scholarly journals Expanding the genetic code of Salmonella with non-canonical amino acids

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Qinglei Gan ◽  
Brent P. Lehman ◽  
Thomas A. Bobik ◽  
Chenguang Fan
Keyword(s):  
Amino Acids ◽  
Genetic Code

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.

On the Optimization of the Physicochemical Distances between Amino Acids in the Evolution of the Genetic Code

1994 ◽  
Vol 168 (1) ◽  
pp. 43-51 ◽  
Author(s):  
Massimo Di Giulio ◽  
M.Rosaria Capobianco ◽  
Mario Medugno
Keyword(s):  
Amino Acids ◽  
Genetic Code

scholarly journals Genetic code as an image of the mirror image. Supplement 1

2019 ◽  
Author(s):  
Miloje M. Rakočević
Keyword(s):  
Amino Acids ◽  
Genetic Code ◽  
Binary Tree ◽  
Mirror Symmetry ◽  
Essential Feature ◽  
Binary Sequence ◽  
Number System ◽  
Mirror Image ◽  
Chemical Similarity ◽  
Decimal Number

Searching for the answer to the question why – in the generating of the genetic code – only mirror symmetrical left and not right amino acids (AAs) were selected, in a previous work we showed the existence of a double Boolean "triangle" in mirror symmetry, with superposition of the top vertices: 00 -11-22 / 22-11-00 → 00-11-22-11-00 [0 as 000; 1 as 001; 2 as 010] (Rakočević, 2019a). The resulting sequence, summed with the binary sequence of a 6-bit binary tree, split with a mirror in the middle (101/010) [as in Dirac's positron / electron mirror], results in a sequence of decimal number system: 02-13-24-16-05, where a smaller number (010 = 2) was added three times and a larger number (101 = 5) twice (Survey 1). The mirror image of the obtained decimal sequence (20-31-42-61-50) is 100% consistent with the arrangement of protein AAs, arranged according to strict chemical similarity (Rakočević, 2019a, Table 3). Starting from this result, the paper of which this is a supplement, presents new insights and new examples of mirror symmetry valid for the genetic code, showing that mirror symmetry is also in other respects an essential feature of the genetic code. In this Supplement are given the further new insights.

scholarly journals Making Sense of “Nonsense” and More: Challenges and Opportunities in the Genetic Code Expansion, in the World of tRNA Modifications

2022 ◽  
Vol 23 (2) ◽  
pp. 938
Author(s):  
Olubodun Michael Lateef ◽  
Michael Olawale Akintubosun ◽  
Olamide Tosin Olaoba ◽  
Sunday Ocholi Samson ◽  
Malgorzata Adamczyk
Keyword(s):  
Amino Acids ◽  
Genetic Code ◽  
Protein Design ◽  
Side Chains ◽  
Vast Number ◽  
Trna Modifications ◽  
Wide Range ◽  
Challenges And Opportunities ◽  
Code Extension ◽  
Genetic Code Expansion

The evolutional development of the RNA translation process that leads to protein synthesis based on naturally occurring amino acids has its continuation via synthetic biology, the so-called rational bioengineering. Genetic code expansion (GCE) explores beyond the natural translational processes to further enhance the structural properties and augment the functionality of a wide range of proteins. Prokaryotic and eukaryotic ribosomal machinery have been proven to accept engineered tRNAs from orthogonal organisms to efficiently incorporate noncanonical amino acids (ncAAs) with rationally designed side chains. These side chains can be reactive or functional groups, which can be extensively utilized in biochemical, biophysical, and cellular studies. Genetic code extension offers the contingency of introducing more than one ncAA into protein through frameshift suppression, multi-site-specific incorporation of ncAAs, thereby increasing the vast number of possible applications. However, different mediating factors reduce the yield and efficiency of ncAA incorporation into synthetic proteins. In this review, we comment on the recent advancements in genetic code expansion to signify the relevance of systems biology in improving ncAA incorporation efficiency. We discuss the emerging impact of tRNA modifications and metabolism in protein design. We also provide examples of the latest successful accomplishments in synthetic protein therapeutics and show how codon expansion has been employed in various scientific and biotechnological applications.

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