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The ancient operational code is embedded in the amino acid substitution matrix and aaRS phylogenies


Shore, JA and Holland, BR and Sumner, JG and Nieselt, K and Wills, PR, The ancient operational code is embedded in the amino acid substitution matrix and aaRS phylogenies, Journal of Molecular Evolution, 88, (2) pp. 136-150. ISSN 0022-2844 (2020) [Refereed Article]

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Copyright 2019 Springer Science+Business Media, LLC, part of Springer Nature

DOI: doi:10.1007/s00239-019-09918-z


The underlying structure of the canonical amino acid substitution matrix (aaSM) is examined by considering stepwise improvements in the differential recognition of amino acids according to their chemical properties during the branching history of the two aminoacyl-tRNA synthetase (aaRS) superfamilies. The evolutionary expansion of the genetic code is described by a simple parameterization of the aaSM, in which (i) the number of distinguishable amino acid types, (ii) the matrix dimension and (iii) the number of parameters, each increases by one for each bifurcation in an aaRS phylogeny. Parameterized matrices corresponding to trees in which the size of an amino acid sidechain is the only discernible property behind its categorization as a substrate, exclusively for a Class I or II aaRS, provide a significantly better fit to empirically determined aaSM than trees with random bifurcation patterns. A second split between polar and nonpolar amino acids in each Class effects a vastly greater further improvement. The earliest Class-separated epochs in the phylogenies of the aaRS reflect these enzymes’ capability to distinguish tRNAs through the recognition of acceptor stem identity elements via the minor (Class I) and major (Class II) helical grooves, which is how the ancient operational code functioned. The advent of tRNA recognition using the anticodon loop supports the evolution of the optimal map of amino acid chemistry found in the later genetic code, an essentially digital categorization, in which polarity is the major functional property, compensating for the unrefined, haphazard differentiation of amino acids achieved by the operational code.

Item Details

Item Type:Refereed Article
Keywords:amino acid substitution matrix, aminoacyl-tRNA synthetase, aaRS phylogeny, code expansion, parameterized matrices, size, polarity
Research Division:Mathematical Sciences
Research Group:Applied mathematics
Research Field:Biological mathematics
Objective Division:Expanding Knowledge
Objective Group:Expanding knowledge
Objective Field:Expanding knowledge in the biological sciences
UTAS Author:Shore, JA (Mrs Julia Shore)
UTAS Author:Holland, BR (Professor Barbara Holland)
UTAS Author:Sumner, JG (Associate Professor Jeremy Sumner)
ID Code:141851
Year Published:2020
Funding Support:Australian Research Council (DP150100088)
Web of Science® Times Cited:5
Deposited By:Mathematics
Deposited On:2020-11-26
Last Modified:2022-08-23

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