The Root of the Universal Tree of Life Inferred from Anciently Duplicated Genes Encoding Components of the Protein-Targeting Machinery

@article{Gribaldo1998TheRO,
  title={The Root of the Universal Tree of Life Inferred from Anciently Duplicated Genes Encoding Components of the Protein-Targeting Machinery},
  author={Simonetta Gribaldo and Piero Cammarano},
  journal={Journal of Molecular Evolution},
  year={1998},
  volume={47},
  pages={508-516}
}
Abstract. The key protein of the signal recognition particle (termed SRP54 for Eucarya and Ffh for Bacteria) and the protein (termed SRα for Eucarya and Ftsy for bacteria) involved in the recognition and binding of the ribosome SRP nascent polypeptide complex are the products of an ancient gene duplication that appears to predate the divergence of all extant taxa. The paralogy of the genes encoding the two proteins (both of which are GTP triphosphatases) is argued by obvious sequence… 

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References

SHOWING 1-10 OF 27 REFERENCES

The root of the universal tree and the origin of eukaryotes based on elongation factor phylogeny.

It is found that a combined data set of EF-Tu and EF-G sequences favors placement of the eukaryotes within the Archaea, as the sister group to the Crenarchaeota.

Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplications.

  • J. R. BrownW. Doolittle
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 1995
This study derives a rooting for the universal tree using aminoacyl-tRNA synthetase genes, an extensive multigene family whose divergence likely preceded that of prokaryotes and eukaryotes.

Molecular evolution of SRP cycle components: functional implications.

This analysis provides insight into the significance of structural variation in SRP RNA and identifies novel conserved motifs in protein components of this pathway, and hypothesizes that a component of the Srp68/72p heterodimer serves as the GDS for both Srp54p and SR alpha.

Horizontal transfer of ATPase genes--the tree of life becomes a net of life.

Archaea and the prokaryote-to-eukaryote transition.

This review considers the cumulative knowledge about the Archaea in relationship to the Bacteria and Eucarya and the recent use of molecular phylogenetic approaches to reconstructing the tree of life.

Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes.

A composite phylogenetic tree with two clusters corresponding to different proteins, from which the evolutionary relationship of the primary kingdoms is determined uniquely is proposed, revealing that archaebacteria are more closely related to eukaryotes than to eubacteria for all the cases.

Model for signal sequence recognition from amino-acid sequence of 54K subunit of signal recognition particle

The sequence of a complementary DNA clone of SRP54 is presented which predicts a protein that contains a putative GTP-binding domain and an unusually methionine-rich domain and the properties of this latter domain suggest that it contains the signal sequence binding site.

Homology of 54K protein of signal-recognition particle, docking protein and two E. coli proteins with putative GTP–binding domains

To understand the molecular nature of the interaction between the signal sequence and its receptor(s) the authors have characterized a complementary DNA coding for the 54K protein of SRP.

Evolution of the vacuolar H+-ATPase: implications for the origin of eukaryotes.

It is reported that the same vacuolar H-ATPase subunits are approximately equal to 50% identical to the alpha and beta subunits, respectively, of the sulfur-metabolizing Sulfolobus acidocaldarius, an archaebacterium (Archaeobacterium).