Evidence that an amoeba acquired a chloroplast by retaining part of an engulfed eukaryotic alga.

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Abstract
Chlorarachniophytes are amoeboid algae with unusual chloroplasts. Instead of the usual two membranes that surround the chloroplasts of plants, green algae, and red algae, the chloroplasts of chlorarachniophytes have four bounding membranes. The extra membranes may reflect an unusual origin of chlorarachniophyte chloroplasts. Rather than inheriting the organelle directly from their ancestors, chlorarachniophytes may have adopted the chloroplast of an algal cell ingested as prey. Parts of the algal cell are postulated to remain within the amoeba as a reduced eukaryotic endosymbiont [Hibberd, D. J. & Norris, R. E. (1984) J. Phycol. 20, 310-330]. A small nucleus-like structure, proposed to be a vestige of the endosymbiont's nucleus, is located in a space between the second and third chloroplast membranes. We cloned and sequenced nuclear-type rRNA genes from chlorarachniophytes and found two highly divergent genes. In situ hybridization shows that one gene is expressed by the amoebal (host) nucleus and the other is expressed by the putative endosymbiont nucleus, suggesting that the latter is indeed a foreign genome. Transcripts from the endosymbiont gene accumulate in the small cytoplasmic compartment between the second and third chloroplast membranes, which we believe to be the remnant cytoplasm of the endosymbiont. Using the endosymbiont gene as a probe, we identified three small chromosomes belonging to the endosymbiont nucleus. This knowledge should allow a detailed molecular analysis of the role of the endosymbiont's genome and cytoplasm in the partnership.