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Assessing functional divergence in EF-1alpha and its paralogs in eukaryotes and archaebacteria
Yuji Inagaki1, Christian Blouin, Edward Susko
1Program in Evolutionary Biology, Canadian Institute for Advanced Research and Genome Atlantic, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 1X5, Canada. yinagai@dal.ca
Nucleic Acids Research
|July 11, 2003
Summary
Functional divergence analysis reveals distinct evolutionary paths for eukaryotic EF-1alpha and its paralogs. Sites involved in binding eEF-1beta or aminoacyl-tRNA differ between orthologs and paralogs, suggesting new functions for HBS1.
Area of Science:
- Evolutionary biology
- Molecular biology
- Biochemistry
Background:
- Phylogenetic methods analyze protein family evolution.
- Eukaryotic EF-1alpha (eEF-1alpha) has orthologs and paralogs with potentially divergent functions.
Purpose of the Study:
- Assess functional divergence between eEF-1alpha, archaebacterial EF-1alpha (aEF-1alpha), and paralogs eRF3 and HBS1.
- Identify functionally divergent (FD) sites and their relation to known binding sites.
Main Methods:
- Phylogenetic analysis of multiple sequence alignments.
- Detection of functionally divergent sites.
- Comparison of FD sites with putative EF-1beta and aminoacyl-tRNA (aa-tRNA) binding sites.
Main Results:
- Evolutionary modes of aEF-1alpha, HBS1, and eRF3 differ significantly from eEF-1alpha.
- FD sites between eEF-1alpha and paralogs overlap with EF-1beta/aa-tRNA binding sites.
- These sites in eRF3 and HBS1 are released from functional constraints, indicating no binding.
Conclusions:
- eRF3 does not bind aa-tRNA, consistent with experimental data.
- HBS1's function may not be 'EF-1alpha-like'.
- HBS1 might function in stop codon-independent peptide release.