Rooting the Ribosomal Tree of Life
Abstract
The origin of the genetic code and the rooting of the tree of life (ToL) are two of the most challenging problems in the study of life's early evolution. Although both have been the focus of numerous investigations utilizing a variety of methods, until now, each problem has been addressed independently. Typically, attempts to root the ToL have relied on phylogenies of genes with ancient duplications, which are subject to artifacts of tree reconstruction and horizontal gene transfer, or specific physiological characters believed to be primitive, which are often based on subjective criteria. Here, we demonstrate a unique method for rooting based on the identification of amino acid usage biases comprising the residual signature of a more primitive genetic code. Using a phylogenetic tree of concatenated ribosomal proteins, our analysis of amino acid compositional bias detects a strong and unique signal associated with the early expansion of the genetic code, placing the root of the translation machinery along the bacterial branch.
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The earliest amino acids used by life fit a temperate origin, not a hot one.
“Work on the addition of amino acids to the canonical repertoire suggest that the first amino acids used by life are also consistent with a temperate, rather than hot, origin of life (Brooks et al. 2002;Zeldovich et al. 2007;Fournier and Gogarten 2010).”
From Environmental Adaptation from the Origin of Life to the Last Universal Common Ancestor (2018) · cites this paper as Fournier and Gogarten 2010
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Self-citation
- Authors
- Fournier, G. P., & Gogarten, J. P.
- Affiliations
- University of Connecticut (US)
- Corresponding author
- Gogarten, J. P.
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-03-01
- Volume
- 27
- Issue
- 8
- Pages
- 1792-1801
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- OpenAlex
- W2163186086
- Cited by
- 72
- References
- 65
- Citations by year
- 2026: 3 · 2025: 3 · 2024: 4 · 2023: 4 · 2022: 8 · 2021: 5 · 2020: 5 · 2019: 2 · 2017: 4 · 2016: 3 · 2015: 7 · 2014: 3 · 2013: 3 · 2012: 4
- FWCI
- 2.73
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Molecular Biology and Evolution (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Science Foundation
- National Aeronautics and Space Administration
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Physical Sciences › Physics and Astronomy › Astronomy and Astrophysics › Origins and Evolution of Life
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- origin of the genetic code, ribosomal proteins, genetic code expansion, translation machinery, early evolution of life, horizontal gene transfer
- MeSH terms
- Amino Acid Sequence, Genetic Code, Molecular Sequence Data, Phylogeny, Ribosomal Proteins, Ribosomes, Sequence Alignment, Evolution, Molecular, Gene Transfer, Horizontal
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