ACS Chemical Biology (3) Youngman, E. M., McDonald, M. E., and Green, R. (2008) Peptide release on the ribosome: mechanism and implications for translational control. Annu. Rev. Microbiol. 62, 353−373. (4) Frolova, L., Le Goﬀ, X., Rasmussen, H. H., Cheperegin, S., Drugeon, G., Kress, M., Arman, I., Haenni, A. L., Celis, J. E., Philippe, M., Justesen, J., and Kisselev, L. (1994) A highly conserved eukaryotic protein family possessing properties of polypeptide chain release factor. Nature 372, 701−703. (5) Dontsova, M., Frolova, L., Vassilieva, J., Piendl, W., Kisselev, L., and Garber, M. (2000) Translation termination factor aRF1 from the archaeon Methanococcus jannaschii is active with eukaryotic ribosomes. FEBS Lett. 472, 213−216. (6) Scolnick, E., Tompkins, R., Caskey, T., and Nirenberg, M. (1968) Release factors diﬀering in speciﬁcity for terminator codons. Proc. Natl. Acad. Sci. U.S.A. 61, 768−774. (7) Gibson, D. G., Glass, J. I., Lartigue, C., Noskov, V. N., Chuang, R. Y., Algire, M. A., Benders, G. A., Montague, M. G., Ma, L., Moodie, M. M., Merryman, C., Vashee, S., Krishnakumar, R., Assad-Garcia, N., Andrews-Pfannkoch, C., Denisova, E. A., Young, L., Qi, Z. Q., Segall- Shapiro, T. H., Calvey, C. H., Parmar, P. P., Hutchison, C. A., 3rd, Smith, H. O., and Venter, J. C. (2010) Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329, 52−56. (8) Wang, L., Brock, A., Herberich, B., and Schultz, P. G. (2001) Expanding the genetic code of Escherichia coli. Science 292, 498−500. (9) Wang, L., and Schultz, P. G. (2005) Expanding the genetic code. Angew. Chem., Int. Ed. 44, 34−66. (10) Wang, Q., Parrish, A. R., and Wang, L. (2009) Expanding the genetic code for biological studies. Chem. Biol. 16, 323−336. (11) Wu, X., and Schultz, P. G. (2009) Synthesis at the interface of chemistry and biology. J. Am. Chem. Soc. 131, 12497−12515. (12) Liu, C. C., and Schultz, P. G. (2010) Adding new chemistries to the genetic code. Annu. Rev. Biochem. 79, 413−444. (13) Johnson, D. B., Xu, J., Shen, Z., Takimoto, J. K., Schultz, M. D., Schmitz, R. J., Xiang, Z., Ecker, J. R., Briggs, S. P., and Wang, L. (2011) RF1 knockout allows ribosomal incorporation of unnatural amino acids at multiple sites. Nat. Chem. Biol. 7, 779−786. (14) Anderson, J. C., Wu, N., Santoro, S. W., Lakshman, V., King, D. S., and Schultz, P. G. (2004) An expanded genetic code with a functional quadruplet codon. Proc. Natl. Acad. Sci. U.S.A. 101, 7566− 7571. (15) Huang, Y., Russell, W. K., Wan, W., Pai, P. J., Russell, D. H., and Liu, W. (2010) A convenient method for genetic incorporation of multiple noncanonical amino acids into one protein in Escherichia coli. Mol. Biosyst. 6, 683−686. (16) Isaacs, F. J., Carr, P. A., Wang, H. H., Lajoie, M. J., Sterling, B., Kraal, L., Tolonen, A. C., Gianoulis, T. A., Goodman, D. B., Reppas, N. B., Emig, C. J., Bang, D., Hwang, S. J., Jewett, M. C., Jacobson, J. M., and Church, G. M. (2011) Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science 333, 348−353. (17) Lozupone, C., Knight, R., and Landweber, L. (2001) The molecular basis of nuclear genetic code change in ciliates. Curr. Biol. 11, 65−74. (18) Inagaki, Y., and Doolittle, W. F. (2001) Class I release factors in ciliates with variant genetic codes. Nucleic Acids Res. 29, 921−927. (19) Inagaki, Y., Bessho, Y., and Osawa, S. (1993) Lack of peptide- release activity responding to codon UGA in Mycoplasma capricolum. Nucleic Acids Res. 21, 1335−1338. (20) Gerdes, S. Y., Scholle, M. D., Campbell, J. W., Balazsi, G., Ravasz, E., Daugherty, M. D., Somera, A. L., Kyrpides, N. C., Anderson, I., Gelfand, M. S., Bhattacharya, A., Kapatral, V., D’Souza, M., Baev, M. V., Grechkin, Y., Mseeh, F., Fonstein, M. Y., Overbeek, R., Barabasi, A. L., Oltvai, Z. N., and Osterman, A. L. (2003) Experimental determination and system level analysis of essential genes in Escherichia coli MG1655. J. Bacteriol. 