3,011
Views
14
CrossRef citations to date
0
Altmetric
Review - Solicited

tRNA engineering for manipulating genetic code

, &
Pages 453-460 | Received 12 Apr 2017, Accepted 13 Jun 2017, Published online: 06 Sep 2017

References

  • Robertson SA, Noren CJ, Anthony-Cahill SJ, Griffith MC, Schultz PG. The use of 5′-phospho-2 deoxyribocytidylylriboadenosine as a facile route to chemical aminoacylation of tRNA. Nucleic Acids Res 1989; 17:9649-60; PMID:2602139; https://doi.org/10.1093/nar/17.23.9649
  • Murakami H, Ohta A, Ashigai H, Suga H. A highly flexible tRNA acylation method for non-natural polypeptide synthesis. Nat Methods 2006; 3:357-9; PMID:16628205; https://doi.org/10.1038/nmeth877
  • Goto Y, Katoh T, Suga H. Flexizymes for genetic code reprogramming. Nat Protoc 2011; 6:779-90; PMID:21637198; https://doi.org/10.1038/nprot.2011.331
  • Wang L, Brock A, Herberich B, Schultz PG. Expanding the genetic code of Escherichia coli. Science 2001; 292:498-500; PMID:11313494; https://doi.org/10.1126/science.1060077
  • Ai HW. Biochemical analysis with the expanded genetic lexicon. Anal Bioanal Chem 2012; 403:2089-102; PMID:22322380; https://doi.org/10.1007/s00216-012-5784-2
  • Chin JW, Cropp TA, Anderson JC, Mukherji M, Zhang Z, Schultz PG. An expanded eukaryotic genetic code. Science 2003; 301:964-7; PMID:12920298; https://doi.org/10.1126/science.1084772
  • Liu CC, Schultz PG. Adding new chemistries to the genetic code. Annu Rev Biochem 2010; 79:413-44; PMID:20307192; https://doi.org/10.1146/annurev.biochem.052308.105824
  • Noren C, Anthony-Cahill S, Griffith M, Schultz P. A general method for site-specific incorporation of unnatural amino acids into proteins. Science 1989; 244:182-8; PMID:2649980; https://doi.org/10.1126/science.2649980
  • Johnson DB, Xu J, Shen Z, Takimoto JK, Schultz MD, Schmitz RJ, Xiang Z, Ecker JR, Briggs SP, Wang L. RF1 knockout allows ribosomal incorporation of unnatural amino acids at multiple sites. Nat Chem Biol 2011; 7:779-86; PMID:21926996; https://doi.org/10.1038/nchembio.657
  • Hohsaka T, Ashizuka Y, Murakami H, Sisido M. Incorporation of nonnatural amino acids into streptavidin through in vitro frame-shift suppression. J Am Chem Soc 1996; 118:9778-79; https://doi.org/10.1021/ja9614225
  • Tan Z, Forster A, Blacklow S, Cornish V. Amino acid backbone specificity of the Escherichia coli translation machinery. J Am Chem Soc 2004; 126:12752-3; PMID:15469251; https://doi.org/10.1021/ja0472174
  • Fujino T, Goto Y, Suga H, Murakami H. Reevaluation of the D-amino acid compatibility with the elongation event in translation. J Am Chem Soc 2013; 135:1830-7; PMID:23301668; https://doi.org/10.1021/ja309570x
  • Achenbach J, Jahnz M, Bethge L, Paal K, Jung M, Schuster M, Albrecht R, Jarosch F, Nierhaus KH, Klussmann S. Outwitting EF-Tu and the ribosome: translation with D-amino acids. Nucleic Acids Res 2015; 43:5687-98; PMID:26026160; https://doi.org/10.1093/nar/gkv566
  • Fujino T, Goto Y, Suga H, Murakami H. Ribosomal synthesis of peptides with multiple β-amino acids. J Am Chem Soc 2016; 138:1962-9; PMID:26807980; https://doi.org/10.1021/jacs.5b12482
  • Katoh T, Tajima K, Suga H. Consecutive Elongation of D-Amino Acids in Translation. Cell Chem Biol 2017; 24:46-54; PMID:28042044; https://doi.org/10.1016/j.chembiol.2016.11.012
  • Xie J, Schultz PG. An expanding genetic code. Methods 2005; 36:227-38; PMID:16076448; https://doi.org/10.1016/j.ymeth.2005.04.010
