The presence of plastids in diverse eukaryotic lineages that have lost the capacity for photosynthesis is well documented. The metabolic functions of such organelles, however, are poorly understood except in the case of the apicoplast in the Apicomplexa, a group of intracellular parasites including Plasmodium falciparum, and the plastid of the green alga Helicosporidium sp., a parasite for which the only host-free stage identified in nature so far is represented by cysts. As a first step in the reconstruction of plastid functions in a nonphotosynthetic, predominantly free-living organism, we searched for expressed sequence tags (ESTs) that correspond to nucleus-encoded plastid-targeted polypeptides in the green alga Prototheca wickerhamii. From 3,856 ESTs, we found that 71 unique sequences (235 ESTs) correspond to different nucleus-encoded putatively plastid-targeted polypeptides. The identified proteins predict that carbohydrate, amino acid, lipid, tetrapyrrole, and isoprenoid metabolism as well as de novo purine biosynthesis and oxidoreductive processes take place in the plastid of P. wickerhamii. Mg-protoporphyrin accumulation and, therefore, plastid-to-nucleus signaling might also occur in this nonphotosynthetic organism, as we identified a transcript which encodes subunit I of Mg-chelatase, the enzyme which catalyzes the first committed step in chlorophyll synthesis. Our data indicate a far more complex metabolism in P. wickerhamii's plastid compared with the metabolic pathways predicted to be located in the apicoplast of P. falciparum and the plastid of Helicosporidium sp.The presence of plastids in eukaryotic cells is generally associated with the ability to perform photosynthesis; these light-harvesting organelles are the product of primary endosymbiosis in the chlorophyte, streptophyte, rhodophyte, and glaucophyte lineages, while in other groups, such as the apicomplexan parasites, heterokonts, euglenoids, and chlorarachniophytes, the plastid was acquired through secondary endosymbiosis. However, colorless plastids with various degrees of functional and structural degeneration, relative to their photosynthetically competent homologues, have been identified in several of these evolutionarily diverse eukaryotic lineages (2, 45, 61). The loss of plastid-encoded photosynthesis-related genes has been documented in plastids from achlorophyllic lineages among green algae (29, 51), land plants (63, 64), dictyochophytes (45), and euglenoids (16), but the functional role of these plastids is largely unknown.The discovery of a relict plastid (the apicoplast) in several apicomplexan parasites, i.e., Plasmodium falciparum (62), Toxoplasma gondii (28, 32), and Eimeria tenella (7), whose impaired functioning leads to the delayed-death of the parasite (15), has greatly enhanced studies aimed to understand the roles of such plastids in cellular metabolism. In the malarial parasite P. falciparum, metabolic pathways such as fatty acid synthesis (59), non-mevalonate isopentenyl diphosphate synthesis (25), and tetrapyrrole ...