Recent emergence of the modern genetic code: a proposal

doi:10.1016/S0168-9525(02)02647-1

Trends in Genetics

Volume 18, Issue 5, 1 May 2002, Pages 245-248

https://doi.org/10.1016/S0168-9525(02)02647-1 Get rights and content

Abstract

This article proposes that the genetic code was not fully formed before the divergence of life into three kingdoms. Rather, at least arginine and tryptophan evolved after the diversification of archaea, bacteria and eukaryotes, and were spread by horizontal gene transfer. Evidence for this hypothesis is based on data suggesting that enzymes for biosynthesis of arginine and tryptophan, and for arginine tRNA ligase, have shorter divergence times than the underlying lineages. Also, many of these genes display ‘star’ phylogenies. This proposal is an extension of the idea that the genetic code was unified because of the evolutionary pressure from horizontal gene transfer. These considerations further undermine the need to postulate the existence of a ‘last common ancestor’; a simpler model would be that multiple lineages gave rise to life today.

Section snippets

Age of the last common ancestor

In 1996, Doolittle et al. [6] suggested that archaea, bacteria and eukaryotes diverged only about 1800—2200 million years (Myr) ago. This was based on examining 57 different genes from the three kingdoms for which calibration points were available, and then averaging the divergence times. The Doolittle study has been confirmed by another study that determined the age of 13 genes and obtained an average divergence time of 2200 Myr [7]. However, there is abundant evidence for the presence of

Star phylogenies

The most parsimonious phylogenetic tree for several of the genes listed in Table 1 takes the shape of a star. A star phylogeny is encountered when eukaryotes, remotely related archaea and remotely related bacteria are all approximately equally related to one another [10]. Fig. 1a shows a typical pattern for arginine tRNA ligase. The star in this example arises from the relatively short internal branches compared with the much longer external branches. Furthermore, the arrangement of clades

Evolution of the genetic code

In an earlier paper, I suggested that the unity of the genetic code was the outcome of an evolutionary mechanism in which horizontal gene transfer was a major factor [17]. In the early 1980s, there were two competing explanations for the unity of the code. One posited that the unity of the genetic code was the result of functional constraints such that certain amino acids would only fit, at the mechanistic level, with certain codons 18., 19., 20.. The second notion was that all life descended

LCA

One of the obvious conclusions from these considerations is that the existence of a single homologous trait found in the three kingdoms does not necessarily imply that the LCA carried that trait. It is not even necessary to postulate the existence of such an ancestor, as has been suggested by Woese [30] and Doolittle [31]. It is simpler to posit that, since the origin of life, multiple lineages emerged and that multiple lineages are responsible for the so-called ‘LCA’. The LCA is an unnecessary

Acknowledgements

I thank Hy Hartman and Steve Daubert for useful suggestions.

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Trends in Genetics

OpinionRecent emergence of the modern genetic code: a proposal

Abstract

Section snippets

Age of the last common ancestor

Star phylogenies

Evolution of the genetic code

LCA

Acknowledgements

Genome Res.

J. Mol. Evol.

J. Mol. Evol.

Trends Genet.

Origins Life

Prokaryotic genomes: the emerging paradigm of genome-based microbiology

Curr. Opin. Genet. Dev.

The universal ancestor

Proc. Natl. Acad. Sci. U. S. A.

Phylogenetic classification and the universal tree

Science

Horizontal gene transfer among genomes: the complexity hypothesis

Proc. Natl. Acad. Sci. U. S. A.

Determining divergence times of the major kingdoms of living organisms with a protein clock

Science

Dating the age of the last common ancestor of all living organisms with a protein clock

Determining the relative rates of change for prokaryotic and eukaryotic proteins with anciently duplicated paralogs

J. Mol. Evol.

Determining divergence times with a protein clock: update and reevaluation

Proc. Natl. Acad. Sci. U. S. A.

On the occurrence of horizontal gene transfer among an arbitrarily chosen group of 26 genes

J. Mol. Evol.

Phylogenetic analysis of the aminoacyl-tRNA synthases

J. Mol. Evol.

Opinion
Recent emergence of the modern genetic code: a proposal