Title:
METHOD FOR PRODUCING PEPTIDE CONTAINING NON-NATURAL AMINO ACID
Document Type and Number:
WIPO Patent Application WO/2021/117848
Kind Code:
A1
Abstract:
It has been found that in a translation system including a ribosome that includes modified L31 protein, by virtue of translating mRNA coding a peptide containing a non-natural amino acid, the translation amount of said peptide can be increased. It has also been found that the relative amount of by-products can also be reduced by using said ribosome. The modified L31 protein in the present invention has an amino acid sequence of wild Escherichia coli L31 protein with six or more amino acid residues from the C terminal deleted.
Inventors:
YOSHII SAKIKO (JP)
SHIMOMURA KOICHIRO (JP)
ISHINO SOU (JP)
SHIMOMURA KOICHIRO (JP)
ISHINO SOU (JP)
Application Number:
PCT/JP2020/046213
Publication Date:
June 17, 2021
Filing Date:
December 11, 2020
Export Citation:
Assignee:
CHUGAI PHARMACEUTICAL CO LTD (JP)
International Classes:
C12N15/31; C07K7/04; C07K7/64; C12N1/15; C12N1/19; C12N1/21; C12N5/10; C12N15/09; C12N15/11; C12N15/63; C12P21/02; C40B30/04; C40B40/10; G01N33/15; G01N33/50
Domestic Patent References:
| WO2018174078A1 | 2018-09-27 | |||
| WO2013100132A1 | 2013-07-04 | |||
| WO2018143145A1 | 2018-08-09 | |||
| WO2018225864A1 | 2018-12-13 | |||
| WO2016148044A1 | 2016-09-22 | |||
| WO2008117833A1 | 2008-10-02 | |||
| WO2012074129A1 | 2012-06-07 | |||
| WO2017150732A1 | 2017-09-08 | |||
| WO2013100132A1 | 2013-07-04 | |||
| WO2018225851A1 | 2018-12-13 | |||
| WO2018143145A1 | 2018-08-09 | |||
| WO2018225864A1 | 2018-12-13 | |||
| WO2020138336A1 | 2020-07-02 |
Foreign References:
| JP2004173627A | 2004-06-24 | |||
| JPH078289A | 1995-01-13 |
Other References:
UETA, M. ET AL.: "Ribosomal protein L31 in Escherichia coli contributes to ribosome subunit association and translation, whereas short L31 cleaved by protease 7 reduces both activities", GENES TO CELLS, vol. 22, 2017, pages 452 - 471, XP055835088
UEDA, MASAMI ET AL.: "3P-0236 A translation activity of Escherichia coli ribosome is 40% higher than a conventional measured value - Effects of L31 protein damage are excluded", 39TH ANNUAL CONFERENCE OF THE MOLECULAR BIOLOGY SOCIETY OF JAPAN; NOV. 30 - DEC. 2, 2016, vol. 39, 30 November 2015 (2015-11-30) - 2 December 2016 (2016-12-02), JP, pages 3P-0236, XP009537476
DATABASE UniprotKB [online] 7 November 2018 (2018-11-07), XP055835090, Database accession no. A0A377B8T0
MAINI, R.UMEMOTO, S.SUGA, H.: "Ribosome-mediated synthesis of natural product-like peptides via cell-free translation", CURRENT OPINION IN CHEMICAL BIOLOGY, vol. 34, 2016, pages 44 - 52, XP029806922, DOI: 10.1016/j.cbpa.2016.06.006
HARTMAN, M. C.JOSEPHSON, K.LIN, C. W.SZOSTAK, J. W.: "An expanded set of amino acid analogs for the ribosomal translation of unnatural peptides", PLOS ONE, vol. 2, 2007, pages e972