185, 5673−5684. (21) Rydeń, S., and Isaksson, L. (1984) 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. Letters (22) Mukai, T., Hayashi, A., Iraha, F., Sato, A., Ohtake, K., Yokoyama, S., and Sakamoto, K. (2010) Codon reassignment in the Escherichia coli genetic code. Nucleic Acids Res. 38, 8188−8195. (23) Datsenko, K., and Wanner, B. (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl. Acad. Sci. U.S.A. 97, 6640−6645. (24) Studier, F. W., Daegelen, P., Lenski, R. E., Maslov, S., and Kim, J. F. (2009) Understanding the diﬀerences between genome sequences of Escherichia coli B strains REL606 and BL21(DE3) and comparison of the E. coli B and K-12 genomes. J. Mol. Biol. 394, 653−680. (25) Kang, Y., Durfee, T., Glasner, J. D., Qiu, Y., Frisch, D., Winterberg, K. M., and Blattner, F. R. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186, 4921−4930. (26) Posfai, G., Plunkett, G., 3rd, Feher, T., Frisch, D., Keil, G. M., Umenhoﬀer, K., Kolisnychenko, V., Stahl, B., Sharma, S. S., de Arruda, M., Burland, V., Harcum, S. W., and Blattner, F. R. (2006) Emergent properties of reduced-genome Escherichia coli. Science 312, 1044−1046. (27) Uno, M., Ito, K., and Nakamura, Y. (1996) Functional speciﬁcity of amino acid at position 246 in the tRNA mimicry domain of bacterial release factor 2. Biochimie 78, 935−943. (28) Dincbas-Renqvist, V., Engstrom, A., Mora, L., Heurgue-Hamard, V., Buckingham, R., and Ehrenberg, M. (2000) A post-translational modiﬁcation in the GGQ motif of RF2 from Escherichia coli stimulates termination of translation. EMBO J. 19, 6900−6907. (29) Nakamura, Y., Gojobori, T., and Ikemura, T. (2000) Codon usage tabulated from international DNA sequence databases: status for the year 2000. Nucleic Acids Res. 28, 292. (30) Jeong, H., Barbe, V., Lee, C. H., Vallenet, D., Yu, D. S., Choi, S. H., Couloux, A., Lee, S. W., Yoon, S. H., Cattolico, L., Hur, C. G., Park, H. S., Segurens, B., Kim, S. C., Oh, T. K., Lenski, R. E., Studier, F. W., Daegelen, P., and Kim, J. F. (2009) Genome sequences of Escherichia coli B strains REL606 and BL21(DE3). J. Mol. Biol. 394, 644−652. (31) Durfee, T., Nelson, R., Baldwin, S., Plunkett, G., 3rd, Burland, V., Mau, B., Petrosino, J. F., Qin, X., Muzny, D. M., Ayele, M., Gibbs, R. A., Csorgo, B., Posfai, G., Weinstock, G. M., and Blattner, F. R. (2008) The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse. J. Bacteriol. 190, 2597−2606. (32) Zhang, S., Ryden-Aulin, M., Kirsebom, L. A., and Isaksson, L. A. (1994) Genetic implication for an interaction between release factor one and ribosomal protein L7/L12 in vivo. J. Mol. Biol. 242, 614−618. (33) Ito, K., Uno, M., and Nakamura, Y. (1998) Single amino acid substitution in prokaryote polypeptide release factor 2 permits it to terminate translation at all three stop codons. Proc. Natl. Acad. Sci. U.S.A. 95, 8165−8169. (34) Dahlgren, A., and Ryden-Aulin, M. (2000) A novel mutation in ribosomal protein S4 that aﬀects the function of a mutated RF1. Biochimie 82, 683−691. (35) Kaczanowska, M., and Ryden-Aulin, M. (2004) Temperature sensitivity caused by mutant release factor 1 is suppressed by mutations that aﬀect 16S rRNA maturation. J. Bacteriol. 186, 3046− 3055. (36) Yang, T. T., Cheng, L., and Kain, S. R. (1996) Optimized codon usage and chromophore mutations provide enhanced sensitivity with the green ﬂuorescent protein. Nucleic Acids Res. 24, 4592−4593. (37) Murgola, E. J. (2005) Translational suppression: when two wrongs do make a right, in tRNA: Structure, Biosynthesis, and Function (Soll, D., and RajBhandary, U. L., Eds.), pp 491−509, ASM Press, Washington, DC. (38) Wang, L., and Schultz, P. G. (2001) A general approach for the generation of orthogonal tRNAs. Chem. Biol. 8, 883−890. (39) Wang, L., Zhang, Z., Brock, A., and Schultz, P. G. (2003) Addition of the keto functional group to the genetic code of Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 100, 56−61. (40) Takimoto, J. K., Adams, K. L., Xiang, Z., and Wang, L. (2009) Improving orthogonal tRNA-synthetase recognition for eﬃcient unnatural amino acid incorporation and application in mammalian cells. Mol. Biosyst. 5, 931−934. 1343 dx.doi.org/10.1021/cb300229q | ACS Chem. Biol. 2012, 7, 1337−1344