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Journal of Molecular Evolution

, Volume 80, Issue 3–4, pp 171–185 | Cite as

Ancestral Reconstruction of a Pre-LUCA Aminoacyl-tRNA Synthetase Ancestor Supports the Late Addition of Trp to the Genetic Code

  • G. P. Fournier
  • E. J. Alm
Original Article

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.

Keywords

Ancestral sequence reconstruction Genetic code Tryptophanyl-tRNA synthetase Tyrosyl-tRNA synthetase Tryptophan 

Notes

Acknowledgments

This work was supported by the National Science Foundation Grant 0936234, NASA Astrobiology Institute Grant NNA08CN84A, and an appointment from the NASA Postdoctoral Program to GPF at the Massachusetts Institute of Technology. We thank Mathieu Groussin and Bastien Boussau for helpful discussions and their assistance with implementing non-homogeneous ancestral reconstruction models.

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

239_2015_9672_MOESM1_ESM.xlsx (10.4 mb)
Homogeneous ancestral reconstruction of TyrRS/TrpRS paralog ancestor, per-site amino acid probabilities. Sites within majority topology regions are labeled V(vertical), sites within proposed partial HGT regions are labeled R1-R3(recombined). Combined alignment sites refer to the native sequence alignment, and match the numbering used throughout the manuscript. Topology-specific alignment sites refer to the provided FASTA format sequence alignments for each topology region (V, R1, R2, R3). As R regions were removed from the V alignment, these numberings differ. Numbering in the “prob” column headings refers to each internal node reconstruction. The mapping of these nodes to the phylogeny is provided in Online Resource 11. For each node, “max” refers to the maximum-likelihood AA for each site. Supplementary material 1 (XLSX 10629 kb)
239_2015_9672_MOESM2_ESM.xlsx (10.4 mb)
Non-homogeneous ancestral reconstruction of TyrRS/TrpRS paralog ancestor, per-site amino acid probabilities. Sites within majority topology regions are labeled V(vertical), sites within proposed partial HGT regions are labeled R1-R3(recombined). Combined alignment sites refer to the native sequence alignment, and match the numbering used throughout the manuscript. Topology-specific alignment sites refer to the provided FASTA format sequence alignments for each topology region (V, R1, R2, R3). As R regions were removed from the V alignment, these numberings differ. Numbering in the “prob” column headings refers to each internal node reconstruction. The mapping of these nodes to the phylogeny is provided in Online Resource X. For each node, “max” refers to the maximum-likelihood AA for each site. Supplementary material 2 (XLSX 10649 kb)
239_2015_9672_MOESM3_ESM.xlsx (53 kb)
Table of species names and abbreviations used in online trees and alignments. Supplementary material 3 (XLSX 52 kb)
239_2015_9672_MOESM4_ESM.fasta (182 kb)
FASTA format alignment of TyrRS/TrpRS protein sequences, with partial HGT regions removed. Supplementary material 4 (FASTA 183 kb)
239_2015_9672_MOESM5_ESM.fasta (7 kb)
FASTA format alignment of TyrRS/TrpRS protein sequences, proposed partial HGT region R1. Supplementary material 5 (FASTA 7 kb)
239_2015_9672_MOESM6_ESM.fasta (13 kb)
FASTA format alignment of TyrRS/TrpRS protein sequences, proposed partial HGT region R2. Supplementary material 6 (FASTA 13 kb)
239_2015_9672_MOESM7_ESM.fasta (4 kb)
FASTA format alignment of TyrRS/TrpRS protein sequences, proposed partial HGT region R3. Supplementary material 7 (FASTA 5 kb)
239_2015_9672_MOESM8_ESM.pdf (10 kb)
Phylogeny for proposed partial HGT region R1. Supplementary material 8 (PDF 10 kb)
239_2015_9672_MOESM9_ESM.pdf (10 kb)
Phylogeny for proposed partial HGT region R2. Supplementary material 9 (PDF 10 kb)
239_2015_9672_MOESM10_ESM.pdf (10 kb)
Phylogeny for proposed partial HGT region R3. Supplementary material 10 (PDF 10 kb)
239_2015_9672_MOESM11_ESM.pdf (13 kb)
Phylogeny with mapping for ancestral node reconstruction numberings. Supplementary material 11 (PDF 12 kb)

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.Department of Earth, Atmospheric, and Planetary SciencesMassachusetts Institute of TechnologyCambridgeUSA
  2. 2.Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeUSA

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