Highly reproductive Escherichia coli cells with no specific assignment to the UAG codon

Scientific Reports

Volumn 5, Issue , 2015, Pages

  Mukai, Takahito ^a   Hoshi, Hiroko ^a,b   Ohtake, Kazumasa ^a   Takahashi, Mihoko ^a   Yamaguchi, Atsushi ^a   Hayashi, Akiko ^a   Yokoyama, Shigeyuki ^a   Sakamoto, Kensaku ^a  

^a RIKEN   (Japan)

^b MAEBASHI INSTITUTE OF TECHNOLOGY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ESCHERICHIA COLI PROTEIN; PRFA PROTEIN, E COLI; RECOMBINANT PROTEIN; STOP CODON; TRANSLATION TERMINATION FACTOR;

BACTERIAL GENOME; ESCHERICHIA COLI; GENE INACTIVATION; GENETIC ENGINEERING; GENETICS; GENOMICS; METABOLISM; PROTEIN PROCESSING; PROTEIN SYNTHESIS; STOP CODON;

CODON, TERMINATOR; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE KNOCKOUT TECHNIQUES; GENETIC ENGINEERING; GENOME, BACTERIAL; GENOMICS; PEPTIDE TERMINATION FACTORS; PROTEIN BIOSYNTHESIS; PROTEIN PROCESSING, POST-TRANSLATIONAL; RECOMBINANT PROTEINS;

EID: 84929598343     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep09699     Document Type: Article

References (45)

