Structural Basis for Genetic-Code Expansion with Various Bulky Lysine Derivatives by an Engineered Pyrrolysyl-tRNA Synthetase

2018 ◽  
Author(s):  
Tatsuo Yanagisawa ◽  
Mitsuo Kuratani ◽  
Eiko Seki ◽  
Nobumasa Hino ◽  
Kensaku Sakamoto ◽  
...  
Keyword(s):  
Genetic Code ◽  
Trna Synthetase ◽  
Structural Basis ◽  
Genetic Code Expansion

scholarly journals Structural basis of nonnatural amino acid recognition by an engineered aminoacyl-tRNA synthetase for genetic code expansion

2005 ◽  
Vol 102 (5) ◽  
pp. 1366-1371 ◽  
Author(s):  
T. Kobayashi ◽  
K. Sakamoto ◽  
T. Takimura ◽  
R. Sekine ◽  
V. P. Kelly ◽  
...  
Keyword(s):  
Amino Acid ◽  
Genetic Code ◽  
Trna Synthetase ◽  
Structural Basis ◽  
Aminoacyl Trna Synthetase ◽  
Genetic Code Expansion ◽  
Nonnatural Amino Acid ◽  
Amino Acid Recognition

scholarly journals Structural Basis for Genetic-Code Expansion with Bulky Lysine Derivatives by an Engineered Pyrrolysyl-tRNA Synthetase

2019 ◽  
Vol 26 (7) ◽  
pp. 936-949.e13 ◽  
Author(s):  
Tatsuo Yanagisawa ◽  
Mitsuo Kuratani ◽  
Eiko Seki ◽  
Nobumasa Hino ◽  
Kensaku Sakamoto ◽  
...  
Keyword(s):  
Genetic Code ◽  
Trna Synthetase ◽  
Structural Basis ◽  
Genetic Code Expansion

scholarly journals Transferability of N-terminal mutations of pyrrolysyl-tRNA synthetase in one species to that in another species on unnatural amino acid incorporation efficiency

Amino Acids ◽  
2020 ◽  
Author(s):  
Thomas L. Williams ◽  
Debra J. Iskandar ◽  
Alexander R. Nödling ◽  
Yurong Tan ◽  
Louis Y. P. Luk ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Genetic Code ◽  
Unnatural Amino Acids ◽  
Trna Synthetase ◽  
Unnatural Amino Acid ◽  
Amino Acid Incorporation ◽  
Acid Incorporation ◽  
Genetic Code Expansion ◽  
Incorporation Efficiency

AbstractGenetic code expansion is a powerful technique for site-specific incorporation of an unnatural amino acid into a protein of interest. This technique relies on an orthogonal aminoacyl-tRNA synthetase/tRNA pair and has enabled incorporation of over 100 different unnatural amino acids into ribosomally synthesized proteins in cells. Pyrrolysyl-tRNA synthetase (PylRS) and its cognate tRNA from Methanosarcina species are arguably the most widely used orthogonal pair. Here, we investigated whether beneficial effect in unnatural amino acid incorporation caused by N-terminal mutations in PylRS of one species is transferable to PylRS of another species. It was shown that conserved mutations on the N-terminal domain of MmPylRS improved the unnatural amino acid incorporation efficiency up to five folds. As MbPylRS shares high sequence identity to MmPylRS, and the two homologs are often used interchangeably, we examined incorporation of five unnatural amino acids by four MbPylRS variants at two temperatures. Our results indicate that the beneficial N-terminal mutations in MmPylRS did not improve unnatural amino acid incorporation efficiency by MbPylRS. Knowledge from this work contributes to our understanding of PylRS homologs which are needed to improve the technique of genetic code expansion in the future.

scholarly journals High-throughput aminoacyl-tRNA synthetase engineering for genetic code expansion in yeast

2021 ◽  
Author(s):  
Jessica T. Stieglitz ◽  
James A. Van Deventer
Keyword(s):  
Genetic Code ◽  
High Throughput ◽  
Trna Synthetase ◽  
Noncanonical Amino Acids ◽  
Trna Synthetases ◽  
E Coli ◽  
Biological Studies ◽  
Screening Strategies ◽  
Genetic Code Expansion ◽  
Translation Systems

