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Adaptive Properties of the Genetically Encoded Amino Acid Alphabet Are Inherited from Its Subsets

Life uses a common set of 20 coded amino acids (CAAs) to construct proteins. This set was likely canonicalized during early evolution; before this, smaller amino acid sets were gradually expanded as new synthetic, proofreading and coding mechanisms became biologically available. Many possible subset...

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Autores principales: Ilardo, Melissa, Bose, Rudrarup, Meringer, Markus, Rasulev, Bakhtiyor, Grefenstette, Natalie, Stephenson, James, Freeland, Stephen, Gillams, Richard J., Butch, Christopher J., Cleaves, H. James
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6713743/
https://www.ncbi.nlm.nih.gov/pubmed/31462646
http://dx.doi.org/10.1038/s41598-019-47574-x
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author Ilardo, Melissa
Bose, Rudrarup
Meringer, Markus
Rasulev, Bakhtiyor
Grefenstette, Natalie
Stephenson, James
Freeland, Stephen
Gillams, Richard J.
Butch, Christopher J.
Cleaves, H. James
author_facet Ilardo, Melissa
Bose, Rudrarup
Meringer, Markus
Rasulev, Bakhtiyor
Grefenstette, Natalie
Stephenson, James
Freeland, Stephen
Gillams, Richard J.
Butch, Christopher J.
Cleaves, H. James
author_sort Ilardo, Melissa
collection PubMed
description Life uses a common set of 20 coded amino acids (CAAs) to construct proteins. This set was likely canonicalized during early evolution; before this, smaller amino acid sets were gradually expanded as new synthetic, proofreading and coding mechanisms became biologically available. Many possible subsets of the modern CAAs or other presently uncoded amino acids could have comprised the earlier sets. We explore the hypothesis that the CAAs were selectively fixed due to their unique adaptive chemical properties, which facilitate folding, catalysis, and solubility of proteins, and gave adaptive value to organisms able to encode them. Specifically, we studied in silico hypothetical CAA sets of 3–19 amino acids comprised of 1913 structurally diverse α-amino acids, exploring the adaptive value of their combined physicochemical properties relative to those of the modern CAA set. We find that even hypothetical sets containing modern CAA members are especially adaptive; it is difficult to find sets even among a large choice of alternatives that cover the chemical property space more amply. These results suggest that each time a CAA was discovered and embedded during evolution, it provided an adaptive value unusual among many alternatives, and each selective step may have helped bootstrap the developing set to include still more CAAs.
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spelling pubmed-67137432019-09-13 Adaptive Properties of the Genetically Encoded Amino Acid Alphabet Are Inherited from Its Subsets Ilardo, Melissa Bose, Rudrarup Meringer, Markus Rasulev, Bakhtiyor Grefenstette, Natalie Stephenson, James Freeland, Stephen Gillams, Richard J. Butch, Christopher J. Cleaves, H. James Sci Rep Article Life uses a common set of 20 coded amino acids (CAAs) to construct proteins. This set was likely canonicalized during early evolution; before this, smaller amino acid sets were gradually expanded as new synthetic, proofreading and coding mechanisms became biologically available. Many possible subsets of the modern CAAs or other presently uncoded amino acids could have comprised the earlier sets. We explore the hypothesis that the CAAs were selectively fixed due to their unique adaptive chemical properties, which facilitate folding, catalysis, and solubility of proteins, and gave adaptive value to organisms able to encode them. Specifically, we studied in silico hypothetical CAA sets of 3–19 amino acids comprised of 1913 structurally diverse α-amino acids, exploring the adaptive value of their combined physicochemical properties relative to those of the modern CAA set. We find that even hypothetical sets containing modern CAA members are especially adaptive; it is difficult to find sets even among a large choice of alternatives that cover the chemical property space more amply. These results suggest that each time a CAA was discovered and embedded during evolution, it provided an adaptive value unusual among many alternatives, and each selective step may have helped bootstrap the developing set to include still more CAAs. Nature Publishing Group UK 2019-08-28 /pmc/articles/PMC6713743/ /pubmed/31462646 http://dx.doi.org/10.1038/s41598-019-47574-x Text en © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Ilardo, Melissa
Bose, Rudrarup
Meringer, Markus
Rasulev, Bakhtiyor
Grefenstette, Natalie
Stephenson, James
Freeland, Stephen
Gillams, Richard J.
Butch, Christopher J.
Cleaves, H. James
Adaptive Properties of the Genetically Encoded Amino Acid Alphabet Are Inherited from Its Subsets
title Adaptive Properties of the Genetically Encoded Amino Acid Alphabet Are Inherited from Its Subsets
title_full Adaptive Properties of the Genetically Encoded Amino Acid Alphabet Are Inherited from Its Subsets
title_fullStr Adaptive Properties of the Genetically Encoded Amino Acid Alphabet Are Inherited from Its Subsets
title_full_unstemmed Adaptive Properties of the Genetically Encoded Amino Acid Alphabet Are Inherited from Its Subsets
title_short Adaptive Properties of the Genetically Encoded Amino Acid Alphabet Are Inherited from Its Subsets
title_sort adaptive properties of the genetically encoded amino acid alphabet are inherited from its subsets
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6713743/
https://www.ncbi.nlm.nih.gov/pubmed/31462646
http://dx.doi.org/10.1038/s41598-019-47574-x
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