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Adaptive properties of the genetically encoded amino acid alphabet are inherited from its subsets

Adaptive properties of the genetically encoded amino acid alphabet are inherited from its subsets
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 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.

2045-2322
Ilardo, Melissa
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Bose, Rudrarup
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Meringer, Markus
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Rasulev, Bakhtiyor
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Grefenstette, Natalie
364517b0-c9ee-4502-b28f-0d3276d836ad
Stephenson, James
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Freeland, Stephen
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Gillams, Richard J.
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Butch, Christopher J.
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Cleaves, H. James
a60d382d-f1ef-492c-86c6-b5e544acc01d
Ilardo, Melissa
c02b378e-d488-44f7-88cb-42522d0dfd01
Bose, Rudrarup
8309131c-c403-4d09-9e0a-6766168ae2d0
Meringer, Markus
1773b450-058f-4aae-9624-e37d141db676
Rasulev, Bakhtiyor
49d6ee0a-2958-415b-b889-460cbbefefb6
Grefenstette, Natalie
364517b0-c9ee-4502-b28f-0d3276d836ad
Stephenson, James
16b29e75-cc40-4407-a885-21d80426607c
Freeland, Stephen
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Gillams, Richard J.
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Butch, Christopher J.
fcdcbe35-39ae-4bae-b3c2-de8b2167c2f8
Cleaves, H. James
a60d382d-f1ef-492c-86c6-b5e544acc01d

Ilardo, Melissa, Bose, Rudrarup, Meringer, Markus, Rasulev, Bakhtiyor, Grefenstette, Natalie, Stephenson, James, Freeland, Stephen, Gillams, Richard J., Butch, Christopher J. and Cleaves, H. James (2019) Adaptive properties of the genetically encoded amino acid alphabet are inherited from its subsets. Scientific Reports, 9 (1), [12468]. (doi:10.1038/s41598-019-47574-x).

Record type: Article

Abstract

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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Accepted/In Press date: 8 July 2019
e-pub ahead of print date: 28 August 2019

Identifiers

Local EPrints ID: 434261
URI: http://eprints.soton.ac.uk/id/eprint/434261
ISSN: 2045-2322
PURE UUID: 418816e4-169e-4332-a694-22989180bc0f
ORCID for Richard J. Gillams: ORCID iD orcid.org/0000-0002-8597-8723

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Date deposited: 18 Sep 2019 16:30
Last modified: 07 Oct 2020 02:15

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Contributors

Author: Melissa Ilardo
Author: Rudrarup Bose
Author: Markus Meringer
Author: Bakhtiyor Rasulev
Author: Natalie Grefenstette
Author: James Stephenson
Author: Stephen Freeland
Author: Richard J. Gillams ORCID iD
Author: Christopher J. Butch
Author: H. James Cleaves

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