Title:
MODIFICATION OF D AND T ARMS OF TRNA ENHANCING D-AMINO ACID AND β-AMINO ACID UPTAKE
Document Type and Number:
WIPO Patent Application WO/2019/077887
Kind Code:
A1
Abstract:
The purpose of the present invention is to provide a novel translation system by which a peptide, wherein non-protein amino acids are consecutively bonded, can be synthesized by translation in a cell-free translation system. Provided is a tRNA which contains the base sequence represented by SEQ ID NO: 1 and encodes non-protein amino acids.
Inventors:
SUGA HIROAKI (JP)
KATO TAKAYUKI (JP)
KATO TAKAYUKI (JP)
Application Number:
PCT/JP2018/031814
Publication Date:
April 25, 2019
Filing Date:
August 28, 2018
Export Citation:
Assignee:
UNIV TOKYO (JP)
International Classes:
C12N15/09; C12P21/00; C40B40/06; C40B40/08; C40B40/10; C40B50/06
Domestic Patent References:
| WO2011049157A1 | 2011-04-28 | |||
| WO2012074130A1 | 2012-06-07 | |||
| WO2012074129A1 | 2012-06-07 | |||
| WO2015030014A1 | 2015-03-05 | |||
| WO2008117833A1 | 2008-10-02 | |||
| WO2012074129A1 | 2012-06-07 |
Foreign References:
| JP2008125396A | 2008-06-05 |
Other References:
KATO, T. ET AL.: "Essential structural elements in tRNAPro for EF-P-mediated alleviation of translation stalling", NATURE COMMUNICATIONS, vol. 7, 2016, pages 11657, XP055598164
KOJIMA, TATSUYA ET AL.: "Genetic Code Reprogramming", SEIBUTSU BUTSURI, vol. 52, no. 1, pages 004 - 009, XP055598167
KATO, T. ET AL.: "Consecutive Elongation of D- Amino Acids in Translation,", CELL CHEMICAL BIOLOGY, vol. 24, no. 1, 29 December 2016 (2016-12-29), pages 46 - 54, XP029890372
KATO, T. ET AL.: "Logical engineering of D-arm and I-stem of tRNA that enhances D-amino acid incorporation", NUCLEIC ACIDS RESEARCH, vol. 45, no. 22, 16 November 2017 (2017-11-16), pages 12601 - 12610, XP055598170
MURAKAMI, H. ET AL., NAT. METHODS, vol. 3, 2006, pages 357 - 359
GOTO, Y. ET AL., NAT. PROTOC., vol. 6, 2011, pages 779 - 790
GOTO, Y. ET AL., RNA, vol. 14, 2008, pages 1390 - 1398
FUJINO, T. ET AL., J. AM. CHEM. SOC., vol. 135, 2013, pages 1830 - 1837
KATOH, T. ET AL., CELL CHEM. BIOL., vol. 24, 2017, pages 46 - 54
KAWAKAMI, T. ET AL., CHEM BIOL, vol. 15, 2008, pages 32 - 42
KAWAKAMI, T. ET AL., J AM CHEM SOC, vol. 135, 2013, pages 12297 - 12304
FUJINO, T. ET AL., J AM CHEM SOC, vol. 138, 2016, pages 1962 - 1969
OHTA, A. ET AL., CHEM BIOL, vol. 14, 2007, pages 1315 - 1322
DEDKOVA, L.M. ET AL., J. AM. CHEM. SOC., vol. 125, 2003, pages 6616 - 6617
DEDKOVA, L.M. ET AL., BIOCHEMISTRY, vol. 45, 2006, pages 15541 - 15551
ACHENBACH, J. ET AL., NUCLEIC ACIDS RES, vol. 43, 2015, pages 5687 - 5698
HECKLER, T. G. ET AL., J. BIOL. CHEM., vol. 258, 1983, pages 4492 - 4495
MAINI, R. ET AL., BIOCHEMISTRY, vol. 54, 2015, pages 3694 - 3706
IQBAL, E. S. ET AL., ORG. BIOMOL. CHEM., vol. 16, 2018, pages 1073 - 1078
DEDKOVA, L. M. ET AL., BIOCHEMISTRY, vol. 51, 2011, pages 401 - 415
MAINI, R. ET AL., BIOORG. MED. CHEM., vol. 21, 2013, pages 1088 - 1096
CZEKSTER, C. M. ET AL., J. AM. CHEM. SOC., vol. 138, 2016, pages 5194 - 5197
H. F. KUNG ET AL., THE JOURNAL OF BIOLOGICAL CHEMISTRY, vol. 252, no. 19, 1977, pages 6889 - 6894
M. C. GONZA ET AL., PROCEEDING OF NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 82, 1985, pages 1648 - 1652
