Abstract
Plastids and mitochondria derive from prokaryotic symbionts that lost most of their genes after the establishment of endosymbiosis. In consequence, relatively few of the thousands of different proteins in these organelles are actually encoded there. Most are now specified by nuclear genes. The most direct way to reconstruct the evolutionary history of plastids and mitochondria is to sequence and analyze their relatively small genomes. However, understanding the functional diversification of these organelles requires the identification of their complete protein repertoires – which is the ultimate goal of organellar proteomics. In the meantime, judicious combination of proteomics-based data with analyses of nuclear genes that include interspecies comparisons and/or predictions of subcellular location is the method of choice. Such genome-wide approaches can now make use of the entire sequences of plant nuclear genomes that have emerged since 2000. Here I review the results of these attempts to reconstruct the evolution and functions of plant DNA-containing organelles, focusing in particular on data from nuclear genomes. In addition, I discuss proteomic approaches to the direct identification of organellar proteins and briefly refer to ongoing research on non-coding nuclear DNAs of organellar origin (specifically, nuclear mitochondrial DNA and nuclear plastid DNA).
Highlights
The progenitors of the non-nuclear DNA-containing organelles of plants – plastids and mitochondria – were originally acquired as cyanobacterial and proteobacterial endosymbionts, respectively
As yet, no single prediction program and no single proteomics experiment can accurately identify the full complement of proteins located in plastids or mitochondria
At least for model plants like C. reinhardtii and A. thaliana, a combination of predictions, largescale fluorescence tagging, epitope tagging, proteomics of multiple subfractions of organelles, and studies of individual genes/proteins will remain the method of choice for identifying entire organelle proteomes
Summary
The progenitors of the non-nuclear DNA-containing organelles of plants – plastids and mitochondria – were originally acquired as cyanobacterial and proteobacterial endosymbionts, respectively (reviewed in 1–4). An early phylogenomic study compared all protein-coding genes from only one plant species (A. thaliana) with the genes from several animals, yeasts, and combined sets of bacteria and Archaea[33] and identified 3848 plantspecific proteins, of which about 27% were predicted to localize to chloroplasts or mitochondria. Mitochondria The first phylogenomic approach that indirectly addressed the evolution of nuclear genes for mitochondrial proteins compared the nuclear protein-coding genes from Saccharomyces cerevisiae to the ones encoded by Bacteria and Archaea and found that about 75% of all yeast nuclear genes of tentatively prokaryotic origin are more similar to eubacterial than to archaebacterial homologs[41] This suggested that the common ancestor of eukaryotes may have possessed a majority of eubacterial genes, though it is still unclear how many of these come from the ancestral mitochondrial genome. NUPTs and NUMTs can account for several hundred kbps of nuclear genomes, ranging from very small insertions to larger segments of mtDNA and/or ptDNA >100 kbps in length[63], which further facilitates study of the fate of alien DNA in the nuclear genome
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