Bull Chem Soc Jpn, 91, 410-419 (2018)
"Artificial Division of Codon Boxes for Expansion of the Amino Acid Repertoire of Ribosomal Polypeptide Synthesis."
Y. Iwane; T. Katoh; Y. Goto; H. Suga
Methods Mol Biol, 1728, 17-47 (2018)
"Highly selective inhibition of histone demethylases by de novo macrocyclic peptides."
A. Kawamura; M. Munzel; T. Kojima; C. Yapp; B. Bhushan; Y. Goto; A. Tumber; T. Katoh; O.N. King; T. Passioura; L.J. Walport; S.B. Hatch; S. Madden; S. Muller; P.E. Brennan; R. Chowdhury; R.J. Hopkinson; H. Suga; C.J. Schofield
Nature Communications, 8, 14773 (2017)
"Dissection of goadsporin biosynthesis by in vitro reconstitution leading to designer analogues expressed in vivo."
T. Ozaki; K. Yamashita; Y. Goto; M. Shimomura; S. Hayashi; S. Asamizu; Y. Sugai; H. Ikeda; H. Suga; H. Onaka
Nature Communications, 8, 14207 (2017)
"Efficient siRNA Delivery by Lipid Nanoparticles Modified with a Nonstandard Macrocyclic Peptide for EpCAM-Targeting."
Y. Sakurai; W. Mizumura; M. Murata; T. Hada; S. Yamamoto; K. Ito; K. Iwasaki; T. Katoh; Y. Goto; A. Takagi; M. Kohara; H. Suga; H. Harashima
Mol Pharm, 14, 3290-3298 (2017)
"Conformational and chemical selection by a trans-acting editing domain."
E.M. Danhart; M. Bakhtina; W.A. Cantara; A.B. Kuzmishin; X. Ma; B.L. Sanford; M. Kosutic; Y. Goto; H. Suga; K. Nakanishi; R. Micura; M.P. Foster; K. Musier-Forsyth
Proc. Natl. Acad. Sci. USA, 114, E6774-E6783 (2017)
"Quality control by trans-editing factor prevents global mistranslation of non-protein amino acid alpha-aminobutyrate."
J.M. Bacusmo; A.B. Kuzmishin; W.A. Cantara; Y. Goto; H. Suga; K. Musier-Forsyth
RNA Biol, 0 (2017)
"Characterization of the stereochemical configuration of lanthionines formed by the lanthipeptide synthetase GeoM."
N. Garg; Y. Goto; T. Chen; W.A. van der Donk
Biopolymers, 106, 834-842 (2016)
"Expanding the amino acid repertoire of ribosomal polypeptide synthesis via the artificial division of codon boxes."
Y. Iwane; A. Hitomi; H. Murakami; T. Katoh; Y. Goto; H. Suga
Nature chemistry, 8, 317-325 (2016)
"A Post-translational Cyclodehydratase, PatD, Tolerates Sequence Variation in the C-terminal Region of Substrate Peptides."
Y. Goto; H. Suga
Chem Lett, 45, 1247-1249 (2016)
"Ribosomal synthesis of peptides with multiple beta-amino acids."
T. Fujino; Y. Goto; H. Suga; H. Murakami
J. Am. Chem. Soc., 138, 1962-1969 (2016)
"Homologous trans-editing factors with broad tRNA specificity prevent mistranslation caused by serine/threonine misactivation."
Z. Liu; O. Vargas-Rodriguez; Y. Goto; E.M. Novoa; L. Ribas de Pouplana; H. Suga; K. Musier-Forsyth
Proceedings of the National Academy of Sciences of the United States of America, 112, 6027-6032 (2015)
"A Fluorescent Imaging Probe Based on a Macrocyclic Scaffold That Binds to Cellular EpCAM."
K. Iwasaki; Y. Goto; T. Katoh; T. Yamashita; S. Kaneko; H. Suga
Journal of molecular evolution, 81, 210-217 (2015)
"Recent developments of engineered translational machineries for the incorporation of non-canonical amino acids into polypeptides."
N. Terasaka; Y. Iwane; A.S. Geiermann; Y. Goto; H. Suga
International journal of molecular sciences, 16, 6513-6531 (2015)
"Ancestral AlaX editing enzymes for control of genetic code fidelity are not tRNA-specific."