M. Y. PAVLOVM. EHRENBERG, ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, vol. 328, no. 1, 1996, pages 9 - 16
Y. SHIMIZU ET AL., NATURE BIOTECHNOLOGY, vol. 19, no. 8, 2001, pages 751 - 755
H. OHASHI ET AL., BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, vol. 352, no. 1, 2007, pages 270 - 276
KAWAKAMI, T. ET AL., NATURE CHEMICAL BIOLOGY, vol. 5, 2009, pages 888 - 890
YAMAGISHI, Y. ET AL., CHEMBIOCHEM, vol. 10, 2009, pages 1469 - 1472
SAKO, Y. ET AL., JOURNAL OF AMERICAN CHEMICAL SOCIETY, vol. 130, 2008, pages 7932 - 7934
GOTO, Y. ET AL., ACS CHEMICAL BIOLOGY, vol. 3, 2008, pages 120 - 129
KAWAKAMI T. ET AL., CHEMISTRY & BIOLOGY, vol. 15, 2008, pages 32 - 42
UDE, S. ET AL.: "Translation elongation factor EF-P alleviates ribosome stalling at polyproline stretches", SCIENCE, vol. 339, 2013, pages 82 - 5
DOERFEL, L.K. ET AL.: "EF-P is essential for rapid synthesis of proteins containing consecutive proline residues", SCIENCE, vol. 339, 2013, pages 85 - 8
KATOH, T.WOHLGEMUTH, I.NAGANO, M.RODNINA, M.V.SUGA, H.: "Essential structural elements in tRNA(Pro) for EF-P-mediated alleviation of translation stalling", NAT COMMUN, vol. 7, 2016, pages 11657
LARIVIERE, F.J.WOLFSON, A.D.UHLENBECK, O.C.: "Uniform binding of aminoacyl-tRNAs to elongation factor Tu by thermodynamic compensation", SCIENCE, vol. 294, 2001, pages 165 - 8
DALE, T.SANDERSON, L.E.UHLENBECK, O.C.: "The affinity of elongation factor Tu for an aminoacyl-tRNA is modulated by the esterified amino acid", BIOCHEMISTRY, vol. 43, 2004, pages 6159 - 66
BECKER, H.D.KERN, D.: "Thermus thermophilus: a link in evolution of the tRNA-dependent amino acid amidation pathways", PROC NATL ACAD SCI U S A, vol. 95, 1998, pages 12832 - 7
STANZEL, M.SCHON, A.SPRINZL, M.: "Discrimination against misacylated tRNA by chloroplast elongation factor Tu", EUR J BIOCHEM, vol. 219, 1994, pages 435 - 9
SCHRADER, J.M.CHAPMAN, S.J.UHLENBECK, O.C.: "Tuning the affinity of aminoacyl-tRNA to elongation factor Tu for optimal decoding", PROC NATL ACAD SCI U S A, vol. 108, 2011, pages 5215 - 20
HASEGAWA, T.YOKOGAWA, T.: "Escherichia coli proline tRNA: structure and recognition sites for prolyl-tRNA synthetase", NUCLEIC ACIDS SYMP. SER., vol. 44, 2000, pages 7 - 8
PAVLOV, M.Y. ET AL.: "Slow peptide bond formation by proline and other N-alkylamino acids in translation", PROC NATL ACAD SCI U S A, vol. 106, 2009, pages 50 - 4
DOERFEL, L.K. ET AL.: "Entropic Contribution of Elongation Factor P to Proline Positioning at the Catalytic Center of the Ribosome", J AM CHEM SOC, vol. 137, 2015, pages 12997 - 3006
WOHLGEMUTH, I.BRENNER, S.BERINGER, M.RODNINA, M.V.: "Modulation of the rate of peptidyl transfer on the ribosome by the nature of substrates", J BIOL CHEM, vol. 283, 2008, pages 32229 - 35
JOHANSSON, M. ET AL.: "pH-sensitivity of the ribosomal peptidyl transfer reaction dependent on the identity of the A-site aminoacyl-tRNA", PROC NATL ACAD SCI U S A, vol. 108, 2011, pages 79 - 84
MELNIKOV, S. ET AL.: "Molecular insights into protein synthesis with proline residues", EMBO REP, vol. 17, 2016, pages 1776 - 1784
DRIGGERS, E.M.HALE, S.P.LEE, J.TERRETT, N.K.: "The exploration of macrocycles for drug discovery--an underexploited structural class", NAT REV DRUG DISCOV, vol. 7, 2008, pages 608 - 24, XP055151640, DOI: 10.1038/nrd2590
