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Crystal structures reveal an elusive functional domain of pyrrolysyl-tRNA synthetase.

Suzuki T, Miller C, Guo LT, Ho JML, Bryson DI, Wang YS, Liu DR, Söll D
Nat Chem Biol 13 1261-1266 (2017)
Cited: 52 times
EuropePMC logo PMID: 29035363

Abstract

Pyrrolysyl-tRNA synthetase (PylRS) is a major tool in genetic code expansion using noncanonical amino acids, yet its structure and function are not completely understood. Here we describe the crystal structure of the previously uncharacterized essential N-terminal domain of this unique enzyme in complex with tRNAPyl. This structure explains why PylRS remains orthogonal in a broad range of organisms, from bacteria to humans. The structure also illustrates why tRNAPyl recognition by PylRS is anticodon independent: the anticodon does not contact the enzyme. Then, using standard microbiological culture equipment, we established a new method for laboratory evolution-a noncontinuous counterpart of the previously developed phage-assisted continuous evolution. With this method, we evolved novel PylRS variants with enhanced activity and amino acid specificity. Finally, we employed an evolved PylRS variant to determine its N-terminal domain structure and show how its mutations improve PylRS activity in the genetic encoding of a noncanonical amino acid.

Reviews - 5ud5 mentioned but not cited (1)

  1. Personalized Medicine in Mitochondrial Health and Disease: Molecular Basis of Therapeutic Approaches Based on Nutritional Supplements and Their Analogs. Tragni V, Primiano G, Tummolo A, Cafferati Beltrame L, La Piana G, Sgobba MN, Cavalluzzi MM, Paterno G, Gorgoglione R, Volpicella M, Guerra L, Marzulli D, Servidei S, De Grassi A, Petrosillo G, Lentini G, Pierri CL. Molecules 27 3494 (2022)

Articles - 5ud5 mentioned but not cited (6)

  1. Crystal structures reveal an elusive functional domain of pyrrolysyl-tRNA synthetase. Suzuki T, Miller C, Guo LT, Ho JML, Bryson DI, Wang YS, Liu DR, Söll D. Nat Chem Biol 13 1261-1266 (2017)
  2. Engineering aminoacyl-tRNA synthetases for use in synthetic biology. Krahn N, Tharp JM, Crnković A, Söll D. Enzymes 48 351-395 (2020)
  3. Ancestral archaea expanded the genetic code with pyrrolysine. Guo LT, Amikura K, Jiang HK, Mukai T, Fu X, Wang YS, O'Donoghue P, Söll D, Tharp JM. J Biol Chem 298 102521 (2022)
  4. Expanding the Scope of Orthogonal Translation with Pyrrolysyl-tRNA Synthetases Dedicated to Aromatic Amino Acids. Tseng HW, Baumann T, Sun H, Wang YS, Ignatova Z, Budisa N. Molecules 25 E4418 (2020)
  5. Linker and N-Terminal Domain Engineering of Pyrrolysyl-tRNA Synthetase for Substrate Range Shifting and Activity Enhancement. Jiang HK, Lee MN, Tsou JC, Chang KW, Tseng HW, Chen KP, Li YK, Wang YS. Front Bioeng Biotechnol 8 235 (2020)
  6. tRNA shape is an identity element for an archaeal pyrrolysyl-tRNA synthetase from the human gut. Krahn N, Zhang J, Melnikov SV, Tharp JM, Villa A, Patel A, Howard RJ, Gabir H, Patel TR, Stetefeld J, Puglisi J, Söll D. Nucleic Acids Res 52 513-524 (2024)


Reviews citing this publication (14)