E.M. Novoa; O. Vargas-Rodriguez; S. Lange; Y. Goto; H. Suga; K. Musier-Forsyth; L. Ribas de Pouplana
The Journal of biological chemistry, 290, 10495-10503 (2015)
"Selection-based discovery of macrocyclic peptides for the next generation therapeutics."
T. Morioka; N.D. Loik; C.J. Hipolito; Y. Goto; H. Suga
Current opinion in chemical biology, 26C, 34-41 (2015)
"Structural basis for potent inhibition of SIRT2 deacetylase by a macrocyclic peptide inducing dynamic structural change."
K. Yamagata; Y. Goto; H. Nishimasu; J. Morimoto; R. Ishitani; N. Dohmae; N. Takeda; R. Nagai; I. Komuro; H. Suga; O. Nureki
Structure, 22, 345-352 (2014)
"Selection-based discovery of druglike macrocyclic peptides."
T. Passioura; T. Katoh; Y. Goto; H. Suga
Annu. Rev. Biochem., 83, 727-752 (2014)
"One-pot synthesis of azoline-containing peptides in a cell-free translation system integrated with a posttranslational cyclodehydratase."
Y. Goto; Y. Ito; Y. Kato; S. Tsunoda; H. Suga
Chem. Biol., 21, 766-774 (2014)
"Investigating the role of a backbone to substrate hydrogen bond in OMP decarboxylase using a site-specific amide to ester substitution."
B.J. Desai; Y. Goto; A. Cembran; A.A. Fedorov; S.C. Almo; J. Gao; H. Suga; J.A. Gerlt
Proc. Natl. Acad. Sci. USA, 111, 15066-15071 (2014)
"Distinct tRNA recognition strategies used by a homologous family of editing domains prevent mistranslation."
M. Das; O. Vargas-Rodriguez; Y. Goto; H. Suga; K. Musier-Forsyth
Nucleic Acids Res., 42, 3943-3953 (2014)
"Nonstandard peptide expression under the genetic code consisting of reprogrammed dual sense codons."
Y. Goto; M. Iseki; A. Hitomi; H. Murakami; H. Suga
ACS Chem. Biol., 8, 2630-2634 (2013)
"Reevaluation of the D-amino acid compatibility with the elongation event in translation."
T. Fujino; Y. Goto; H. Suga; H. Murakami
J. Am. Chem. Soc., 135, 1830-1837 (2013)
"Charging of tRNAs using ribozymes and selection of cyclic peptides containing thioethers."
P.C. Reid; Y. Goto; T. Katoh; H. Suga
Methods Mol. Biol., 805, 335-348 (2012)
"Selective thioether macrocyclization of peptides having the N-terminal 2-chloroacetyl group and competing two or three cysteine residues in translation."
K. Iwasaki; Y. Goto; T. Katoh; H. Suga
Org. Biomol. Chem., 10, 5783-5786 (2012)
"Flexizymes as a tRNA acylation tool facilitating genetic code reprogramming."
Y. Goto; H. Suga
Methods Mol. Biol., 848, 465-478 (2012)
"Lantibiotics from Geobacillus thermodenitrificans."
N. Garg; W. Tang; Y. Goto; S.K. Nair; W.A. van der Donk
Proc. Natl. Acad. Sci. USA, 109, 5241-5246 (2012)
"Natural product-like macrocyclic N-methyl-peptide inhibitors against a ubiquitin ligase uncovered from a ribosome-expressed de novo library."
Y. Yamagishi; I. Shoji; S. Miyagawa; T. Kawakami; T. Katoh; Y. Goto; H. Suga
Chem. Biol., 18, 1562-1570 (2011)
"Ribosomal synthesis of backbone-macrocyclic peptides containing gamma-amino acids."
Y. Ohshiro; E. Nakajima; Y. Goto; S. Fuse; T. Takahashi; T. Doi; H. Suga
Chembiochem, 12, 1183-1187 (2011)
"Ribosomal synthesis of backbone macrocyclic peptides."
T. Katoh; Y. Goto; M.S. Reza; H. Suga
Chem. Commun., 47, 9946-9958 (2011)
"Mechanistic studies of Ser/Thr dehydration catalyzed by a member of the LanL lanthionine synthetase family."
Y. Goto; A. Okesli; W.A. van der Donk
Biochemistry, 50, 891-898 (2011)
"Preparation of materials for flexizyme reactions and genetic code reprogramming."
Y. Goto; T. Katoh; H. Suga
Protoc. Exchange, 779-790 (2011)
"Flexizymes for genetic code reprogramming."