UETA MWADA CBESSHO YMAEDA MWADA A, GENES CELLS, vol. 22, no. 5, May 2017 (2017-05-01), pages 452 - 471
LILLEORG SREIER KREMME JLIIV A., J MOL BIOL., vol. 429, no. 7, 7 April 2017 (2017-04-07), pages 1067 - 1080
J MOL BIOL., 2017
CHADANI YNIWA TIZUMI TSUGATA NNAGAO ASUZUKI TCHIBA SITO KTAGUCHI H, MOL CELL., vol. 68, no. 3, 2 November 2017 (2017-11-02), pages 528 - 539
MOL CELL, 2017
KUNKEL ET AL., PROC. NATL. ACAD. SCI. USA, vol. 82, 1985, pages 488 - 492
PROC. NATL. ACAD. SCI. USA, vol. 87, 1990, pages 2264 - 2268
PROC. NATL. ACAD. SCI. USA, vol. 90, 1993, pages 5873
ALTSCHUL SF ET AL., J. MOL. BIOL., vol. 215, 1990, pages 403
J. AM. CHEM. SOC., vol. 131, no. 14, 15 April 2009 (2009-04-15), pages 5040 - 1
NOWAK ET AL., SCIENCE, vol. 268, 1995, pages 439 - 442
ERICKSON ET AL., METHODS ENZYMOL, vol. 101, 1983, pages 674 - 690
GASIOR ET AL., J BIOL CHEM, vol. 254, 1979, pages 3965 - 3969
BARTON ET AL., METHODS ENZYMOL, vol. 275, 1996, pages 35 - 57
SWERDEL ET AL., COMP BIOCHEM PHYSIOL B, vol. 93, 1989, pages 803 - 806
SHIMIZU ET AL., NAT BIOTECH, vol. 19, 2001, pages 751 - 755
NAT. BIOTECHNOL., vol. 19, 2001, pages 751 - 5
SHIMIZU, Y.INOUE, A.TOMARI, Y.SUZUKI, T.YOKOGAWA, T.NISHIKAWA, K.UEDA, T., METHODS MOL. BIOL., vol. 607, 2010, pages 11 - 21
J. AM. CHEM. SOC., vol. 127, 2005, pages 11727 - 35
KWON, I. ET AL.: "Breaking the degeneracy of the genetic code", J. AM. CHEM. SOC., vol. 125, 2003, pages 7512 - 3
KAWAKAMI, T. ET AL.: "Ribosomal synthesis of polypeptoids and peptoid-peptide hybrids", J. AM. CHEM. SOC., vol. 130, 2008, pages 16861 - 3
KAWAKAMI, T. ET AL.: "Diverse backbone-cyclized peptides via codon reprogramming", NAT. CHEM. BIOL., vol. 5, 2009, pages 888 - 90, XP055143411, DOI: 10.1038/nchembio.259
DEDKOVA LM ET AL.: "Construction of modified ribosomes for incorporation of D-amino acids into proteins", BIOCHEMISTRY, vol. 45, 2006, pages 15541 - 51
DOI Y ET AL.: "Elongation factor Tu mutants expand amino acid tolerance of protein biosynthesis system", J AM CHEM SOC., vol. 129, 2007, pages 14458 - 62
PARK HS ET AL.: "Expanding the genetic code of Escherichia coli with phosphoserine", SCIENCE, vol. 333, 2011, pages 1151 - 4, XP055014139, DOI: 10.1126/science.1207203
BIOCHEMISTRY, vol. 42, 2003, pages 9598 - 608
ANDERSON, JC.SCHULTZ, PG., CHEM. BIOL., vol. 10, 2003, pages 1077 - 84
PROC. NATL. ACAD. SCI. USA., vol. 99, 2002, pages 9715 - 20
KIGA, D.SAKAMOTO, K.KODAMA, K.KIGAWA, T.MATSUDA, T.YABUKI, T.SHIROUZU, M.HARADA, Y.NAKAYAMA, H.TAKIO, K., SCIENCE, vol. 301, 2003, pages 964 - 7
CHIN, JW.CROPP, TA.ANDERSON, JC.MUKHERJI, M.ZHANG, Z.SCHULTZ, PG.CHIN, JW., PROC. NATL. ACAD. SCI. USA., vol. 103, 2006, pages 4356 - 61
HARTMAN, MCJOSEPHSON, K.SZOSTAK, JW.: "Second, a method in which tRNAs are aminoacylated in vitro, and then the amino acids are chemically modified can also be used", J. AM. CHEM. SOC., vol. 130, 2008, pages 6131 - 6