Protein expression with genetically encoded noncanonical amino acids (ncAAs) benefits a broad range of applications, from the discovery of biological therapeutics to fundamental biological studies. A major factor limiting the use of ncAAs is the lack of orthogonal translation systems (OTSs) that support efficient genetic code expansion at repurposed stop codons. Aminoacyl-tRNA synthetases (aaRSs) have been extensively evolved in E. coli but are not always orthogonal in eukaryotes. In this work, we use a yeast display-based ncAA incorporation reporter platform with fluorescence-activated cell sorting (FACS) to screen libraries of aaRSs in high throughput for 1) incorporation of ncAAs not previously encoded in yeast; 2) improvement of the performance of an existing aaRS; 3) highly selective OTSs capable of discriminating between closely related ncAA analogs; and 4) OTSs exhibiting enhanced polyspecificity to support translation with structurally diverse sets of ncAAs. The number of previously undiscovered aaRS variants we report in this work more than doubles the total number of translationally active aaRSs available for genetic code manipulation in yeast. The success of myriad screening strategies has important implications related to the fundamental properties and evolvability of aaRSs. Furthermore, access to OTSs with diverse activities and specific/polyspecific properties are invaluable for a range of applications within chemical biology, synthetic biology, and protein engineering.

scholarly journals Pyrrolysyl-tRNA Synthetase, an Aminoacyl-tRNA Synthetase for Genetic Code Expansion

2016 ◽  
Vol 89 (2) ◽  
Author(s):  
Ana Crnković ◽  
Tateki Suzuki ◽  
Dieter Söll ◽  
Noah M. Reynolds
Keyword(s):  
Genetic Code ◽  
Trna Synthetase ◽  
Aminoacyl Trna Synthetase ◽  
Genetic Code Expansion

Fully Productive Cell-Free Genetic Code Expansion by Structure-Based Engineering of Methanomethylophilus alvus Pyrrolysyl-tRNA Synthetase

2020 ◽  
Vol 9 (4) ◽  
pp. 718-732 ◽  
Author(s):  
Eiko Seki ◽  
Tatsuo Yanagisawa ◽  
Mitsuo Kuratani ◽  
Kensaku Sakamoto ◽  
Shigeyuki Yokoyama
Keyword(s):  
Genetic Code ◽  
Trna Synthetase ◽  
Genetic Code Expansion

scholarly journals Functional replacement of the endogenous tyrosyl-tRNA synthetase–tRNATyr pair by the archaeal tyrosine pair in Escherichia coli for genetic code expansion

2010 ◽  
Vol 38 (11) ◽  
pp. 3682-3691 ◽  
Author(s):  
Fumie Iraha ◽  
Kenji Oki ◽  
Takatsugu Kobayashi ◽  
Satoshi Ohno ◽  
Takashi Yokogawa ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Genetic Code ◽  
Trna Synthetase ◽  
Genetic Code Expansion ◽  
Functional Replacement

scholarly journals Pyrrolysyl-tRNA synthetase: An ordinary enzyme but an outstanding genetic code expansion tool

2014 ◽  
Vol 1844 (6) ◽  
pp. 1059-1070 ◽  
Author(s):  
Wei Wan ◽  
Jeffery M. Tharp ◽  
Wenshe R. Liu
Keyword(s):  
Genetic Code ◽  
Trna Synthetase ◽  
Genetic Code Expansion

scholarly journals Simplified Methodology for a Modular and Genetically Expanded Protein Synthesis in Cell-Free Systems

2019 ◽  
Author(s):  
Yonatan Chemla ◽  
Eden Ozer ◽  
Michael Shaferman ◽  
Ben Zaad ◽  
Rambabu Dandela ◽  
...  
Keyword(s):  
Amino Acids ◽  
Genetic Code ◽  
Unnatural Amino Acids ◽  
High Efficiency ◽  
Living Cells ◽  
Trna Synthetase ◽  
Complex Nature ◽  
Reporter Protein ◽  
A Cell ◽  
Genetic Code Expansion

ABSTRACTGenetic code expansion, which enables the site-specific incorporation of unnatural amino acids into proteins, has emerged as a new and powerful tool for protein engineering. Currently, it is mainly utilized inside living cells for a myriad of applications. However, utilization of this technology in a cell-free, reconstituted platform has several advantages over living systems. The common limitations to the employment of these systems are the laborious and complex nature of its preparation and utilization. Herein, we describe a simplified method for the preparation of this system from Escherichia coli cells, which is specifically adapted for the expression of the components needed for cell-free genetic code expansion. In addition, we propose and demonstrate a modular approach to its utilization. By this approach, it is possible to prepare and store different extracts, harboring various translational components, and mix and match them as needed for more than four years retaining its high efficiency. We demonstrate this with the simultaneous incorporation of two different unnatural amino acids into a reporter protein. Finally, we demonstrate the advantage of cell-free systems over living cells for the incorporation of δ-thio-boc-lysine into ubiquitin by using the methanosarcina mazei wild-type pyrrolysyl tRNACUA and tRNA-synthetase pair, which can not be achieved in a living cell.

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