Overexpression of aminoacyl-tRNA synthetases for efficient...

Chemistry: molecular biology and microbiology – Micro-organism – tissue cell culture or enzyme using process... – Recombinant dna technique included in method of making a...

Reexamination Certificate

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C435S320100, C435S325000, C435S006120, C435S183000, C435S348000, C435S366000, C435S410000, C435S419000, C435S254100, C435S254110, C435S243000, C435S252300, C530S350000

Reexamination Certificate

active

06586207

ABSTRACT:

Throughout this application various publications are referenced. The disclosures of these publications in their entireties are hereby incorporated by reference into this application in order to more fully describe the state of the art to which this invention pertains.
FIELD OF INVENTION
The present invention relates to novel compositions and methods, for incorporating amino acid analogues into proteins in vivo, by overexpression of aminoacyl-tRNA synthetases.
BACKGROUND OF INVENTION
Expanding the scope of biological polymerizations to include non-natural monomers, is an area of growing interest, with important theoretical and practical consequences. An early and critically important example of such studies was the demonstration that “dideoxy” nucleotide monomers can serve as substrates for DNA polymerases. Advances in DNA sequencing (F. Sanger, S. Nicklen, A. R. Coulson,
Proc. Natl. Acad. Sci. USA
1977, 74, 5463-5467), DNA base pairing models (M. J. Lutz, S. A. Benner, S. Hein, G. Breipohl, E. Uhlmann,
J. Am. Chem. Soc.
1997, 119, 3177-3178; J. C. Morales, E. T. Kool,
Nature Struct. Biol.
1998, 5, 950-954), materials synthesis (W. H. Park, R. W. Lenz, S. Goodwin,
Macromolecules
1998, 31, 1480-1486; Y. Doi, S. Kitamura, H. Abe,
Macromolecules
1995, 28, 4822-4828), and cell surface engineering (K. J. Yarema, L. K. Mahal, R. E. Bruehl, E. C. Rodriguez, C. R. Bertozzi,
J. Biol. Chem.
1998, 273, 31168-31179; L. K. Mahal, K. J. Yarema, C. R. Bertozzi,
Science
1997, 276, 1125-1128; Saxon, E. and Bertozzi, C. R.
Science
2000, 287, 2007-2010) have resulted from the recognition of non-natural monomers by the enzymes that control these polymerizations.
Recent investigations have shown the incorporation of modified or completely “synthetic” bases into nucleic acids (Matray, T. J.; Kool, E. T.
Nature
1999, 399, 704; Kool, E. T.
Biopolymers
1998, 48, 3; Morales, J. C. ; Kool, E. T.
Nature Struct. Biol.
1998, 5, 950; Guckian, K. M. ; Kool, E. T. ;
Angew. Chem. Int. Ed. Eng.
1998, 36, 2825; Liu, D. Y. ; Moran, S.; Kool, E. T.
Chem. Biol.
1997, 4, 919; Moran, S.; Ren, R. X. F.; Kool, E. T.
Proc. Natl. Acad. Sci. USA
1997, 94, 10506; Moran, S. et al.
J. Am. Chem. Soc.
1997, 119, 2056; Benner, S. A. et al.
Pure Appl. Chem.
1998, 70, 263; Lutz, M. J.; Horlacher J.; Benner, S. A.
Bioorg. Med. Chem. Lett.
1998, 8, 1149; Lutz, M. J. ; Held, H. A. ; Hottiger, M.; Hubscher, U.; Benner, S. A.
Nuc. Acids Res.
1996, 24, 1308; Horlacher, J. et al.
Proc. Natl. Acad. Sci. USA
1995, 92, 6329; Switzer, C. Y. ; Moroney, S. E. ; Benner, S. A.
Biochemistry
1993, 32, 10489; Lutz, M. J.; Horlacher, J.; Benner, S. A.
Bioorg. Med. Chem. Lett.
1998, 8, 499; Switzer, C.; Moroney, S. E. ; Benner, S. A.
J. Am. Chem. Soc.
1989, 111, 8322; Piccirilli, J. A. ; Krauch, T.; Moroney, S. E. ; Benner, S. A.
Nature
1990, 343, 33), while materials researchers have exploited the broad substrate range of the poly(&bgr;-hydroxyalkanoate) (PHA) synthases to prepare novel poly(&bgr;-hydroxyalkanoate)s (PHAs) with unusual physical properties (Kim, Y. B.; Rhee, Y. H.; Lenz, R. W.
Polym. J.
1997, 29, 894; Hazer, B.; Lenz, R. W.; Fuller, R. C.
Polymer
1996, 37, 5951; Lenz, R. W. ; Kim, Y. B. ; Fuller, R. C.
FEMS Microbiol. Rev.
1992, 103, 207; Park, W. H.; Lenz, R. W.;
Goodwin, S. Macromolecules
1998, 31, 1480; Ballistreri, A. et al.
Macromolecules
1995, 28, 3664; Doi, Y.; Kitamura, S.; Abe, H.
Macromolecules
1995, 28, 4822).
Novel polymeric materials with unusual physical and/or chemical properties are also useful in polymer chemistry. The last several decades have shown many advances in synthetic polymer chemistry that provide the polymer chemist with increasing control over the structure of macromolecules (Szwarc, M.
Nature
1956, 178, 1168-1169 Szwarc, M.
Nature