  1. Reprogramming the genetic code. de la Torre D, Chin JW. Nat Rev Genet 22 169-184 (2021)
  2. Upgrading aminoacyl-tRNA synthetases for genetic code expansion. Vargas-Rodriguez O, Sevostyanova A, Söll D, Crnković A. Curr Opin Chem Biol 46 115-122 (2018)
  3. Site-Specific Labeling of Proteins Using Unnatural Amino Acids. Lee KJ, Kang D, Park HS. Mol Cells 42 386-396 (2019)
  4. Therapeutic applications of genetic code expansion. Huang Y, Liu T. Synth Syst Biotechnol 3 150-158 (2018)
  5. Naturally Occurring tRNAs With Non-canonical Structures. Krahn N, Fischer JT, Söll D. Front Microbiol 11 596914 (2020)
  6. Aminoacyl-tRNA Synthetases and tRNAs for an Expanded Genetic Code: What Makes them Orthogonal? Melnikov SV, Söll D. Int J Mol Sci 20 E1929 (2019)
  7. Strategies for Improving Small-Molecule Biosensors in Bacteria. Miller CA, Ho JML, Bennett MR. Biosensors (Basel) 12 64 (2022)
  8. Versatility of Synthetic tRNAs in Genetic Code Expansion. Hoffman KS, Crnković A, Söll D. Genes (Basel) 9 E537 (2018)
  9. Plasticity and Constraints of tRNA Aminoacylation Define Directed Evolution of Aminoacyl-tRNA Synthetases. Crnković A, Vargas-Rodriguez O, Söll D. Int J Mol Sci 20 E2294 (2019)
  10. Synthesis at the interface of virology and genetic code expansion. Kelemen RE, Erickson SB, Chatterjee A. Curr Opin Chem Biol 46 164-171 (2018)
  11. Unconventional genetic code systems in archaea. Meng K, Chung CZ, Söll D, Krahn N. Front Microbiol 13 1007832 (2022)
  12. Update of the Pyrrolysyl-tRNA Synthetase/tRNAPyl Pair and Derivatives for Genetic Code Expansion. Gong X, Zhang H, Shen Y, Fu X. J Bacteriol 205 e0038522 (2023)
  13. Improving the Efficiency and Orthogonality of Genetic Code Expansion. Fu X, Huang Y, Shen Y. Biodes Res 2022 9896125 (2022)
  14. Virus-assisted directed evolution of biomolecules. Jewel D, Pham Q, Chatterjee A. Curr Opin Chem Biol 76 102375 (2023)

