Phosphoinositide (PI) 3-kinases, which phosphorylate the D-3 position of the inositol ring, function in several different signalling pathways. The phosphatidylinositol (PtdIns)-specific PI 3-kinase of yeast (Vps34p) is part of a receptor signalling protein complex associated with the trans-Golgi membranes, whereas PI 3-kinases that phosphorylate polyphosphoinositides in animal cells form a major receptor-controlled signalling pathway in the plasma membrane. Recent studies have indicated the presence of active PLC, PLD, and PI 3-kinase-dependent signalling systems in the unicellular green alga Chlamydomonas, and PtdIns-3P in Chlamydomonas shows a particularly high rate of turnover. Here we report the cloning of the Chlamydomonas Vps34p, and some characterisation of its properties, regulation and localisation. A single-copy 12 kb gene was present. The corresponding protein of 122 kDa had full-length homology with Vps34ps from other species, but it contained a novel spacer-like insert region of 148 amino acid residues between homology region 2 (HR2) and the C-terminal catalytic core domain, and three other shorter putative inserts. Available cDNAs were used to assemble a pBluescript clone expressing a recombinant protein which had PtdIns-specific 3-kinase activity. However, an unexpected observation was that recombinant proteins containing the complete catalytic core, but lacking HR2, had no lipid kinase activity, pointing to a previously unsuspected role for this domain, possibly in substrate binding. VPS34 mRNA and protein levels, as determined by RNAse protection assays and by immunological methods respectively, were low in all cell stages that were examined. Western blotting of subcellular fractions revealed that most of Vps34p in cell lysates of cw-15 (a cell wall-deficient mutant) could be recovered in a NP-40-resistant 100000 x g pellet, suggesting that the enzyme may have a location different from that found in higher plants.