SUBTELNY, AO.HARTMAN, MC.SZOSTAK, JW: "Third, tRNAs in which CA has been removed from the 3'-end CCA sequence can be linked with a separately prepared aminoacylated pdCpA by using RNA ligase to obtain aminoacyl tRNAs", BIOCHEMISTRY, vol. 23, 1984, pages 1468 - 73
HECKLER, TG.CHANG, LH.ZAMA, Y.NAKA, T.CHORGHADE, MS.HECHT, SM: "There is also aminoacylation by flexizymes, which are ribozymes that allow tRNAs to carry active esters of various unnatural amino acids", J. AM. CHEM. SOC., vol. 124, 2002, pages 6834 - 5
CHEM. COMMUN. (CAMB, no. 34, 2005, pages 4321 - 3
HASHIMOTO, N.NINOMIYA, K.ENDO, T.SISIDO, M.: "Fifth, aminoacylation is also possible by linking an amino acid active ester to a PNA that is complementary to a sequence close to the 3'-end of a tRNA and adding this to the tRNA", J. AM. CHEM. SOC., vol. 126, 2004, pages 15984 - 9
PROC. NATL. ACAD. SCI. USA., vol. 94, 1997, pages 12297 - 302
ROBERTS, R.W.SZOSTAK, J.W., FEBS LETT., vol. 414, 1997, pages 405 - 8
NUCLEIC ACIDS RES., vol. 37, no. 16, 2009, pages e108
PROC. NATL. ACAD. SCI. USA., vol. 91, 1994, pages 9022 - 6
NUCLEIC ACIDSRES., vol. 33, 2005, pages e10
PROC. NATL. ACAD. SCI. USA., vol. 101, 2004, pages 2806 - 10
NAT. BIOTECHNOL., vol. 16, 1998, pages 652 - 6
KRAMER, W.FRITZ, H.-J.: "Oligonucleotide-directed construction of mutagenesis via gapped duplex DNA", METHODS IN ENZYMOLOGY, vol. 154, 1987, pages 350 - 367
SOUTHERN, E.M., JOURNAL OF MOLECULAR BIOLOGY, vol. 98, 1975, pages 503
MANDEL, M., HIGA, A., JOURNAL OF MOLECULAR BIOLOGY, vol. 53, 1970, pages 158 - 162
HANAHAN, D., JOURNAL OF MOLECULAR BIOLOGY, vol. 166, 1983, pages 557 - 580
WARD ET AL., NATURE, vol. 341, 1989, pages 544 - 546
FASEB J., vol. 6, 1992, pages 2422 - 2427
BETTER ET AL., SCIENCE, vol. 240, 1988, pages 1041 - 1043
LEI, S. P. ET AL., J. BACTERIOL., vol. 169, 1987, pages 4379
NUCLEIC ACIDS. RES., vol. 18, no. 17, 1990, pages 5322
MULLIGAN ET AL., NATURE, vol. 277, 1979, pages 108
MIZUSHIMA ET AL., NUCLEIC ACIDS RES., vol. 18, 1990, pages 5322
VALLE ET AL., NATURE, vol. 291, 1981, pages 358 - 340
PROC. NATL. ACAD. SCI. USA, vol. 77, 1980, pages 4216 - 4220
PROC. NATL. ACAD. SCI. USA, vol. 60, 1968, pages 1275
HELV. CHIM. ACTA, vol. 90, pages 297 - 310
YOKOGAWA TKITAMURA YNAKAMURA DOHNO SNISHIKAWA K, NUCLEIC ACIDS RESEARCH, vol. 38, 2010, pages e89
BMC BIOTECHNOLOGY, vol. 8, 2008, pages 41
PROTEIN SCIENCE, vol. 108, no. 4, 1990, pages 673 - 6
See also references of EP 4074829A4
UEDA, MASAMI ET AL.: "3P-0236 A translation activity of Escherichia coli ribosome is 40% higher than a conventional measured value - Effects of L31 protein damage are excluded", 39TH ANNUAL CONFERENCE OF THE MOLECULAR BIOLOGY SOCIETY OF JAPAN; NOV. 30 - DEC. 2, 2016, vol. 39, 30 November 2015 (2015-11-30) - 2 December 2016 (2016-12-02), JP, pages 3P-0236, XP009537476
DATABASE UniprotKB [online] 7 November 2018 (2018-11-07), XP055835090, Database accession no. A0A377B8T0
