Repurposing the translation apparatus for synthetic biology

Current Opinion in Chemical Biology

Volumn 28, Issue , 2015, Pages 83-90

  Des Soye, Benjamin J ^a,b   Patel, Jaymin R ^c   Isaacs, Farren J ^c   Jewett, Michael C ^a,b,d  

^a NORTHWESTERN UNIVERSITY   (United States)

^b Northwestern University   (United States)

^c YALE UNIVERSITY   (United States)

^d Northwestern University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA DIRECTED RNA POLYMERASE III; PHOSPHOSERINE; TRANSFER RNA; AMINO ACID;

CELL FREE SYSTEM; CELL VIABILITY; CROSS REACTION; ESSENTIAL GENE; GENETIC CODE; GENOME; MEMBRANE PERMEABILITY; METHANOCALDOCOCCUS JANNASCHII; NONHUMAN; NONSENSE MEDIATED MRNA DECAY; OPEN READING FRAME; POINT MUTATION; PROMOTER REGION; PROTEIN SYNTHESIS; REVIEW; RIBOSOME SUBUNIT; STOP CODON; SYNTHETIC BIOLOGY; ANIMAL; GENETIC ENGINEERING; GENETICS; HUMAN; PROCEDURES;

EUKARYOTA;

AMINO ACIDS; ANIMALS; GENETIC CODE; GENETIC ENGINEERING; HUMANS; PROTEIN BIOSYNTHESIS; SYNTHETIC BIOLOGY;

EID: 84937046954     PISSN: 13675931     EISSN: 18790402     Source Type: Journal    
DOI: 10.1016/j.cbpa.2015.06.008     Document Type: Review

References (75)

