Nucleic Acids Research, 2003, Vol. 31, No. 14 4227-4237
© 2003 Oxford University Press
Assessing functional divergence in EF-1
and its paralogs in eukaryotes and archaebacteria
Program 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 and 1 Department of Mathematics and Statistics and Genome Atlantic, Dalhousie University, Halifax, Nova Scotia B3H 3J5, Canada
*To whom correspondence should be addressed. Tel: +1 902 494 2881; Fax: +1 902 494 1355; Email: yinagai{at}dal.ca
+AY185331–AY185338
A number of methods have recently been published that use phylogenetic information extracted from large multiple sequence alignments to detect sites that have changed properties in related protein families. In this study we use such methods to assess functional divergence between eukaryotic EF-1
(eEF-1), archaebacterial EF-1 (aEF-1) and two eukaryote-specific EF-1 paralogs—eukaryotic release factor 3 (eRF3) and Hsp70 subfamily B suppressor 1 (HBS1). Overall, the evolutionary modes of aEF-1, HBS1 and eRF3 appear to significantly differ from that of eEF-1. However, functionally divergent (FD) sites detected between aEF-1 and eEF-1 only weakly overlap with sites implicated as putative EF-1ß or aminoacyl-tRNA (aa-tRNA) binding residues in EF-1, as expected based on the shared ancestral primary translational functions of these two orthologs. In contrast, FD sites detected between eEF-1 and its paralogs significantly overlap with the putative EF-1ß and/or aa-tRNA binding sites in EF-1. In eRF3 and HBS1, these sites appear to be released from functional constraints, indicating that they bind neither eEF-1ß nor aa-tRNA. These results are consistent with experimental observations that eRF3 does not bind to aa-tRNA, but do not support the ‘EF-1-like’ function recently proposed for HBS1. We re-assess the available genetic data for HBS1 in light of our analyses, and propose that this protein may function in stop codon-independent peptide release.
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