MAINI, R.UMEMOTO, S.SUGA, H.: "Ribosome-mediated synthesis of natural product-like peptides via cell-free translation", CURRENT OPINION IN CHEMICAL BIOLOGY, vol. 34, 2016, pages 44 - 52, XP029806922, DOI: 10.1016/j.cbpa.2016.06.006
HARTMAN, M. C.JOSEPHSON, K.LIN, C. W.SZOSTAK, J. W.: "An expanded set of amino acid analogs for the ribosomal translation of unnatural peptides", PLOS ONE, vol. 2, 2007, pages e972
UETA MWADA CBESSHO YMAEDA MWADA A, GENES CELLS, vol. 22, no. 5, May 2017 (2017-05-01), pages 452 - 471
LILLEORG SREIER KREMME JLIIV A., J MOL BIOL., vol. 429, no. 7, 7 April 2017 (2017-04-07), pages 1067 - 1080
J MOL BIOL., 2017
CHADANI YNIWA TIZUMI TSUGATA NNAGAO ASUZUKI TCHIBA SITO KTAGUCHI H, MOL CELL., vol. 68, no. 3, 2 November 2017 (2017-11-02), pages 528 - 539
MOL CELL, 2017
KUNKEL ET AL., PROC. NATL. ACAD. SCI. USA, vol. 82, 1985, pages 488 - 492
PROC. NATL. ACAD. SCI. USA, vol. 87, 1990, pages 2264 - 2268
PROC. NATL. ACAD. SCI. USA, vol. 90, 1993, pages 5873
ALTSCHUL SF ET AL., J. MOL. BIOL., vol. 215, 1990, pages 403
J. AM. CHEM. SOC., vol. 131, no. 14, 15 April 2009 (2009-04-15), pages 5040 - 1
NOWAK ET AL., SCIENCE, vol. 268, 1995, pages 439 - 442
ERICKSON ET AL., METHODS ENZYMOL, vol. 101, 1983, pages 674 - 690
GASIOR ET AL., J BIOL CHEM, vol. 254, 1979, pages 3965 - 3969
BARTON ET AL., METHODS ENZYMOL, vol. 275, 1996, pages 35 - 57
SWERDEL ET AL., COMP BIOCHEM PHYSIOL B, vol. 93, 1989, pages 803 - 806
SHIMIZU ET AL., NAT BIOTECH, vol. 19, 2001, pages 751 - 755
NAT. BIOTECHNOL., vol. 19, 2001, pages 751 - 5
SHIMIZU, Y.INOUE, A.TOMARI, Y.SUZUKI, T.YOKOGAWA, T.NISHIKAWA, K.UEDA, T., METHODS MOL. BIOL., vol. 607, 2010, pages 11 - 21
J. AM. CHEM. SOC., vol. 127, 2005, pages 11727 - 35
KWON, I. ET AL.: "Breaking the degeneracy of the genetic code", J. AM. CHEM. SOC., vol. 125, 2003, pages 7512 - 3
KAWAKAMI, T. ET AL.: "Ribosomal synthesis of polypeptoids and peptoid-peptide hybrids", J. AM. CHEM. SOC., vol. 130, 2008, pages 16861 - 3
KAWAKAMI, T. ET AL.: "Diverse backbone-cyclized peptides via codon reprogramming", NAT. CHEM. BIOL., vol. 5, 2009, pages 888 - 90, XP055143411, DOI: 10.1038/nchembio.259
DEDKOVA LM ET AL.: "Construction of modified ribosomes for incorporation of D-amino acids into proteins", BIOCHEMISTRY, vol. 45, 2006, pages 15541 - 51
DOI Y ET AL.: "Elongation factor Tu mutants expand amino acid tolerance of protein biosynthesis system", J AM CHEM SOC., vol. 129, 2007, pages 14458 - 62
PARK HS ET AL.: "Expanding the genetic code of Escherichia coli with phosphoserine", SCIENCE, vol. 333, 2011, pages 1151 - 4, XP055014139, DOI: 10.1126/science.1207203
BIOCHEMISTRY, vol. 42, 2003, pages 9598 - 608
ANDERSON, JC.SCHULTZ, PG., CHEM. BIOL., vol. 10, 2003, pages 1077 - 84
PROC. NATL. ACAD. SCI. USA., vol. 99, 2002, pages 9715 - 20
KIGA, D.SAKAMOTO, K.KODAMA, K.KIGAWA, T.MATSUDA, T.YABUKI, T.SHIROUZU, M.HARADA, Y.NAKAYAMA, H.TAKIO, K., SCIENCE, vol. 301, 2003, pages 964 - 7