  • Park HS, Hohn MJ, Umehara T, Guo LT, Osborne EM, Benner J, Noren CJ, Rinehart J, Soll D. Expanding the genetic code of Escherichia coli with phosphoserine. Science 2011; 333:1151-4; PMID:21868676; https://doi.org/10.1126/science.1207203
  • Ohta A, Murakami H, Higashimura E, Suga H. Synthesis of polyester by means of genetic code reprogramming. Chem Biol 2007; 14:1315-22; PMID:18096500; https://doi.org/10.1016/j.chembiol.2007.10.015
  • Murakami H, Kourouklis D, Suga H. Using a solid-phase ribozyme aminoacylation system to reprogram the genetic code. Chem Biol 2003; 10:1077-84; PMID:14652075; https://doi.org/10.1016/j.chembiol.2003.10.010
  • Cload ST, Liu DR, Froland WA, Schultz PG. Development of improved tRNAs for in vitro biosynthesis of proteins containing unnatural amino acids. Chem Biol 1996; 3:1033-8; PMID:9000011; https://doi.org/10.1016/S1074-5521(96)90169-6
  • Kawakami T, Murakami H, Suga H. Ribosomal synthesis of polypeptoids and peptoid-peptide hybrids. J Am Chem Soc 2008; 130:16861-3; PMID:19053417; https://doi.org/10.1021/ja806998v
  • Kawakami T, Ishizawa T, Murakami H. Extensive reprogramming of the genetic code for genetically encoded synthesis of highly N-alkylated polycyclic peptidomimetics. J Am Chem Soc 2013; 135:12297-304; PMID:23899321; https://doi.org/10.1021/ja405044k
  • Terasaka N, Hayashi G, Katoh T, Suga H. An orthogonal ribosome-tRNA pair via engineering of the peptidyl transferase center. Nat Chem Biol 2014; 10:555-7; PMID:24907900; https://doi.org/10.1038/nchembio.1549
  • Dale T, Sanderson LE, Uhlenbeck OC. The affinity of elongation factor Tu for an aminoacyl-tRNA is modulated by the esterified amino acid. Biochemistry 2004; 43:6159-66; PMID:15147200; https://doi.org/10.1021/bi036290o
  • Dale T, Uhlenbeck OC. Amino acid specificity in translation. Trends Biochem Sci 2005; 30:659-65; PMID:16260144; https://doi.org/10.1016/j.tibs.2005.10.006
  • Doi Y, Ohtsuki T, Shimizu Y, Ueda T, Sisido M. Elongation factor Tu mutants expand amino acid tolerance of protein biosynthesis system. J Am Chem Soc 2007; 129:14458-62; PMID:17958427; https://doi.org/10.1021/ja075557u
  • Shimizu Y, Inoue A, Tomari Y, Suzuki T, Yokogawa T, Nishikawa K, Ueda T. Cell-free translation reconstituted with purified components. Nat Biotechnol 2001; 19:751-5; PMID:11479568; https://doi.org/10.1038/90802
  • Iwane Y, Hitomi A, Murakami H, Katoh T, Goto Y, Suga H. Expanding the amino acid repertoire of ribosomal polypeptide synthesis via the artificial division of codon boxes. Nat Chem 2016; 8:317-25; PMID:27001726; https://doi.org/10.1038/nchem.2446
  • Komine Y, Adachi T, Inokuchi H, Ozeki H. Genomic organization and physical mapping of the transfer RNA genes in Escherichia coli K12. J Mol Biol 1990; 212:579-98; PMID:PMID:2184240; https://doi.org/10.1016/0022-2836(90)90224-A
  • Murphy FVt, Ramakrishnan V. Structure of a purine-purine wobble base pair in the decoding center of the ribosome. Nat Struct Mol Biol 2004; 11:1251-2; PMID:15558050; https://doi.org/10.1038/nsmb866
  • Gustilo EM, Vendeix FA, Agris PF. tRNA's modifications bring order to gene expression. Curr Opin Microbiol 2008; 11:134-40; PMID:18378185; https://doi.org/10.1016/j.mib.2008.02.003
  • Crick FH. Codon—anticodon pairing: the wobble hypothesis. J Mol Biol 1966; 19:548-55; PMID:5969078; https://doi.org/10.1016/S0022-2836(66)80022-0