1. van Hest J.C.M., Kiick K.L., Tirrell D.A. Efficient incorporation of unsaturated methionine analogues into proteins in vivo. J Am Chem Soc 2000, 122:1282-1288. 10.1021/Ja992749j.
2. Ngo J.T., Tirrell D.A. Noncanonical amino acids in the interrogation of cellular protein synthesis. Acc Chem Res 2011, 44:677-685. 10.1021/ar200144y.
3. Chin J.W. Expanding and reprogramming the genetic code of cells and animals. Annu Rev Biochem 2014, 83:379-408. 10.1146/annurev-biochem-060713-035737.
4. Dumas A., Lercher e.L., Spicer C.D., Davis B.G. Designing logical codon reassignment-expanding the chemistry in biology. Chem Sci 2014, 6:50-69.
5. Chin J.W., et al. Addition of p-azido-l-phenylaianine to the genetic code of Escherichia coli. J Am Chem Soc 2002, 124:9026-9027. 10.1021/Ja027007w.
6. Yang H., Srivastava P., Zhang C., Lewis J.C. A general method for artificial metalloenzyme formation through strain-promoted azide-alkyne cycloaddition. Chembiochem 2014, 15:223-227. 10.1002/cbic.201300661.
7. Cho H., et al. Optimized clinical performance of growth hormone with an expanded genetic code. Proc Natl Acad Sci U S A 2011, 108:9060-9065. 10.1073/pnas.1100387108.
8. Tada S., et al. Genetic PEGylation. PLoS One 2012, 7:e49235. 10.1371/journal.pone.0049235.
9. Park H.S., et al. Expanding the genetic code of Escherichia coli with phosphoserine. Science 2011, 333:1151-1154. 10.1126/science.1207203.
10. Lee S., et al. A facile strategy for selective incorporation of phosphoserine into histones. Angew Chem 2013, 52:5771-5775. 10.1002/anie.201300531.
11. Neumann H., Peak-Chew S.Y., Chin J.W. Genetically encoding N(epsilon)-acetyllysine in recombinant proteins. Nat Chem Biol 2008, 4:232-234. 10.1038/nchembio.73.
12. Ai H.W., Lee J.W., Schultz P.G. A method to site-specifically introduce methyllysine into proteins in E. coli. Chem Commun 2010, 46:5506-5508. 10.1039/c0cc00108b.
13. Wang L., Brock A., Herberich B., Schultz P.G. Expanding the genetic code of Escherichia coli. Science 2001, 292:498-500. 10.1126/science.1060077.
14. Wang L., Xie J., Schultz P.G. Expanding the genetic code. Annu Rev Biophys Biomol Struct 2006, 35:225-249. 10.1146/annurev.biophys.35.101105.121507.
15. Santoro S.W., Wang L., Herberich B., King D.S., Schultz P.G. An efficient system for the evolution of aminoacyl-tRNA synthetase specificity. Nat Biotechnol 2002, 20:1044-1048. 10.1038/nbt742.
16. Nozawa K., et al. Pyrrolysyl-tRNA synthetase-tRNA(Pyl) structure reveals the molecular basis of orthogonality. Nature 2009, 457:1163-1167. 10.1038/nature07611.
17. Fekner T., Chan M.K. The pyrrolysine translational machinery as a genetic-code expansion tool. Curr Opin Chem Biol 2011, 15:387-391. 10.1016/j.cbpa.2011.03.007.
18. Wan W., Tharp J.M., Liu W.R. Pyrrolysyl-tRNA synthetase: an ordinary enzyme but an outstanding genetic code expansion tool. Biochim Biophys Acta 2014, 1844:1059-1070. 10.1016/j.bbapap.2014.03.002.
19. Li W.T., et al. Specificity of pyrrolysyl-tRNA synthetase for pyrrolysine and pyrrolysine analogs. J Mol Biol 2009, 385:1156-1164. 10.1016/j.jmb.2008.11.032.
20. Ellefson J.W., et al. Directed evolution of genetic parts and circuits by compartmentalized partnered replication. Nat Biotechnol 2014, 32:97-101. 10.1038/nbt.2714.
21. Chin J.W., et al. An expanded eukaryotic genetic code. Science 2003, 301:964-967. 10.1126/science.1084772.
22. Ai H.W., Shen W., Brustad E., Schultz P.G. Genetically encoded alkenes in yeast. Angew Chem 2010, 49:935-937. 10.1002/anie.200905590.
23. Zhang Y., Wang L., Schultz P.G., Wilson I.A. Crystal structures of apo wild-type M. jannaschii tyrosyl-tRNA synthetase (TyrRS) and an engineered TyrRS specific for O-methyl-l-tyrosine. Protein Sci 2005, 14:1340-1349. 10.1110/ps.041239305.
24. Haruna K., Alkazemi M.H., Liu Y., Soll D., Englert M. Engineering the elongation factor Tu for efficient selenoprotein synthesis. Nucleic Acids Res 2014, 42:9976-9983. 10.1093/nar/gku691.
25. O'Donoghue P., Ling J., Wang Y.S., Soll D. Upgrading protein synthesis for synthetic biology. Nat Chem Biol 2013, 9:594-598. 10.1038/nchembio.1339.
26. Rackham O., Chin J.W. A network of orthogonal ribosome×mRNA pairs. Nat Chem Biol 2005, 1:159-166. 10.1038/nchembio719.
27. Wang K., Neumann H., Peak-Chew S.Y., Chin J.W. Evolved orthogonal ribosomes enhance the efficiency of synthetic genetic code expansion. Nat Biotechnol 2007, 25:770-777. 10.1038/nbt1314.
