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A Closer Look at Non-random Patterns Within Chemistry Space for a Smaller, Earlier Amino Acid Alphabet

Mayer-Bacon, Christopher and Meringer, Markus and Havel, Riley and Aponte, José C. and Freeland, Stephen J. (2022) A Closer Look at Non-random Patterns Within Chemistry Space for a Smaller, Earlier Amino Acid Alphabet. Journal of Molecular Evolution, 90, pp. 307-323. Springer Nature. doi: 10.1007/s00239-022-10061-5. ISSN 0022-2844.

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Official URL: https://link.springer.com/article/10.1007/s00239-022-10061-5


Recent findings, in vitro and in silico, are strengthening the idea of a simpler, earlier stage of genetically encoded proteins which used amino acids produced by prebiotic chemistry. These findings motivate a re-examination of prior work which has identified unusual properties of the set of twenty amino acids found within the full genetic code, while leaving it unclear whether similar patterns also characterize the subset of prebiotically plausible amino acids. We have suggested previously that this ambiguity may result from the low number of amino acids recognized by the definition of prebiotic plausibility used for the analysis. Here, we test this hypothesis using significantly updated data for organic material detected within meteorites, which contain several coded and non-coded amino acids absent from prior studies. In addition to confirming the well-established idea that "late" arriving amino acids expanded the chemistry space encoded by genetic material, we find that a prebiotically plausible subset of coded amino acids generally emulates the patterns found in the full set of 20, namely an exceptionally broad and even distribution of volumes and an exceptionally even distribution of hydrophobicities (quantified as logP) over a narrow range. However, the strength of this pattern varies depending on both the size and composition the library used to create a background (null model) for a random alphabet, and the precise definition of exactly which amino acids were present in a simpler, earlier code. Findings support the idea that a small sample size of amino acids caused previous ambiguous results, and further improvements in meteorite analysis, and/or prebiotic simulations will further clarify the nature and extent of unusual properties. We discuss the case of sulfur-containing amino acids as a specific and clear example and conclude by reviewing the potential impact of better understanding the chemical "logic" of a smaller forerunner to the standard amino acid alphabet.

Item URL in elib:https://elib.dlr.de/187335/
Document Type:Article
Title:A Closer Look at Non-random Patterns Within Chemistry Space for a Smaller, Earlier Amino Acid Alphabet
AuthorsInstitution or Email of AuthorsAuthor's ORCID iD
Mayer-Bacon, ChristopherUniversity of Maryland Baltimore Countyhttps://orcid.org/0000-0002-5863-7712
Meringer, MarkusMarkus.Meringer (at) dlr.dehttps://orcid.org/0000-0001-8526-2429
Havel, RileyUniversity of Central FloridaUNSPECIFIED
Aponte, José C.NASA Goddard Space Flight CenterUNSPECIFIED
Freeland, Stephen J.University of Hawaii, NASA Astribiology InstituteUNSPECIFIED
Date:6 June 2022
Journal or Publication Title:Journal of Molecular Evolution
Refereed publication:Yes
Open Access:No
Gold Open Access:No
In ISI Web of Science:Yes
DOI :10.1007/s00239-022-10061-5
Page Range:pp. 307-323
Publisher:Springer Nature
Keywords:abiogenesis, chemistry space, amino acids, computational chemistry, evolution
HGF - Research field:Aeronautics, Space and Transport
HGF - Program:Space
HGF - Program Themes:Space Exploration
DLR - Research area:Raumfahrt
DLR - Program:R EW - Space Exploration
DLR - Research theme (Project):R - Planetary Evolution and Life
Location: Oberpfaffenhofen
Institutes and Institutions:Remote Sensing Technology Institute > Atmospheric Processors
Deposited By: Meringer, Dr.rer.nat. Markus
Deposited On:11 Jul 2022 13:01
Last Modified:12 Jul 2022 14:48

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