  • Yamagishi Y, Shoji I, Miyagawa S, Kawakami T, Katoh T, Goto Y, Suga H. Natural product-like macrocyclic N-methyl-peptide inhibitors against a ubiquitin ligase uncovered from a ribosome-expressed de novo library. Chem Biol 2011; 18:1562-70; PMID:22195558; https://doi.org/10.1016/j.chembiol.2011.09.013
  • Forster AC, Tan Z, Nalam MN, Lin H, Qu H, Cornish VW, Blacklow SC. Programming peptidomimetic syntheses by translating genetic codes designed de novo. Proc Natl Acad Sci USA 2003; 100:6353-7; PMID:12754376; https://doi.org/10.1073/pnas.1132122100
  • Josephson K, Hartman MC, Szostak JW. Ribosomal synthesis of unnatural peptides. J Am Chem Soc 2005; 127:11727-35; PMID:16104750; https://doi.org/10.1021/ja0515809
  • Sismour AM, Benner SA. The use of thymidine analogs to improve the replication of an extra DNA base pair: a synthetic biological system. Nucleic Acids Res 2005; 33:5640-6; PMID:16192575; https://doi.org/10.1093/nar/gki873
  • Switzer C, Moroney SE, Benner SA. Enzymatic incorporation of a new base pair into DNA and RNA. J Am Chem Soc 1989; 111:8322-23; https://doi.org/10.1021/ja00203a067
  • Dedkova LM, Fahmi NE, Golovine SY, Hecht SM. Enhanced D-amino acid incorporation into protein by modified ribosomes. J Am Chem Soc 2003; 125:6616-17; PMID:12769555; https://doi.org/10.1021/ja035141q
  • Dedkova LM, Fahmi NE, Golovine SY, Hecht SM. Construction of modified ribosomes for incorporation of D-amino acids into proteins. Biochemistry 2006; 45:15541-51; PMID:17176075; https://doi.org/10.1021/bi060986a
  • Dedkova LM, Fahmi NE, Paul R, del Rosario M, Zhang L, Chen S, Feder G, Hecht SM. β-Puromycin selection of modified ribosomes for in vitro incorporation of β-amino acids. Biochemistry 2012; 51:401-15; PMID:22145951; https://doi.org/10.1021/bi2016124
  • Maini R, Nguyen DT, Chen S, Dedkova LM, Chowdhury SR, Alcala-Torano R, Hecht SM. Incorporation of β-amino acids into dihydrofolate reductase by ribosomes having modifications in the peptidyltransferase center. Bioorg Med Chem 2013; 21:1088-96; PMID:23375097; https://doi.org/10.1016/j.bmc.2013.01.002
  • Rao AR, Varshney U. Specific interaction between the ribosome recycling factor and the elongation factor G from Mycobacterium tuberculosis mediates peptidyl-tRNA release and ribosome recycling in Escherichia coli. EMBO J 2001; 20:2977-86; PMID:11387230; https://doi.org/10.1093/emboj/20.11.2977
  • Hayashi Y, Morimoto J, Suga H. In vitro selection of anti-Akt2 thioether-macrocyclic peptides leading to isoform-selective inhibitors. ACS Chem Biol 2012; 7:607-13; PMID:22273180; https://doi.org/10.1021/cb200388k
  • Morimoto J, Hayashi Y, Suga H. Discovery of macrocyclic peptides armed with a mechanism-based warhead: isoform-selective inhibition of human deacetylase SIRT2. Angew Chem Int Ed Engl 2012; 51:3423-7; PMID:PMID:22374802; https://doi.org/10.1002/anie.201108118
  • Tanaka Y, et al. Structural basis for the drug extrusion mechanism by a MATE multidrug transporter. Nature 2013; 496:247-51; PMID:23535598; https://doi.org/10.1038/nature12014
  • Nemoto N, Miyamoto-Sato E, Husimi Y, Yanagawa H. In vitro virus: bonding of mRNA bearing puromycin at the 3′-terminal end to the C-terminal end of its encoded protein on the ribosome in vitro. FEBS Lett 1997; 414:405-8; PMID:9315729; https://doi.org/10.1016/S0014-5793(97)01026-0
  • Roberts RW, Szostak JW. RNA-peptide fusions for the in vitro selection of peptides and proteins. Proc Natl Acad Sci USA 1997; 94:12297-302; PMID:9356443

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.