Abstract. The major surface macromolecules of the protozoan parasite Leishmania major, gp63 (a metalloprotease), and lipophosphoglycan (a polysaccharide), are glycosylphosphatidylinositol (GPI) anchored. We expressed a cytoplasmic glycosylphosphatidylinositol phospholipase C (GPI-PLC) in L. major in order to examine the topography of the protein-GPI and polysaccharide-GPI pathways. In L. major cells expressing GPI-PLC, cell-associated gp63 could not be detected in immunoblots. Pulse-chase analysis revealed that gp63 was secreted into the culture medium with a half-time of 5.5 h. Secreted gp63 lacked anti-cross reacting determinant epitopes, and was not metabolically labeled with [3H]ethanolamine, indicating that it never received a GPI anchor. Further, the quantity of putative protein-GPI intermediates decreased ,,ol0-fold. In striking contrast, lipophosphoglycan levels were unaltered. However, GPI-PLC cleaved polysaccharide-GPI intermediates (glycoinositol phospholipids) in vitro. Thus, reactions specific to the polysaccharide-GPI pathway are comparianentalized in vivo within the endoplasmic reticulum, thereby sequestering polysaccharide-GPI intermediates from GPI-PLC cleavage. On the contrary, protein-GPI synthesis at least up to production of Man(lat)Man(lot4)GlcN-(lat)-myo-inositol-l-phospholipid is cytosolic. To our knowledge this represents the first use of a catabolic enzyme in vivo to elucidate the topography of biosynthetic pathways.GPI-PLC causes a protein-GPI-negative phenotype in L. major, even when genes for GPI biosynthesis are functional. This phenotype is remarkably similar to that of some GPI mutants of mammalian cells: implications for paroxysmal nocturnal hemoglobinuria and Thy-l-negative T-lymphoma are discussed. LYCOSYLPHOSPHATIDYLINOSITOL (GP1) t anchors attach a diverse group of macromolecules to membranes in eukaryotes (see 19, 22 for recent reviews). The plasma membrane of the protozoan parasite Trypmwsoma brucei is covered with about 107 molecules of the variant surface glycoprotein (VSG), a GPI-anchored molePlease address all correspondence to Dr. K. Mensa-Wilmot, Department of Zoology, University of Georgia, Athens, Georgia 30602.1. Abbreviations used in this paper: CRD, cross-reacting determinant; dol-P-Man, dolichol-phosphoryl-mannose; eGPI-PLC, recombinant glycosylphosphatidylinositol phospholipase C; EtN, ethanolamine; gp63, 63-kD GPI-anchored glycoprotein of Leishmania parasites; GIPL, glycoinositol phospholipid; GPI, glycosylphosphatidylinositol; GPI-PLC, glycosylphosphatidylinositol phospholipnse C; Gall, Galactofuranose; GleN, glucosamine; GIcNAC, N-acetyl glucosamine; LP-1, putative protein-GPI precursor (possibly EtN-phospho-ManrGlcN-PI); LP-2, putative protein-GPl precursor; LPG, lipophosphoglycan; Man, mannose; mfVSG, membraneform VSG; PI, phosphatidylinositol; PNH, paroxysmal nocturnal hemoglobinuria; UDP-GIcNAc, uridine 5'-diphospho N-acetylglucosamine; VSG, variant surface glycoprotein of Trypanosoma brucei.cule. The VSG GPI consists of dimyristoylphosphatidylinositol l...