28. Jewett M.C., Fritz B.R., Timmerman L.E., Church G.M. In vitro integration of ribosomal RNA synthesis, ribosome assembly, and translation. Mol Syst Biol 2013, 9:678. 10.1038/msb.2013.31.
29. Fritz B.R., Jewett M.C. The impact of transcriptional tuning on in vitro integrated rRNA transcription and ribosome construction. Nucleic Acids Res 2014, 42:6774-6785. 10.1093/nar/gku307.
30. Liu Y., Fritz B.R., Anderson M.J., Schoborg J.A., Jewett M.C. Characterizing and alleviating substrate limitations for improved in vitro ribosome construction. ACS Synth Biol 2014, 10.1021/sb5002467.
31. Hong S.H., Kwon Y.C., Jewett M.C. Non-standard amino acid incorporation into proteins using Escherichia coli cell-free protein synthesis. Front Chem 2014, 2:34. 10.3389/fchem.2014.00034.
32. Hong S.H., et al. Cell-free protein synthesis from a release factor 1 deficient Escherichia coli activates efficient and multiple site-specific nonstandard amino acid incorporation. ACS Synth Biol 2014, 3:398-409. 10.1021/sb400140t.
33. Lajoie M.J., et al. Genomically recoded organisms expand biological functions. Science 2013, 342:357-360. 10.1126/science.1241459.
34. Johnson D.B., et al. RF1 knockout allows ribosomal incorporation of unnatural amino acids at multiple sites. Nat Chem Biol 2011, 7:779-786. 10.1038/nchembio.657.
35. Mukai T., et al. Codon reassignment in the Escherichia coli genetic code. Nucleic Acids Res 2010, 38:8188-8195. 10.1093/nar/gkq707.
36. Heinemann I.U., et al. Enhanced phosphoserine insertion during Escherichia coli protein synthesis via partial UAG codon reassignment and release factor 1 deletion. FEBS Lett 2012, 586:3716-3722. 10.1016/j.febslet.2012.08.031.
37. Hong S.H., et al. Improving cell-free protein synthesis through genome engineering of Escherichia coli lacking release factor 1. Chembiochem 2015, 10.1002/cbic.201402708.
38. Isaacs F.J., et al. Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science 2011, 333:348-353. 10.1126/science.1205822.
39. Rovner A.J., et al. Recoded organisms engineered to depend on synthetic amino acids. Nature 2015, 518:89-93. 10.1038/nature14095.
40. Mandell D.J., et al. Biocontainment of genetically modified organisms by synthetic protein design. Nature 2015, 518:55-60. 10.1038/nature14121.
41. Wan W., et al. A facile system for genetic incorporation of two different noncanonical amino acids into one protein in Escherichia coli. Angew Chem 2010, 49:3211-3214. 10.1002/anie.201000465.
42. Odoi K.A., Huang Y., Rezenom Y.H., Liu W.R. Nonsense and sense suppression abilities of original and derivative Methanosarcina mazei pyrrolysyl-tRNA synthetase-tRNA(Pyl) pairs in the Escherichia coli BL21(DE3) cell strain. PLoS One 2013, 8:e57035. 10.1371/journal.pone.0057035.
43. Anderson J.C., et al. An expanded genetic code with a functional quadruplet codon. Proc Natl Acad Sci U S A 2004, 101:7566-7571. 10.1073/pnas.0401517101.
44. Chatterjee A., Lajoie M.J., Xiao H., Church G.M., Schultz P.G. A bacterial strain with a unique quadruplet codon specifying non-native amino acids. Chembiochem 2014, 15:1782-1786. 10.1002/cbic.201402104.
45. Neumann H., Wang K., Davis L., Garcia-Alai M., Chin J.W. Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome. Nature 2010, 464:441-444. 10.1038/nature08817.
46. Wang K., et al. Optimized orthogonal translation of unnatural amino acids enables spontaneous protein double-labelling and FRET. Nat Chem 2014, 6:393-403. 10.1038/nchem.1919.
47. Sachdeva A., Wang K., Elliott T., Chin J.W. Concerted, rapid, quantitative, and site-specific dual labeling of proteins. J Am Chem Soc 2014, 136:7785-7788. 10.1021/ja4129789.
48. Jewett M.C., Calhoun K.A., Voloshin A., Wuu J.J., Swartz J.R. An integrated cell-free metabolic platform for protein production and synthetic biology. Mol Syst Biol 2008, 4:220. 10.1038/msb.2008.57.
49. Caschera F., Noireaux V. Synthesis of 2.3mg/ml of protein with an all Escherichia coli cell-free transcription-translation system. Biochimie 2014, 99:162-168. 10.1016/j.biochi.2013.11.025.
50. Carlson E.D., Gan R., Hodgman C.E., Jewett M.C. Cell-free protein synthesis: applications come of age. Biotechnol Adv 2012, 30:1185-1194. 10.1016/j.biotechadv.2011.09.016.
51. Bundy B.C., Swartz J.R. Site-specific incorporation of p-propargyloxyphenylalanine in a cell-free environment for direct protein-protein click conjugation. Bioconj Chem 2010, 21:255-263. 10.1021/bc9002844.
