Abstract
BackgroundThe L-Ala-D/L-Glu epimerases (AEEs), a subgroup of the enolase superfamily, catalyze the epimerization of L-Ala-D/L-Glu and other dipeptides in bacteria and contribute to the metabolism of the murein peptide of peptidoglycan. Although lacking in peptidoglycan, land plants possess AEE genes that show high similarity to those in bacteria.ResultsSimilarity searches revealed that the AEE gene is ubiquitous in land plants, from bryophytas to angiosperms. However, other eukaryotes, including green and red algae, do not contain genes encoding proteins with an L-Ala-D/L-Glu_epimerase domain. Homologs of land plant AEE genes were found to only be present in prokaryotes, especially in bacteria. Phylogenetic analysis revealed that the land plant AEE genes formed a monophyletic group with some bacterial homologs. In addition, land plant AEE proteins showed the highest similarity with these bacterial homologs and shared motifs only conserved in land plant and these bacterial AEEs. Integrated information on the taxonomic distribution, phylogenetic relationships and sequence similarity of the AEE proteins revealed that the land plant AEE genes were acquired from bacteria through an ancient horizontal gene transfer (HGT) event. Further evidence revealed that land plant AEE genes had undergone positive selection and formed the main characteristics of exon/intron structures through gaining some introns during the initially evolutionary period in the ancestor of land plants.ConclusionsThe results of this study clearly demonstrated that the ancestor of land plants acquired an AEE gene from bacteria via an ancient HGT event. Other findings illustrated that adaptive evolution through positive selection has contributed to the functional adaptation and fixation of this gene in land plants.
Highlights
The L-Ala-D/L-Glu epimerases (AEEs), a subgroup of the enolase superfamily, catalyze the epimerization of L-Ala-D/L-Glu and other dipeptides in bacteria and contribute to the metabolism of the murein peptide of peptidoglycan
Intron gain/loss was found in some species, the structure of these AEE genes showed highly similarity (Figure 1), illustrating that the main characteristics of the gene structure of this family were formed in the common ancestor of land plants
The gene encoding L-Ala-D/L-Glu epimerase (AEE) was found to be present in all of the available sequenced genomes of land plants, whereas homologs of this gene were not found in any other eukaryotic genome, including those of green and red algae
Summary
The L-Ala-D/L-Glu epimerases (AEEs), a subgroup of the enolase superfamily, catalyze the epimerization of L-Ala-D/L-Glu and other dipeptides in bacteria and contribute to the metabolism of the murein peptide of peptidoglycan. Land plants possess AEE genes that show high similarity to those in bacteria. The frequency of HGT into eukaryotic genomes is possibly lower than in prokaryotes, but HGT has been an important force in the evolution of eukaryotes [5]. The classical example of plant HGT is that the ct-DNA sequences in some tobacco nuclear genomes were probably horizontally acquired from Agrobacterium rhizogenes during ancient infections [10]. Evidence has showed that land plants can recruit genes from species with distinct relationships, such as fungi, bacteria, and other plant species [11,12,13,14,15]. Land plant genes acquired through HGT are quite rare, they might play critical roles in adaptation to environments. Some anciently employed genes have been found to be involved in many plantspecific activities, including xylem formation, plant defense, nitrogen recycling and the biosynthesis of starch, polyamines, hormones and glutathione [14]
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