ArticleJournal of molecular evolution2015
Ancestral Reconstruction of a Pre-LUCA Aminoacyl-tRNA Synthetase Ancestor Supports the Late Addition of Trp to the Genetic Code.
Article in Journal of molecular evolution, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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42 citing papers in PubMed, 76 citations in OpenAlex.
- Resurrecting tRNAs of the Last Universal Common Ancestor (Commonote) Toward Rebuilding the Ancient Translation System.Journal of molecular evolution · 2026Article
- The Evolution of the First Code.Genes · 2026Review
- Universal paralogs provide a window into evolution before the last universal common ancestor.Cell genomics · 2026Review
- Reduced Amino Acid Substitution Matrices Find Traces of Ancient Coding Alphabets in Modern Day Proteins.Molecular biology and evolution · 2025Article
- Structural Enzymology, Phylogenetics, Differentiation, and Symbolic Reflexivity at the Dawn of Biology.Genome biology and evolution · 2025Article
- Order of amino acid recruitment into the genetic code resolved by last universal common ancestor's protein domains.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Order of amino acid recruitment into the genetic code resolved by Last Universal Common Ancestor's protein domains.bioRxiv : the preprint server for biology · 2024Article
- Multisubstrate specificity shaped the complex evolution of the aminotransferase family across the tree of life.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Autocatalytic Selection as a Driver for the Origin of Life.Life (Basel, Switzerland) · 2024Article
- Enzymic recognition of amino acids drove the evolution of primordial genetic codes.Nucleic acids research · 2024Article
- Informatic Capabilities of Translation and Its Implications for the Origins of Life.Journal of molecular evolution · 2023Review
- Origins of Genetic Coding: Self-Guided Molecular Self-Organisation.Entropy (Basel, Switzerland) · 2023Article
- Electron transport chains as a window into the earliest stages of evolution.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Orthogonal translation with 5-cyanotryptophan as an infrared probe for local structural information, electrostatics, and hydrogen bonding.Protein science : a publication of the Protein Society · 2023Article
- The Origin of Translation: Bridging the Nucleotides and Peptides.International journal of molecular sciences · 2022Review
- A Closer Look at Non-random Patterns Within Chemistry Space for a Smaller, Earlier Amino Acid Alphabet.Journal of molecular evolution · 2022Article
- Article
- A consensus view of the proteome of the last universal common ancestor.Ecology and evolution · 2022Article
- Undefining life's biochemistry: implications for abiogenesis.Journal of the Royal Society, Interface · 2022Review
- Amino Acid Specificity of Ancestral Aminoacyl-tRNA Synthetase Prior to the Last Universal Common Ancestor Commonote commonote.Journal of molecular evolution · 2022Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The genetic code was likely complete in its current form by the time of the last universal common ancestor (LUCA). Several scenarios have been proposed for explaining the code's pre-LUCA emergence and expansion, and the relative order of the appearance of amino acids used in translation. One co-evolutionary model of genetic code expansion proposes that at least some amino acids were added to the code by the ancient divergence of aminoacyl-tRNA synthetase (aaRS) families. Of all the amino acids used within the genetic code, Trp is most frequently claimed as a relatively recent addition. We observe that, since TrpRS and TyrRS are paralogous protein families retaining significant sequence similarity, the inferred sequence composition of their ancestor can be used to evaluate this co-evolutionary model of genetic code expansion. We show that ancestral sequence reconstructions of the pre-LUCA paralog ancestor of TyrRS and TrpRS have several sites containing Tyr, yet a complete absence of sites containing Trp. This is consistent with the paralog ancestor being specific for the utilization of Tyr, with Trp being a subsequent addition to the genetic code facilitated by a process of aaRS divergence and neofunctionalization. Only after this divergence could Trp be specifically encoded and incorporated into proteins, including the TyrRS and TrpRS descendant lineages themselves. This early absence of Trp is observed under both homogeneous and non-homogeneous models of ancestral sequence reconstruction. Simulations support that this observed absence of Trp is unlikely to be due to chance or model bias. These results support that the final stages of genetic code evolution occurred well within the "protein world," and that the presence-absence of Trp within conserved sites of ancient protein domains is a likely measure of their relative antiquity, permitting the relative timing of extremely early events within protein evolution before LUCA.
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