Evolution of the genetic code; Evidence from serine codon use disparity in Escherichia coli
Masayori Inouye, Risa Takino, Yojiro Ishida, and Keiko Inouye
PNAS November 17, 2020 117 (46) 28572-28575
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Figure: Escherichia coli (Migula 1895) Castellani và Chalmers 1919
Significance
There are many questions related to the origin of life and how we came to rely on an almost universal system to encode all of life as we know it today. The genetic code is both robust and redundant, yet also full of interesting anomalies. Here we explore one of these anomalies, specifically the existence of two separate boxes/classes of serine codons, AGU/C and UCU/C/A/G. Unlike other synonymous codons encoding an amino acid, these codons for serine require a two-base substitution in order to go from one box to the other and remain a serine. Deciphering how this came to be will provide important insight into the origin of life and the genetic code.
Abstract
Among the 20 amino acids, three of them—leucine (Leu), arginine (Arg), and serine (Ser)—are encoded by six different codons. In comparison, all of the other 17 amino acids are encoded by either 4, 3, 2, or 1 codon. Peculiarly, Ser is separated into two disparate Ser codon boxes, differing by at least two-base substitutions, in contrast to Leu and Arg, of which codons are mutually exchangeable by a single-base substitution. We propose that these two different Ser codons independently emerged during evolution. In this hypothesis, at the time of the origin of life there were only seven primordial amino acids: Valine (coded by GUX [X = U, C, A or G]), alanine (coded by GCX), aspartic acid (coded by GAY [Y = U or C]), glutamic acid (coded by GAZ [Z = A or G]), glycine (coded by GGX), Ser (coded by AGY), and Arg (coded by CGX and AGZ). All of these were derived from GGX for glycine by single-base substitutions. Later in evolution, another class of Ser codons, UCX, were derived from alanine codons, GCX, distinctly different from the other primordial Ser codon, AGY. From the analysis of the Escherichia coli genome, we find extensive disparities in the usage of these two Ser codons, as some genes use only AGY for Ser in their genes. In contrast, others use only UCX, pointing to distinct differences in their origins, consistent with our hypothesis.
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