Beside the nucleus, the plastid and mitochondria, cryptomonads possess a fourth DNA-containing semiautonomous organelle, the nucleomorph. This organell was shown to be the remnant of the nucleus of a former free-living rhodophytic alga, which was engulfed and reduced to a complex plastid by a heterotrophic host cell. By sequencing the three minute nucleomorph chromosomes of the cryptomonad Guillardia theta, we present evidence that the purpose of the nucleomorph is to perpetuate itself, the periplastid space it is embedded in and a eukaryotic expression machinery for the synthesis of 30 nucleomorph-encoded chloroplast proteins (Douglas et al. (2001), Nature 410, 1091-1096). Some of these chloroplast located proteins have homologous sequences in the cyanobacterium Synechocystis sp. PCC6803 but differ from those by an amino-terminal extension which functions as a transit peptide for the translocation to the plastid. Beside proteins of known function (FtsZ, Hlip, CbbX), we identified 11 gene products whose homologs in cyanobacteria do not have any known function. These are the genes of interest we have in part characterized. By knock-out experiments in cyanobacteria and physiological investigations we analyzed the functions of the nucleomorph-encoded proteins in respect to the photosynthesis machinery. Major results so far are the detection of components attached to photosystem II and the creation of mutants with a reduced phycocyanin content.
Chloroplasts contain proteins that are encoded by different genetic systems, the plastid genome and the nuclear chromosomes. By comparing the gene content of plastid genomes of different taxa, some predictions about nuclear-encoded genes for plastid proteins are possible. However, early in evolution, many genes were transferred from the plastid to the cell nucleus and are therefore missing from all known plastid genomes and escape such predictions. By sequencing the miniaturized chromosomes of the nucleomorph of the cryptophyte Guillardia theta, as well as the plastid genome, we uncovered two genes encoding CbbX which are predicted to be involved in plastid function. Our findings suggest that (1) red-type plastid rbcLS genes evolved together with cbbX, which is related to cbbX genes of purple bacteria; (2) early in rhodoplast evolution, the cbbX gene was duplicated and transferred into the nucleus; (3) the plastid-encoded LysR transcriptional activator gene, rbcR, is homologous to rbcR and cbbR transcriptional activator genes of purple bacteria and cyanobacteria; and (4) the ancestral plastid probably harbored both types of form I RuBisCo.
Chromist algae (stramenopiles, cryptophytes, and haptophytes) are major contributors to marine primary productivity. These eukaryotes acquired their plastid via secondary endosymbiosis, whereby an early-diverging red alga was engulfed by a protist and the plastid was retained and its associated nuclear-encoded genes were transferred to the host genome. Current data suggest, however, that chromists are paraphyletic; therefore, it remains unclear whether their plastids trace back to a single secondary endosymbiosis or, alternatively, this organelle has resulted from multiple independent events in the different chromist lineages. Both scenarios, however, predict that plastid-targeted, nucleus-encoded chromist proteins should be most closely related to their red algal homologs. Here we analyzed the biosynthetic pathway of carotenoids that are essential components of all photosynthetic eukaryotes and find a mosaic evolutionary origin of these enzymes in chromists. Surprisingly, about one-third (5/16) of the proteins are most closely related to green algal homologs with three branching within or sister to the early-diverging Prasinophyceae. This phylogenetic association is corroborated by shared diagnostic indels and the syntenic arrangement of a specific gene pair involved in the photoprotective xanthophyll cycle. The combined data suggest that the prasinophyte genes may have been acquired before the ancient split of stramenopiles, haptophytes, cryptophytes, and putatively also dinoflagellates. The latter point is supported by the observed monophyly of alveolates and stramenopiles in most molecular trees. One possible explanation for our results is that the green genes are remnants of a cryptic endosymbiosis that occurred early in chromalveolate evolution; that is, prior to the postulated split of stramenopiles, alveolates, haptophytes, and cryptophytes. The subsequent red algal capture would have led to the loss or replacement of most green genes via intracellular gene transfer from the new endosymbiont. We argue that the prasinophyte genes were retained because they enhance photosynthetic performance in chromalveolates, thus extending the niches available to these organisms. The alternate explanation of green gene origin via serial endosymbiotic or horizontal gene transfers is also plausible, but the latter would require the independent origins of the same five genes in some or all the different chromalveolate lineages.
