The single, ancient origin of chromist plastids

Abstract

A plastid is the site where the energy of photons is captured and used to power the synthesis of sugars. Many photosynthetic proteins, and the rRNAs and tRNAs are encoded on the circular plastid genome, whereas many genes have been transferred to the nucleus (1–3). All plastids are believed to trace their origins to a primary endosymbiotic event in which a previously nonphotosynthetic single-celled protist engulfed a cyanobacterium that eventually became a photosynthetic organelle (4–6). The primordial alga resulting from this primary endosymbiosis then putatively gave rise through vertical evolution to the Chlorophyta, Rhodophyta, and the Glaucophyta (6).

A large body of molecular, phylogenetic, and ultrastructural data suggests that members of the Chlorophyta and Rhodophyta then gave rise to most other algal plastids through secondary endosymbiosis (7, 8). In secondary endosymbiosis, a previously nonphotosynthetic single-celled protist engulfs an existing alga that is then reduced to a secondary plastid (7–9). The red algae are particularly noteworthy in this respect because they are believed to have contributed plastids to at least five evolutionarily distantly related lineages [cryptophytes, haptophytes, stramenopiles (6, 10, 11), apicomplexa (12, 13), and dinoflagellates (14)]. Our laboratory has recently confirmed the red algal origin of the ancestral dinoflagellate plastid by using phylogenetic analyses, but surprisingly, it was found to have arisen through a tertiary endosymbiosis (uptake of a plastid of secondary endosymbiotic origin) of a haptophyte alga (15). In this case, the haptophyte plastid replaced the original dinoflagellate plastid, both of which trace their roots to the red algae. These data underline the importance of plastid endosymbiosis in the evolutionary history of eukaryotes and lead to the present study in which we address a long-standing issue in algal biology, the Chromista hypothesis (10).

Cavalier-Smith (10) proposed that the cryptophytes, haptophytes, and stramenopiles share a common ancestor and together form the kingdom Chromista. These taxa were united primarily on the basis of plastid characters, most importantly the presence of chlorophyll c₂ in a four-membrane bound plastid that was located in the lumen of the endoplasmic reticulum. The cryptophytes were posited as the early divergence in this group with the retention of the remnant endosymbiont nucleus (the nucleomorph) being an ancestral character (10). However, there is presently no convincing phylogenetic evidence in support of the monophyly of the Chromista “host” cells to the exclusion of other eukaryotes (e.g., ref. 6). Therefore, it is not known whether all of the chromist plastids have arisen from multiple, independent endosymbioses (e.g., refs. 3 and 6), or whether some of them (and the host cells that contain them) trace their origins to a single endosymbiotic event followed by separation of the nuclear lineages over evolutionary time (e.g., ref. 13). Assessing chromist monophyly is important not only for algal taxonomy but more generally for understanding the frequency of secondary plastid establishment in protists. Each secondary endosymbiosis entails the stable inheritance of a foreign cell, the large-scale movement of genes from the endosymbiont to the host nucleus, and the reimport of the gene products required for photosynthesis into the organelle to facilitate plastid function (1, 12, 13). Previous phylogenetic analyses of single plastid genes, although clearly supportive of a red algal origin of the secondary plastids of the Chromista, are ambiguous about the number of events that gave rise to them (e.g., refs. 16 and 17). A more recent analysis of 41 proteins from 15 complete plastid genomes, however, with limited taxon sampling of chromists and red algae has suggested that the plastid in cryptophytes and stramenopiles has independent origins (3). And finally, the organization of the plastid genomes in each of these algae is sufficiently different to preclude a clear understanding of their interrelationships (18, 19).

A direct approach to resolving this central problem in organelle evolution is to sample a broad range of plastid genes from red algae and Chromista members to test the hypothesis of independent secondary plastid origins in cryptophytes, haptophytes, and stramenopiles. Such analyses could have three possible outcomes. (i) Demonstration of a well-supported sister-group relationship of individual Chromista plastids with different red algae in plastid gene trees, which would suggest that chromist secondary endosymbioses are independent events. (ii) Alternatively, if the chromist plastid sequences form a strongly supported monophyletic group after extensive taxon sampling, then we would accept the hypothesis that a single secondary endosymbiosis likely explains plastid origin in these algae. Another less parsimonious interpretation of this result is that the same or closely related bangiophytes gave rise independently to the plastids. (iii) A third possibility is that two of the chromist lineages may share a single secondary endosymbiosis and the third gained its plastid although an independent event. To test the Chromista hypothesis, we sequenced 13 small subunit (SSU) rRNA, 29 tufA (plastid elongation factor Tu), and 1 rbcL (ribulose-1,5-bisphosphate carboxylase/oxygenase) plastid-encoded coding region from various red and chromist algae. These sequences were added to a published data set of 36 taxa for which we also had the sequences of psaA (photosystem I P700 chlorophyll a apoprotein A1), psbA (photosystem II reaction center protein D1), and “Form I” rbcL (15), and used to infer a DNA-based phylogeny of red and chromist plastids in a context of broad taxon sampling.

Acknowledgments

Abbreviations

Notes

This paper was submitted directly (Track II) to the PNAS office.

Data deposition: The sequences reported in this paper have been deposited in the GenBank database (accession nos. AF545587–AF545628 and AF546185).