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  1. Continuous evolution of SpCas9 variants compatible with non-G PAMs. Miller SM, Wang T, Randolph PB, Arbab M, Shen MW, Huang TP, Matuszek Z, Newby GA, Rees HA, Liu DR. Nat Biotechnol 38 471-481 (2020)
  2. Mutually orthogonal pyrrolysyl-tRNA synthetase/tRNA pairs. Willis JCW, Chin JW. Nat Chem 10 831-837 (2018)
  3. Engineered triply orthogonal pyrrolysyl-tRNA synthetase/tRNA pairs enable the genetic encoding of three distinct non-canonical amino acids. Dunkelmann DL, Willis JCW, Beattie AT, Chin JW. Nat Chem 12 535-544 (2020)
  4. Methanomethylophilus alvus Mx1201 Provides Basis for Mutual Orthogonal Pyrrolysyl tRNA/Aminoacyl-tRNA Synthetase Pairs in Mammalian Cells. Meineke B, Heimgärtner J, Lafranchi L, Elsässer SJ. ACS Chem Biol 13 3087-3096 (2018)
  5. Phage-Assisted Evolution of Bacillus methanolicus Methanol Dehydrogenase 2. Roth TB, Woolston BM, Stephanopoulos G, Liu DR. ACS Synth Biol 8 796-806 (2019)
  6. Phage-assisted continuous and non-continuous evolution. Miller SM, Wang T, Liu DR. Nat Protoc 15 4101-4127 (2020)
  7. Chimeric design of pyrrolysyl-tRNA synthetase/tRNA pairs and canonical synthetase/tRNA pairs for genetic code expansion. Ding W, Zhao H, Chen Y, Zhang B, Yang Y, Zang J, Wu J, Lin S. Nat Commun 11 3154 (2020)
  8. Arginine Forks Are a Widespread Motif to Recognize Phosphate Backbones and Guanine Nucleobases in the RNA Major Groove. Chavali SS, Cavender CE, Mathews DH, Wedekind JE. J Am Chem Soc 142 19835-19839 (2020)
  9. Systematic molecular evolution enables robust biomolecule discovery. DeBenedictis EA, Chory EJ, Gretton DW, Wang B, Golas S, Esvelt KM. Nat Methods 19 55-64 (2022)
  10. A suppressor tRNA-mediated feedforward loop eliminates leaky gene expression in bacteria. Ho JML, Miller CA, Parks SE, Mattia JR, Bennett MR. Nucleic Acids Res 49 e25 (2021)
  11. Restoration of dystrophin expression in mice by suppressing a nonsense mutation through the incorporation of unnatural amino acids. Shi N, Yang Q, Zhang H, Lu J, Lin H, Yang X, Abulimiti A, Cheng J, Wang Y, Tong L, Wang T, Zhang X, Chen H, Xia Q. Nat Biomed Eng 6 195-206 (2022)
  12. Directed Evolution of Methanomethylophilus alvus Pyrrolysyl-tRNA Synthetase Generates a Hyperactive and Highly Selective Variant. Fischer JT, Söll D, Tharp JM. Front Mol Biosci 9 850613 (2022)
  13. Improved pyrrolysine biosynthesis through phage assisted non-continuous directed evolution of the complete pathway. Ho JML, Miller CA, Smith KA, Mattia JR, Bennett MR. Nat Commun 12 3914 (2021)
  14. Directed Evolution of the Methanosarcina barkeri Pyrrolysyl tRNA/aminoacyl tRNA Synthetase Pair for Rapid Evaluation of Sense Codon Reassignment Potential. Schwark DG, Schmitt MA, Fisk JD. Int J Mol Sci 22 E895 (2021)
  15. Genetic Code Expansion in the Engineered Organism Vmax X2: High Yield and Exceptional Fidelity. González SS, Ad O, Shah B, Zhang Z, Zhang X, Chatterjee A, Schepartz A. ACS Cent Sci 7 1500-1507 (2021)
  16. The Pyrrolysyl-tRNA Synthetase Activity can be Improved by a P188 Mutation that Stabilizes the Full-Length Enzyme. Cho CC, Blankenship LR, Ma X, Xu S, Liu W. J Mol Biol 434 167453 (2022)
  17. Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Zhao H, Ding W, Zang J, Yang Y, Liu C, Hu L, Chen Y, Liu G, Fang Y, Yuan Y, Lin S. Nat Commun 12 7039 (2021)
  18. Enhanced incorporation of subnanometer tags into cellular proteins for fluorescence nanoscopy via optimized genetic code expansion. Mihaila TS, Bäte C, Ostersehlt LM, Pape JK, Keller-Findeisen J, Sahl SJ, Hell SW. Proc Natl Acad Sci U S A 119 e2201861119 (2022)
  19. Synthetic Tyrosine tRNA Molecules with Noncanonical Secondary Structures. Sakamoto K, Hayashi A. Int J Mol Sci 20 E92 (2018)
  20. Development of mammalian cell logic gates controlled by unnatural amino acids. Mills EM, Barlow VL, Jones AT, Tsai YH. Cell Rep Methods 1 100073 (2021)
  21. Ferritin Conjugates With Multiple Clickable Amino Acids Encoded by C-Terminal Engineered Pyrrolysyl-tRNA Synthetase. Wang YH, Jian ML, Chen PJ, Tsou JC, Truong LP, Wang YS. Front Chem 9 779976 (2021)
  22. Inducible directed evolution of complex phenotypes in bacteria. Al'Abri IS, Haller DJ, Li Z, Crook N. Nucleic Acids Res 50 e58 (2022)
  23. Quintuply orthogonal pyrrolysyl-tRNA synthetase/tRNAPyl pairs. Beattie AT, Dunkelmann DL, Chin JW. Nat Chem 15 948-959 (2023)
  24. Engineering mutually orthogonal PylRS/tRNA pairs for dual encoding of functional histidine analogues. Taylor CJ, Hardy FJ, Burke AJ, Bednar RM, Mehl RA, Green AP, Lovelock SL. Protein Sci 32 e4640 (2023)
  25. Genetic code expansion: Synthetases pick up the PACE. Tharp JM, Liu WR. Nat Chem Biol 13 1205-1206 (2017)
  26. Rational Design of Aptamer-Tagged tRNAs. Mukai T. Int J Mol Sci 21 E7793 (2020)
  27. Crystal Structure of Pyrrolysyl-tRNA Synthetase from a Methanogenic Archaeon ISO4-G1 and Its Structure-Based Engineering for Highly-Productive Cell-Free Genetic Code Expansion with Non-Canonical Amino Acids. Yanagisawa T, Seki E, Tanabe H, Fujii Y, Sakamoto K, Yokoyama S. Int J Mol Sci 24 6256 (2023)
  28. Dual stop codon suppression in mammalian cells with genomically integrated genetic code expansion machinery. Meineke B, Heimgärtner J, Caridha R, Block MF, Kimler KJ, Pires MF, Landreh M, Elsässer SJ. Cell Rep Methods 3 100626 (2023)
  29. Focused Engineering of Pyrrolysyl-tRNA Synthetase-Based Orthogonal Translation Systems for the Incorporation of Various Noncanonical Amino Acids. Koch NG, Budisa N. Methods Mol Biol 2676 3-19 (2023)
  30. Structural basis for a degenerate tRNA identity code and the evolution of bimodal specificity in human mitochondrial tRNA recognition. Kuhle B, Hirschi M, Doerfel LK, Lander GC, Schimmel P. Nat Commun 14 4794 (2023)
  31. Transferability of N-terminal mutations of pyrrolysyl-tRNA synthetase in one species to that in another species on unnatural amino acid incorporation efficiency. Williams TL, Iskandar DJ, Nödling AR, Tan Y, Luk LYP, Tsai YH. Amino Acids 53 89-96 (2021)


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