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Evolution of Amino Acid Frequencies in Proteins Over Deep Time: Inferred Order of Introduction of Amino Acids into the Genetic Code
Open accessAbstract
To understand more fully how amino acid composition of proteins has changed over the course of evolution, a method has been developed for estimating the composition of proteins in an ancestral genome. Estimates are based upon the composition of conserved residues in descendant sequences and empirical knowledge of the relative probability of conservation of various amino acids. Simulations are used to model and correct for errors in the estimates. The method was used to infer the amino acid composition of a large protein set in the Last Universal Ancestor (LUA) of all extant species. Relative to the modern protein set, LUA proteins were found to be generally richer in those amino acids that are believed to have been most abundant in the prebiotic environment and poorer in those amino acids that are believed to have been unavailable or scarce. It is proposed that the inferred amino acid composition of proteins in the LUA probably reflects historical events in the establishment of the genetic code.
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“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 Brooks et al. 2002
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Metadata
- Authors
- Brooks, D. J., Fresco, J. R., Lesk, A. M., & Singh, M.
- Affiliations
- Princeton University (US)
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2002-10-01
- Volume
- 19
- Issue
- 10
- Pages
- 1645-1655
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- OpenAlex
- W2079704642
- Cited by
- 192
- References
- 35
- Citations by year
- 2026: 9 · 2025: 8 · 2024: 7 · 2023: 10 · 2022: 7 · 2021: 10 · 2020: 11 · 2019: 15 · 2018: 6 · 2017: 10 · 2016: 7 · 2015: 4 · 2014: 6 · 2013: 8 · 2012: 12
- FWCI
- 2.75
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Molecular Biology and Evolution (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Science Foundation (9972930, 0093399)
- U.S. Department of Defense
- Wellcome Trust
- National Institutes of Health
- National Institute of General Medical Sciences (T32GM007388, 2T32GM07388-22)
- U.S. Army Medical Command
- Topics
- Physical Sciences › Physics and Astronomy › Astronomy and Astrophysics › Origins and Evolution of Life
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Keywords
- amino acid composition, protein evolution, origin of the genetic code, ancestral genome reconstruction, conserved residues, prebiotic amino acids, amino acid availability
- MeSH terms
- Amino Acid Sequence, Amino Acids, Computer Simulation, Genetic Code, Models, Genetic, Probability, Proteins, Time Factors, Conserved Sequence, Evolution, Molecular, Amino Acid Substitution
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