HIPOLITO, C.J.SUGA, H.: "Ribosomal production and in vitro selection of natural product-like peptidomimetics: the FIT and RaPID systems", CURR OPIN CHEM BIOL, vol. 16, 2012, pages 196 - 203
PASSIOURA, T.KATOH, T.GOTO, Y.SUGA, H.: "Selection-based discovery of druglike macrocyclic peptides", ANNU REV BIOCHEM, vol. 83, 2014, pages 727 - 52, XP055561850, DOI: 10.1146/annurev-biochem-060713-035456
SAITO, H.KOUROUKLIS, D.SUGA, H.: "An in vitro evolved precursor tRNA with aminoacylation activity", EMBO J, vol. 20, 2001, pages 1797 - 806, XP002430320, DOI: 10.1093/emboj/20.7.1797
See also references of EP 3699276A4
KOJIMA, TATSUYA ET AL.: "Genetic Code Reprogramming", SEIBUTSU BUTSURI, vol. 52, no. 1, pages 004 - 009, XP055598167
KATO, T. ET AL.: "Consecutive Elongation of D- Amino Acids in Translation,", CELL CHEMICAL BIOLOGY, vol. 24, no. 1, 29 December 2016 (2016-12-29), pages 46 - 54, XP029890372
KATO, T. ET AL.: "Logical engineering of D-arm and I-stem of tRNA that enhances D-amino acid incorporation", NUCLEIC ACIDS RESEARCH, vol. 45, no. 22, 16 November 2017 (2017-11-16), pages 12601 - 12610, XP055598170
MURAKAMI, H. ET AL., NAT. METHODS, vol. 3, 2006, pages 357 - 359
GOTO, Y. ET AL., NAT. PROTOC., vol. 6, 2011, pages 779 - 790
GOTO, Y. ET AL., RNA, vol. 14, 2008, pages 1390 - 1398
FUJINO, T. ET AL., J. AM. CHEM. SOC., vol. 135, 2013, pages 1830 - 1837
KATOH, T. ET AL., CELL CHEM. BIOL., vol. 24, 2017, pages 46 - 54
KAWAKAMI, T. ET AL., CHEM BIOL, vol. 15, 2008, pages 32 - 42
KAWAKAMI, T. ET AL., J AM CHEM SOC, vol. 135, 2013, pages 12297 - 12304
FUJINO, T. ET AL., J AM CHEM SOC, vol. 138, 2016, pages 1962 - 1969
OHTA, A. ET AL., CHEM BIOL, vol. 14, 2007, pages 1315 - 1322
DEDKOVA, L.M. ET AL., J. AM. CHEM. SOC., vol. 125, 2003, pages 6616 - 6617
DEDKOVA, L.M. ET AL., BIOCHEMISTRY, vol. 45, 2006, pages 15541 - 15551
ACHENBACH, J. ET AL., NUCLEIC ACIDS RES, vol. 43, 2015, pages 5687 - 5698
HECKLER, T. G. ET AL., J. BIOL. CHEM., vol. 258, 1983, pages 4492 - 4495
MAINI, R. ET AL., BIOCHEMISTRY, vol. 54, 2015, pages 3694 - 3706
IQBAL, E. S. ET AL., ORG. BIOMOL. CHEM., vol. 16, 2018, pages 1073 - 1078
DEDKOVA, L. M. ET AL., BIOCHEMISTRY, vol. 51, 2011, pages 401 - 415
MAINI, R. ET AL., BIOORG. MED. CHEM., vol. 21, 2013, pages 1088 - 1096
CZEKSTER, C. M. ET AL., J. AM. CHEM. SOC., vol. 138, 2016, pages 5194 - 5197
H. F. KUNG ET AL., THE JOURNAL OF BIOLOGICAL CHEMISTRY, vol. 252, no. 19, 1977, pages 6889 - 6894
M. C. GONZA ET AL., PROCEEDING OF NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 82, 1985, pages 1648 - 1652
M. Y. PAVLOVM. EHRENBERG, ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, vol. 328, no. 1, 1996, pages 9 - 16
Y. SHIMIZU ET AL., NATURE BIOTECHNOLOGY, vol. 19, no. 8, 2001, pages 751 - 755
H. OHASHI ET AL., BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, vol. 352, no. 1, 2007, pages 270 - 276
KAWAKAMI, T. ET AL., NATURE CHEMICAL BIOLOGY, vol. 5, 2009, pages 888 - 890
YAMAGISHI, Y. ET AL., CHEMBIOCHEM, vol. 10, 2009, pages 1469 - 1472
SAKO, Y. ET AL., JOURNAL OF AMERICAN CHEMICAL SOCIETY, vol. 130, 2008, pages 7932 - 7934
GOTO, Y. ET AL., ACS CHEMICAL BIOLOGY, vol. 3, 2008, pages 120 - 129
KAWAKAMI T. ET AL., CHEMISTRY & BIOLOGY, vol. 15, 2008, pages 32 - 42
