Abstract
BackgroundElongation factor G (EFG) is a core translational protein that catalyzes the elongation and recycling phases of translation. A more complex picture of EFG's evolution and function than previously accepted is emerging from analyzes of heterogeneous EFG family members. Whereas the gene duplication is postulated to be a prominent factor creating functional novelty, the striking divergence between EFG paralogs can be interpreted in terms of innovation in gene function.Methodology/Principal FindingsWe present a computational study of the EFG protein family to cover the role of gene duplication in the evolution of protein function. Using phylogenetic methods, genome context conservation and insertion/deletion (indel) analysis we demonstrate that the EFG gene copies form four subfamilies: EFG I, spdEFG1, spdEFG2, and EFG II. These ancient gene families differ by their indispensability, degree of divergence and number of indels. We show the distribution of EFG subfamilies and describe evidences for lateral gene transfer and recent duplications. Extended studies of the EFG II subfamily concern its diverged nature. Remarkably, EFG II appears to be a widely distributed and a much-diversified subfamily whose subdivisions correlate with phylum or class borders. The EFG II subfamily specific characteristics are low conservation of the GTPase domain, domains II and III; absence of the trGTPase specific G2 consensus motif “RGITI”; and twelve conserved positions common to the whole subfamily. The EFG II specific functional changes could be related to changes in the properties of nucleotide binding and hydrolysis and strengthened ionic interactions between EFG II and the ribosome, particularly between parts of the decoding site and loop I of domain IV.Conclusions/SignificanceOur work, for the first time, comprehensively identifies and describes EFG subfamilies and improves our understanding of the function and evolution of EFG duplicated genes.
Highlights
Gene duplication is postulated to have played an important role in prokaryotic evolution; the divergence accumulated in the sequences of new gene copies could be considered as a major contribution to the evolution of novel gene functions [1,2,3]
We focused on the determination of Elongation factor G (EFG) subfamilies
Data from genomes with a single EFG gene were excluded from this analysis, and the first set of sequences (214 EFG sequences) was limited to the 99 genomes that exhibited multiple EFGs
Summary
Gene duplication is postulated to have played an important role in prokaryotic evolution; the divergence accumulated in the sequences of new gene copies could be considered as a major contribution to the evolution of novel gene functions [1,2,3]. EFG together with ribosome recycling factor (RRF) participates in the disassembly of the post-termination ribosomal complex [11,12] These EFG functions, catalyzing translocation and ribosome recycling, are indispensable to cells. Data obtained from complete bacterial genomes have demonstrated that two highly expressed trGTPases genes, tuf (EF-Tu) and fus (EFG), are often represented by multiple copies [4,20]. A large fraction of EFG duplications that have not previously been described were investigated as a separate EFG subfamily (the EFG II subfamily) This group of EFG duplications was chosen owing to its wide distribution among all bacterial species and a high degree of divergence, which could be accompanied by functional novelty. The detailed analysis of the EFG II subfamily is essential for understanding how the duplication events contribute to evolutionary advantage
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