CHIN, JW.CROPP, TA.ANDERSON, JC.MUKHERJI, M.ZHANG, Z.SCHULTZ, PG.CHIN, JW., PROC. NATL. ACAD. SCI. USA., vol. 103, 2006, pages 4356 - 61
HARTMAN, MCJOSEPHSON, K.SZOSTAK, JW.: "Second, a method in which tRNAs are aminoacylated in vitro, and then the amino acids are chemically modified can also be used", J. AM. CHEM. SOC., vol. 130, 2008, pages 6131 - 6
SUBTELNY, AO.HARTMAN, MC.SZOSTAK, JW: "Third, tRNAs in which CA has been removed from the 3'-end CCA sequence can be linked with a separately prepared aminoacylated pdCpA by using RNA ligase to obtain aminoacyl tRNAs", BIOCHEMISTRY, vol. 23, 1984, pages 1468 - 73
HECKLER, TG.CHANG, LH.ZAMA, Y.NAKA, T.CHORGHADE, MS.HECHT, SM: "There is also aminoacylation by flexizymes, which are ribozymes that allow tRNAs to carry active esters of various unnatural amino acids", J. AM. CHEM. SOC., vol. 124, 2002, pages 6834 - 5
CHEM. COMMUN. (CAMB, no. 34, 2005, pages 4321 - 3
HASHIMOTO, N.NINOMIYA, K.ENDO, T.SISIDO, M.: "Fifth, aminoacylation is also possible by linking an amino acid active ester to a PNA that is complementary to a sequence close to the 3'-end of a tRNA and adding this to the tRNA", J. AM. CHEM. SOC., vol. 126, 2004, pages 15984 - 9
PROC. NATL. ACAD. SCI. USA., vol. 94, 1997, pages 12297 - 302
ROBERTS, R.W.SZOSTAK, J.W., FEBS LETT., vol. 414, 1997, pages 405 - 8
NUCLEIC ACIDS RES., vol. 37, no. 16, 2009, pages e108
PROC. NATL. ACAD. SCI. USA., vol. 91, 1994, pages 9022 - 6
NUCLEIC ACIDSRES., vol. 33, 2005, pages e10
PROC. NATL. ACAD. SCI. USA., vol. 101, 2004, pages 2806 - 10
NAT. BIOTECHNOL., vol. 16, 1998, pages 652 - 6
KRAMER, W.FRITZ, H.-J.: "Oligonucleotide-directed construction of mutagenesis via gapped duplex DNA", METHODS IN ENZYMOLOGY, vol. 154, 1987, pages 350 - 367
SOUTHERN, E.M., JOURNAL OF MOLECULAR BIOLOGY, vol. 98, 1975, pages 503
MANDEL, M., HIGA, A., JOURNAL OF MOLECULAR BIOLOGY, vol. 53, 1970, pages 158 - 162
HANAHAN, D., JOURNAL OF MOLECULAR BIOLOGY, vol. 166, 1983, pages 557 - 580
WARD ET AL., NATURE, vol. 341, 1989, pages 544 - 546
FASEB J., vol. 6, 1992, pages 2422 - 2427
BETTER ET AL., SCIENCE, vol. 240, 1988, pages 1041 - 1043
LEI, S. P. ET AL., J. BACTERIOL., vol. 169, 1987, pages 4379
NUCLEIC ACIDS. RES., vol. 18, no. 17, 1990, pages 5322
MULLIGAN ET AL., NATURE, vol. 277, 1979, pages 108
MIZUSHIMA ET AL., NUCLEIC ACIDS RES., vol. 18, 1990, pages 5322
VALLE ET AL., NATURE, vol. 291, 1981, pages 358 - 340
PROC. NATL. ACAD. SCI. USA, vol. 77, 1980, pages 4216 - 4220
PROC. NATL. ACAD. SCI. USA, vol. 60, 1968, pages 1275
HELV. CHIM. ACTA, vol. 90, pages 297 - 310
YOKOGAWA TKITAMURA YNAKAMURA DOHNO SNISHIKAWA K, NUCLEIC ACIDS RESEARCH, vol. 38, 2010, pages e89
BMC BIOTECHNOLOGY, vol. 8, 2008, pages 41
PROTEIN SCIENCE, vol. 108, no. 4, 1990, pages 673 - 6
See also references of EP 4074829A4
Attorney, Agent or Firm:
HARUNA, Masao et al. (JP)
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