UDE, S. ET AL.: "Translation elongation factor EF-P alleviates ribosome stalling at polyproline stretches", SCIENCE, vol. 339, 2013, pages 82 - 5
DOERFEL, L.K. ET AL.: "EF-P is essential for rapid synthesis of proteins containing consecutive proline residues", SCIENCE, vol. 339, 2013, pages 85 - 8
KATOH, T.WOHLGEMUTH, I.NAGANO, M.RODNINA, M.V.SUGA, H.: "Essential structural elements in tRNA(Pro) for EF-P-mediated alleviation of translation stalling", NAT COMMUN, vol. 7, 2016, pages 11657
LARIVIERE, F.J.WOLFSON, A.D.UHLENBECK, O.C.: "Uniform binding of aminoacyl-tRNAs to elongation factor Tu by thermodynamic compensation", SCIENCE, vol. 294, 2001, pages 165 - 8
DALE, T.SANDERSON, L.E.UHLENBECK, O.C.: "The affinity of elongation factor Tu for an aminoacyl-tRNA is modulated by the esterified amino acid", BIOCHEMISTRY, vol. 43, 2004, pages 6159 - 66
BECKER, H.D.KERN, D.: "Thermus thermophilus: a link in evolution of the tRNA-dependent amino acid amidation pathways", PROC NATL ACAD SCI U S A, vol. 95, 1998, pages 12832 - 7
STANZEL, M.SCHON, A.SPRINZL, M.: "Discrimination against misacylated tRNA by chloroplast elongation factor Tu", EUR J BIOCHEM, vol. 219, 1994, pages 435 - 9
SCHRADER, J.M.CHAPMAN, S.J.UHLENBECK, O.C.: "Tuning the affinity of aminoacyl-tRNA to elongation factor Tu for optimal decoding", PROC NATL ACAD SCI U S A, vol. 108, 2011, pages 5215 - 20
HASEGAWA, T.YOKOGAWA, T.: "Escherichia coli proline tRNA: structure and recognition sites for prolyl-tRNA synthetase", NUCLEIC ACIDS SYMP. SER., vol. 44, 2000, pages 7 - 8
PAVLOV, M.Y. ET AL.: "Slow peptide bond formation by proline and other N-alkylamino acids in translation", PROC NATL ACAD SCI U S A, vol. 106, 2009, pages 50 - 4
DOERFEL, L.K. ET AL.: "Entropic Contribution of Elongation Factor P to Proline Positioning at the Catalytic Center of the Ribosome", J AM CHEM SOC, vol. 137, 2015, pages 12997 - 3006
WOHLGEMUTH, I.BRENNER, S.BERINGER, M.RODNINA, M.V.: "Modulation of the rate of peptidyl transfer on the ribosome by the nature of substrates", J BIOL CHEM, vol. 283, 2008, pages 32229 - 35
JOHANSSON, M. ET AL.: "pH-sensitivity of the ribosomal peptidyl transfer reaction dependent on the identity of the A-site aminoacyl-tRNA", PROC NATL ACAD SCI U S A, vol. 108, 2011, pages 79 - 84
MELNIKOV, S. ET AL.: "Molecular insights into protein synthesis with proline residues", EMBO REP, vol. 17, 2016, pages 1776 - 1784
DRIGGERS, E.M.HALE, S.P.LEE, J.TERRETT, N.K.: "The exploration of macrocycles for drug discovery--an underexploited structural class", NAT REV DRUG DISCOV, vol. 7, 2008, pages 608 - 24, XP055151640, DOI: 10.1038/nrd2590
HIPOLITO, C.J.SUGA, H.: "Ribosomal production and in vitro selection of natural product-like peptidomimetics: the FIT and RaPID systems", CURR OPIN CHEM BIOL, vol. 16, 2012, pages 196 - 203
PASSIOURA, T.KATOH, T.GOTO, Y.SUGA, H.: "Selection-based discovery of druglike macrocyclic peptides", ANNU REV BIOCHEM, vol. 83, 2014, pages 727 - 52, XP055561850, DOI: 10.1146/annurev-biochem-060713-035456
SAITO, H.KOUROUKLIS, D.SUGA, H.: "An in vitro evolved precursor tRNA with aminoacylation activity", EMBO J, vol. 20, 2001, pages 1797 - 806, XP002430320, DOI: 10.1093/emboj/20.7.1797
See also references of EP 3699276A4
Attorney, Agent or Firm:
INABA, Yoshiyuki et al. (JP)
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