52. Nehring S., Budisa N., Wiltschi B. Performance analysis of orthogonal pairs designed for an expanded eukaryotic genetic code. PLoS One 2012, 7:e31992. 10.1371/journal.pone.0031992.
53. Loscha K.V., et al. Multiple-site labeling of proteins with unnatural amino acids. Angew Chem 2012, 51:2243-2246. 10.1002/anie.201108275.
54. Gerrits M., et al. Cell-free Protein Expression 2007, 166-180. Landes Bioscience. W. Kudlicki, F. Katzen, R. Bennerr (Eds.).
55. Goerke A.R., Swartz J.R. High-level cell-free synthesis yields of proteins containing site-specific non-natural amino acids. Biotechnol Bioeng 2009, 102:400-416. 10.1002/bit.22070.
56. Shimizu Y., et al. Cell-free translation reconstituted with purified components. Nat Biotechnol 2001, 19:751-755. 10.1038/90802.
57. Ahn J.-H., et al. Preparation method for Escherichia coli S30 extracts completely dependent upon tRNA addition to catalyze cell-free protein synthesis. Biotechnol Bioproc Eng 2006, 11:420-424.
58. Forster A.C., et al. Programming peptidomimetic syntheses by translating genetic codes designed de novo. Proc Natl Acad Sci U S A 2003, 100:6353-6357. 10.1073/pnas.1132122100.
59. Cui Z., Stein V., Tnimov Z., Mureev S., Alexandrov K. Semisynthetic tRNA complement mediates in vitro protein synthesis. J Am Chem Soc 2015, 137:4404-4413. 10.1021/ja5131963.
60. Terasaka N., Hayashi G., Katoh T., Suga H. An orthogonal ribosome-tRNA pair via engineering of the peptidyl transferase center. Nat Chem Biol 2014, 10:555-557. 10.1038/nchembio.1549.
61. Ohuchi M., Murakami H., Suga H. The flexizyme system: a highly flexible tRNA aminoacylation tool for the translation apparatus. Curr Opin Chem Biol 2007, 11:537-542. 10.1016/j.cbpa.2007.08.011.
62. Gautier A., Deiters A., Chin J.W. Light-activated kinases enable temporal dissection of signaling networks in living cells. J Am Chem Soc 2011, 133:2124-2127. 10.1021/ja1109979.
63. Lemke E.A., Summerer D., Geierstanger B.H., Brittain S.M., Schultz P.G. Control of protein phosphorylation with a genetically encoded photocaged amino acid. Nat Chem Biol 2007, 3:769-772. 10.1038/nchembio.2007.44.
64. Wilkins B.J., et al. A cascade of histone modifications induces chromatin condensation in mitosis. Science 2014, 343:77-80. 10.1126/science.1244508.
65. Uttamapinant C., et al. Genetic code expansion enables live-cell and super-resolution imaging of site-specifically labeled cellular proteins. J Am Chem Soc 2015, 137:4602-4605. 10.1021/ja512838z.
66. Greiss S., Chin J.W. Expanding the genetic code of an animal. J Am Chem Soc 2011, 133:14196-14199. 10.1021/ja2054034.
67. Bianco A., Townsley F.M., Greiss S., Lang K., Chin J.W. Expanding the genetic code of Drosophila melanogaster. Nat Chem Biol 2012, 8:748-750. 10.1038/nchembio.1043.
68. Annaluru N., et al. Total synthesis of a functional designer eukaryotic chromosome. Science 2014, 344:55-58. 10.1126/science.1249252.
69. Longman D., Plasterk R.H., Johnstone I.L., Caceres J.F. Mechanistic insights and identification of two novel factors in the C. elegans NMD pathway. Genes Dev 2007, 21:1075-1085. 10.1101/gad.417707.
70. Hancock S.M., Uprety R., Deiters A., Chin J.W. Expanding the genetic code of yeast for incorporation of diverse unnatural amino acids via a pyrrolysyl-tRNA synthetase/tRNA pair. J Am Chem Soc 2010, 132:14819-14824. 10.1021/ja104609m.
71. Ma H., Zhang J., Wu H. Designing Ago2-specific siRNA/shRNA to avoid competition with endogenous miRNAs. Molecular therapy. Nucleic Acids 2014, 3:e176. 10.1038/mtna.2014.27.
72. Meiler J.B.D. ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility. Proteins 2006, 10.1002/prot.21086.
73. Malyshev D., Lavergne D.K., Chen T., Dai T., Foster N., Corrêa J., Romesberg I.F. A semi-synthetic organism with an expanded genetic alphabet. Nature 2014, 10.1038/nature13314.
74. Neumann H., Chin S.A.L.J.W. De novo generation of mutually orthogonal aminoacyl-tRNA synthetase/tRNA pairs. J Am Chem Soc 2010, 10.1021/ja9068722.
75. Zimmerman E.S., Heibeck T.H., Gill A., Li X., Murray C.J., Madlansacay M.R., Tran C., Uter N.T., Yin G., Rivers P.J., et al. Production of site-specific antibody-drug conjugates using optimized non-natural amino acids in a cell-free expression system. Bioconjugate Chem 2014, 25:351-361.