Evolutionary transfer of the chloroplasttufA gene to the nucleus.

Abstract

The endosymbiotic theory proposes the origin of the eukaryotic organelles from once-free-living eubacteria, the nuclear genes encoding organelle proteins having arisen by direct transfer of organelle genes to the nucleus. Most gene transfer appears to have occurred early in evolution, although indirect evidence suggests the possibility of more recent transfers. However, replacement of an organelle gene with a nuclear homolog of clearly organellar ancestry has not yet been demonstrated. Evidence is presented here for the evolutionary transfer of the chloroplast tufA gene to the nucleus, within the green algal lineage giving rise to land plants. The tufA gene, encoding chloroplast protein synthesis elongation factor Tu (EF-Tu), is shown to be chloroplast-encoded in the green alga Chlamydomonas reinhardtii but nuclear-encoded in the flowering plant Arabidopsis thaliana. Complete gene sequences for both the Chlamydomonas and the Arabidopsis tufAs are presented, and the Arabidopsis tufa is shown to be expressed and its RNA polyadenylated. Phylogenetic analysis of EF-Tu sequences supports the origin of the nuclear-encoded TufA gene from a green algal chloroplast-encoded ancestor. This is the first direct evidence of the modern evolutionary transfer of an organelle gene to the nucleus. Chloroplast DNA from green algae was further analyzed and results suggest the universal presence of tufA in chloroplast DNA of all major classes of green algae except the Charophyceae. This is consistent with the proposed origin of land plants from charophycean green algae. Within the Charophyceae results suggest that transfer of the gene to the nucleus occurred early in the evolution of this lineage. An unusual chloroplast tufA from the Coleochaetales, the proposed sister group to land plants, is described, and it is suggested that this gene no longer encodes a fully-functional EF-Tu. It is proposed that an intermediate state existed, during transfer of the tufA gene, in which copies of the gene existed in both chloroplast and nucleus, with this state persisting through separation of the various charophycean orders. Evolution of a new or altered function by one copy of a duplicated gene is proposed to explain the unusual chloroplast tufA of Coleochaete.