The Ancient Operational Code is Embedded in the Amino Acid Substitution Matrix and aaRS Phylogenies
Autor: | Barbara R. Holland, Jeremy G. Sumner, Kay Nieselt, Julia A. Shore, Peter R. Wills |
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Rok vydání: | 2019 |
Předmět: |
0106 biological sciences
Polarity (physics) Minor (linear algebra) Computational biology 010603 evolutionary biology 01 natural sciences Identity (music) Amino Acyl-tRNA Synthetases Evolution Molecular 03 medical and health sciences Matrix (mathematics) Phylogenetics Anticodon Genetics Amino Acids Quantitative Biology - Populations and Evolution Molecular Biology Phylogeny Ecology Evolution Behavior and Systematics 030304 developmental biology Mathematics chemistry.chemical_classification 0303 health sciences Models Genetic Populations and Evolution (q-bio.PE) Genetic code Amino acid Amino Acid Substitution chemistry Genetic Code FOS: Biological sciences Transfer RNA |
Zdroj: | Journal of Molecular Evolution. 88:136-150 |
ISSN: | 1432-1432 0022-2844 |
Popis: | 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. |
Databáze: | OpenAIRE |
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