scholarly journals The e-Dimensionality of Genetic Information

2021 ◽  
Author(s):  
Subhash Kak
Keyword(s):  
Amino Acids ◽  
Genetic Code ◽  
Genetic Information ◽  
Coding Theory ◽  
Rank Order ◽  
Information Space ◽  
Zipf Distribution

This paper provides an explanation for why the assignment of codons to amino acids, which range from 1 to 6, is non-uniform. Since mathematical coding theory demands a near uniform assignment, the answer to this question is important to understand deeper aspects of the structure of the genetic code. Our analysis points to 20 different covering regions in an e-dimensional information space, which is equal to the number of amino acids. It is also shown that the assignment of the codons to the amino acids is fractal-like that is well modeled by the Zipf distribution. It is remarkable that the Zipf distribution that holds for the letter frequencies of words in a language also applies to the rank order of triplets the code for amino acids.

scholarly journals The e-Dimensionality of Genetic Information

2021 ◽  
Author(s):  
Subhash Kak
Keyword(s):  
Amino Acids ◽  
Genetic Code ◽  
Genetic Information ◽  
Coding Theory ◽  
Rank Order ◽  
Information Space ◽  
Zipf Distribution

This paper provides an explanation for why the assignment of codons to amino acids, which range from 1 to 6, is non-uniform. Since mathematical coding theory demands a near uniform assignment, the answer to this question is important to understand deeper aspects of the structure of the genetic code. Our analysis points to 20 different covering regions in an e-dimensional information space, which is equal to the number of amino acids. It is also shown that the assignment of the codons to the amino acids is fractal-like that is well modeled by the Zipf distribution. It is remarkable that the Zipf distribution that holds for the letter frequencies of words in a language also applies to the rank order of triplets the code for amino acids.

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 Determinants of adenine-mutagenesis in diversity-generating retroelements

2020 ◽  
Author(s):  
Sumit Handa ◽  
Andres Reyna ◽  
Timothy Wiryaman ◽  
Partho Ghosh
Keyword(s):  
Amino Acids ◽  
Dark Matter ◽  
Reverse Transcription ◽  
Genetic Information ◽  
Human Microbiome ◽  
Protein Sequences ◽  
Catalytic Efficiency ◽  
Natural World ◽  
In Vitro System

Abstract Diversity-generating retroelements (DGRs) vary protein sequences to the greatest extent known in the natural world. These elements are encoded by constituents of the human microbiome and the microbial ‘dark matter’. Variation occurs through adenine-mutagenesis, in which genetic information in RNA is reverse transcribed faithfully to cDNA for all template bases but adenine. We investigated the determinants of adenine-mutagenesis in the prototypical Bordetella bacteriophage DGR through an in vitro system composed of the reverse transcriptase bRT, Avd protein, and a specific RNA. We found that the catalytic efficiency for correct incorporation during reverse transcription by the bRT-Avd complex was strikingly low for all template bases, with the lowest occurring for adenine. Misincorporation across a template adenine was only somewhat lower in efficiency than correct incorporation. We found that the C6, but not the N1 or C2, purine substituent was a key determinant of adenine-mutagenesis. bRT-Avd was insensitive to the C6 amine of adenine but recognized the C6 carbonyl of guanine. We also identified two bRT amino acids predicted to nonspecifically contact incoming dNTPs, R74 and I181, as promoters of adenine-mutagenesis. Our results suggest that the overall low catalytic efficiency of bRT-Avd is intimately tied to its ability to carry out adenine-mutagenesis.

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 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
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