Cited by 193Origins and Evolution of LifeRNA and protein synthesis mechanismsEvolution and Genetic Dynamics

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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

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Brooks, Dawn J., Fresco, Jacques R., Lesk, Arthur M., Singh, Mona·2002·Molecular Biology and Evolution

DOI 10.1093/oxfordjournals.molbev.a003988

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Abstract

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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Authors: Brooks, D. J., Fresco, J. R., Lesk, A. M., & Singh, M.
Affiliations: Princeton University (US)
ORCID: Fresco, Jacques R.
Lesk, Arthur M.
Singh, Mona
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
DOI: 10.1093/oxfordjournals.molbev.a003988
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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Evolution of Amino Acid Frequencies in Proteins Over Deep Time: Inferred Order of Introduction of Amino Acids into the Genetic Code

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