1956, 178, 1168-1169; Faust, R.; Kennedy, J. P.
Polym. Bull.
1986, 15, 317-323; Schrock, R. R.
Acc. Chem. Res.
1990, 23, 158-165; Corradini, P.
Macromol Symp.
1995, 89, 1-11; Brintzinger, H. H.; Fischer, D.; Mulhaupt, R.; Rieger, B.; Waymouth, R. M.
Angew. Chem. Int. Ed. Engl.
1995, 34, 1143-1170; Dias, E. L.; SonBinh, T. N.; Grubbs, R. H.
J. Am. Chem. Soc.
1997, 119, 3887-3897; Chiefari, J. et al.
Macromolecules
1998, 31, 5559-5562). However, none of these methods have provided the level of control that is the basis of the exquisite catalytic, informational, and signal transduction capabilities of proteins and nucleic acids (Ibba, M.; Soll, D.
Science
1999, 286, 1893-1897). There remains a need for control over protein synthesis to design and produce artificial proteins having advantageous properties.
For this reason, the design and synthesis of artificial proteins that exhibit novel and potentially useful structural properties have been investigated. Harnessing the molecular weight and sequence control provided by in vivo synthesis would permit control of folding, functional group placement, and self-assembly at the angstrom length scale. Proteins that have been produced by in vivo methods exhibit predictable chain-folded lamellar architectures (Krejchi, M. T.; Atkins, E. D. T.; Waddon, A. J.; Fournier, M. J.; Mason, T. L.; Tirrell, D. A.
Science
1994, 265, 1427-1432; Parkhe, A. D.; Fournier, M. J. ; Mason, T. L.; Tirrell, D. A.
Macromolecules
1993, 26(24), 6691-6693; McGrath, K. P.; Fournier, M. J. ; Mason, T. L.; Tirrell, D. A.
J. Am. Chem. Soc.
1992, 114, 727-733; Creel, H. S.; Fournier, M. J.; Mason, T. L.; Tirrell, D. A.
Macromolecules
1991, 24, 1213-1214), unique smectic liquid-crystalline structures with precise layer spacings (Yu, S. M.; Conticello, V.; Zhang, G.; Kayser, C.; Fournier, M. J.; Mason, T. L.; Tirrell, D. A.
Nature
1997, 389, 187-190), and controlled reversible gelation (Petka, W. A.; Hardin, J. L.; McGrath, K. P.; Wirtz, D.; Tirrell, D. A.
Science
1998, 281, 389-392). The demonstrated ability of these protein polymers to form unique macromolecular architectures will be of importance for engineering materials with interesting liquid-crystalline, crystalline, surface, electronic, and optical properties.
Novel chemical and physical properties that can be engineered into protein polymers may be expanded by the precise placement of amino acid analogues. Efforts to incorporate novel amino acids into proteins in vivo have relied on the ability of the translational apparatus to recognize amino acid analogues that differ in structure and functionality from the natural amino acids. The in vivo incorporation of amino acid analogues into proteins is controlled most stringently by the aminoacyl-tRNA synthetases (AARS), the class of enzymes that safeguards the fidelity of amino acid incorporation into proteins (FIG.
1
). The DNA message is translated into an amino acid sequence via the pairing of the codon of the messenger RNA (mRNA) with the complementary anticodon of the aminoacyl-tRNA. Aminoacyl-tRNA synthetases control the fidelity of amino acid attachment to the tRNA. The discriminatory power of the aminoacyl-tRNA synthetase places severe limits on the set of amino acid structures that can be exploited in the engineering of natural and artificial proteins in vivo.
Several strategies for circumventing the specificity of the synthetases have been explored. Introduction of amino acid analogues can be achieved relatively simply via solid-phase peptide synthesis (Merrifield, R. B.
Pure
&
Appl. Chem.
1978, 50, 643-653). While this method circumvents all biosynthetic machinery, the multistep procedure is limited to synthesis of peptides less than or equal to approximately 50 amino acids in length, and is therefore not suitable for producing protein materials of longer amino acid sequences.
Chemical aminoacylation methods, introduced by Hecht and coworkers (Hecht, S. M.
Acc. Chem. Res.
1992, 25, 545; Heckler, T. G.; Roesser, J. R.; Xu, C.; Chang, P.; Hecht, S. M.
Biochemistry
1988, 27, 7254; Hecht, S. M.; Alford, B. L.; Kuroda, Y.; Kitano, S.
J. Biol. Chem.
1978, 253, 4517) and exploited by Schultz, Chamberlin, Dougherty and others (Cornish, V. W.; Mendel, D.; Schultz, P.

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