1. Itakura, K. et al. Expression in Escherichia coli of a chemically synthesized gene for the hormone somatostatin. Science 198, 1056-1063 (1977).
2. Goeddel, D. V. et al. Expression in Escherichia coli of chemically synthesized genes for human insulin. Proc. Natl. Acad. Sci. USA 76, 106-110 (1979).
3. Assenberg, R., Wan, P. T., Geisse, S. & Mayr, L. M. Advances in recombinant protein expression for use in pharmaceutical research. Curr. Opin. Struct. Biol. 23, 393-402 (2013).
4. Mukai, T. et al. Codon reassignment in the Escherichia coli genetic code. Nucleic Acids Res. 38, 8188-8195 (2010).
5. Isaacs, F. J. et al. Precise manipulation of chromosomes in vivo enables genomewide codon replacement. Science 333, 348-353 (2011).
6. Mukai, T. et al. Genetic-code evolution for protein synthesis with non-natural amino acids. Biochem. Biophys. Res. Commun. 411, 757-761 (2011).
7. Johnson, D. B. et al. RF1 knockout allows ribosomal incorporation of unnatural amino acids at multiple sites. Nat. Chem. Biol. 7, 779-786 (2011).
8. Johnson, D. B. et al. Release factor one is nonessential in Escherichia coli. ACS Chem. Biol. 7, 1337-1344 (2012).
9. Heinemann, I. U. et al. Enhanced phosphoserine insertion during Escherichia coli protein synthesis via partial UAG codon reassignment and release factor 1 deletion. FEBS Let. 586, 3716-3722 (2012).
10. Lajoie, M. J. et al. Genomically recoded organisms expand biological functions. Science 342, 357-360 (2013).
11. Rydén, S. M. & Isaksson, L. A. A temperature-sensitive mutant of Escherichia coli that shows enhanced misreading of UAG/A and increased efficiency for some tRNA nonsense suppressors. Mol. Gen. Genet. 193, 38-45 (1984).
12. Crick, F. H. The origin of the genetic code. J. Mol. Biol. 38, 367-379 (1968).
13. Baba, T. et al. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. doi:10.1038/msb4100050 (2006).
14. Eyre-Walker, A. The close proximity of Escherichia coli genes: consequences for stop codon and synonymous codon use. J. Mol. Evol. 42, 73-78 (1996).
15. Mora, L., Heurgué-Hamard, V., de Zamaroczy, M., Kervestin, S. & Buckingham, R. H. Methylation of bacterial release factors RF1 and RF2 is required for normal translation termination in vivo. J. Biol. Chem. 282, 35638-35645 (2007).
16. Ito, K., Uno, M. & Nakamura, Y. Single amino acid substitution in prokaryote polypeptide release factor 2 permits it to terminate translation at all three stop codons. Proc. Natl. Acad. Sci. USA 95, 8165-8169 (1998).
17. Ohtake, K. et al. Efficient decoding of theUAGtriplet as a full-fledged sense codon enhances the growth of a prfA-deficient strain of Escherichia coli. J. Bacteriol. 194, 2606-2613 (2012).
18. Sawitzke, J. A. et al. Probing cellular processes with oligo-mediated recombination and using the knowledge gained to optimize recombineering. J. Mol. Biol. 407, 45-59 (2011).
19. Kthiri, F. et al. Translational defects in a mutant deficient in YajL, the bacterial homolog of the parkinsonism-associated protein DJ-1. J. Bacteriol. 192, 6302-6306 (2010).
20. Zhang, Y. M., Marrakchi, H. & Rock, C. O. The FabR (YijC) transcription factor regulates unsaturated fatty acid biosynthesis in Escherichia coli. J. Biol. Chem. 277, 15558-15565 (2002).
21. Kim, C. H., Axup, J. Y. & Schultz, P. G. Protein conjugation with genetically encoded unnatural amino acids. Curr. Opin. Chem. Biol. 17, 412-419 (2013).
22. Lemke, E. A. The exploding genetic code. Chembiochem 15, 1691-1694 (2014).
23. Liu, C. C. & Schultz, P. G. Recombinant expression of selectively sulfated proteins in Escherichia coli. Nat. Biotechnol. 24, 1436-1440 (2006).
24. Lu, W. et al. Production and characterization of hirudin variant-1 by SUMO fusion technology in E. coli. Mol. Biotechnol. 53, 41-48 (2013).
25. Kim, C. H. et al. Synthesis of bispecific antibodies using genetically encoded unnatural amino acids. J. Am. Chem. Soc. 134, 9918-9921 (2012).
26. Chin, J. W. et al. Addition of p-azido-L-phenylalanine to the genetic code of Escherichia coli. J. Am. Chem. Soc. 124, 9026-9027 (2002).
27. Saxon, E. & Bertozzi, C. R. Cell surface engineering by a modified Staudinger reaction. Science 287, 2007-2010 (2000).
28. Tsao, M. L., Tian, F. & Schultz, P. G. Selective Staudinger modification of proteins containing p-azidophenylalanine. Chembiochem 6, 2147-2149 (2005).
29. Axup, J. Y. et al. Synthesis of site-specific antibody-drug conjugates using unnatural amino acids. Proc. Natl. Acad. Sci. USA 109, 16101-16106 (2012).
30. Wang, K., Neumann, H., Peak-Chew, S. Y. & Chin, J. W. Evolved orthogonal ribosomes enhance the efficiency of synthetic genetic code expansion. Nat. Biotechnol. 25, 770-777 (2007).
31. Petry, S. et al. Crystal structures of the ribosome in complex with release factors RF1 and RF2 bound to a cognate stop codon. Cell 123, 1255-1266 (2005).
32. Keiler, K. C., Weller, P. R. & Sauer, R. T. Role of a peptide tagging system in degradation of protein synthesized from damaged messenger RNA. Science 271, 990-993 (1996).
33. Chadani, Y., Ito, K., Kutsukake, K. & Abo, T. ArfA recruits release factor 2 to rescue stalled ribosomes by peptidyl-tRNA hydrolysis in Escherichia coli. Mol. Microbiol. 86, 37-50 (2012).
34. Chadani, Y. et al. Ribosome rescue by Escherichia coli ArfA (YhdL) in the absence of trans-translation system. Mol. Microbiol. 78, 796-808 (2010).
35. Handa, Y., Inaho, N. & Nameki, N. YaeJ is a novel ribosome-associated protein in Escherichia coli that can hydrolyze peptidyl-tRNA on stalled ribosomes. Nucleic Acids Res. 39, 1739-1748 (2011).
36. Ivanova, N. N. et al. Stop codon reassignments in the wild. Science 344, 909-913.
37. Osawa, S, &Jukes, T. H. Codon reassignment (codon capture) in evolution. J. Mol. Evol. 28, 271-278 (1989).
38. Vakhrusheva,A. A., Kazanov,M.D., Mironov, A. A.&Bazykin, G. A. Evolution of prokaryotic genes by shift of stop codons. J. Mol. Evol. 72, 138-146 (2008).
39. Guo, J., Melancxon, C. E., Lee, H. S., Groff, D. & Schultz, P. G. Evolution of amber suppressor tRNAs for efficient bacterial production of proteins containing nonnatural amino acids. Angew. Chem. Int. Ed. Engl. 48, 9148-9151 (2009).
40. Keseler, I. M. et al. EcoCyc: fusing model organism databases with systems biology. Nucleic Acids Res. 41, D605-D612 (2013).
41. Zhou, J. & Rudd, K. E. EcoGene 3.0. Nucleic Acids Res. 41, D613-D624 (2013).
42. Salgado, H. et al. RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more. Nucleic Acids Res. 41, D203-D213 (2013).
43. Mitra, A., Kesarwani, A. K., Pal, D.&Nagaraja, V. WebGeSTer DB-a transcription terminator database. Nucleic Acids Res. 39, D129-D135 (2011).
44. Wang, H. H. & Church, G. M. Multiplexed genome engineering and genotyping methods applications for synthetic biology and metabolic engineering. Methods in Enzymol. 498, 409-426 (2011).
45. Barbas, C. F. 3rd. et al. Recombinant human Fab fragments neutralize human type 1 immunodeficiency virus in vitro. Proc. Natl. Acad. Sci. USA 89, 9339-9343 (1992).