Y. Goto; T. Katoh; H. Suga
Nat. Protoc., 6, 779-790 (2011)
"Ribosome evolution for two artificial amino acids in E. coli."
G. Hayashi; Y. Goto; H. Suga
Chem. Biol., 17, 320-321 (2010)
"Discovery of unique lanthionine synthetases reveals new mechanistic and evolutionary insights."
Y. Goto; B. Li; J. Claesen; Y. Shi; M.J. Bibb; W.A. van der Donk
PLoS Biol., 8, e1000339 (2010)
"Ribosomal synthesis of cyclic peptides with a fluorogenic oxidative coupling reaction."
Y. Yamagishi; H. Ashigai; Y. Goto; H. Murakami; H. Suga
Chembiochem, 10, 1469-1472 (2009)
"Ribosomal synthesis of peptides with C-terminal lactams, thiolactones, and alkylamides."
E. Nakajima; Y. Goto; Y. Sako; H. Murakami; H. Suga
Chembiochem, 10, 1186-1192 (2009)
"Translation initiation with initiator tRNA charged with exotic peptides."
Y. Goto; H. Suga
J. Am. Chem. Soc., 131, 5040-5041 (2009)
"Ribosomal synthesis of dehydrobutyrine- and methyllanthionine-containing peptides."
Y. Goto; K. Iwasaki; K. Torikai; H. Murakami; H. Suga
Chem. Commun., 3419-3421 (2009)
"Ribosomal synthesis of peptidase-resistant peptides closed by a nonreducible inter-side-chain bond."
Y. Sako; Y. Goto; H. Murakami; H. Suga
ACS Chem. Biol., 3, 241-249 (2008)
"Ligand-stabilized hairpin structures interfere with elongation of human telomere."
M. Hagihara; Y. Goto; K. Nakatani
Chembiochem, 9, 510-513 (2008)
"Reprogramming the translation initiation for the synthesis of physiologically stable cyclic peptides."
Y. Goto; A. Ohta; Y. Sako; Y. Yamagishi; H. Murakami; H. Suga
ACS Chem. Biol., 3, 120-129 (2008)
"Initiating translation with D-amino acids."
Y. Goto; H. Murakami; H. Suga
RNA, 14, 1390-1398 (2008)
"Analysis of mismatched DNA by mismatch binding ligand (MBL)-Sepharose affinity chromatography."
Y. Goto; H. Suda; A. Kobori; K. Nakatani
Anal. Bioanal. Chem., 388, 1165-1173 (2007)
"Small-molecule binding to the nonquadruplex form of the human telomeric sequence."
Y. Goto; S. Hagihara; M. Hagihara; K. Nakatani
Chembiochem, 8, 723-726 (2007)
"Evaluation of mismatch-binding ligands as inhibitors for Rev-RRE interaction."
K. Nakatani; S. Horie; Y. Goto; A. Kobori; S. Hagihara
Bioorg. Med. Chem., 14, 5384-5388 (2006)
"A new ligand binding to G-G mismatch having improved thermal and alkaline stability."
T. Peng; T. Murase; Y. Goto; A. Kobori; K. Nakatani
Bioorg. Med. Chem. Lett., 15, 259-262 (2005)
"Small-molecule ligand induces nucleotide flipping in (CAG)n trinucleotide repeats."
K. Nakatani; S. Hagihara; Y. Goto; A. Kobori; M. Hagihara; G. Hayashi; M. Kyo; M. Nomura; M. Mishima; C. Kojima
Nat. Chem. Biol., 1, 39-43 (2005)
"The binding of guanine-guanine mismatched DNA to naphthyridine dimer immobilized sensor surfaces: kinetic aspects."
K. Nakatani; A. Kobori; H. Kumasawa; Y. Goto; I. Saito
Bioorg. Med. Chem., 12, 3117-3123 (2004)
"Detection of guanine-adenine mismatches by surface plasmon resonance sensor carrying naphthyridine-azaquinolone hybrid on the surface."
S. Hagihara; H. Kumasawa; Y. Goto; G. Hayashi; A. Kobori; I. Saito; K. Nakatani
Nucleic Acids Res., 32, 278-286 (2004)

Publication (Books and reviews in Japanese)

33 Japanese articles/books have been published.

Proceedings

25 articles published in Peptide Science, Nucleic Acids Research Symposium Series, etc.