Preparations of intact trehalose synthase contain three polypeptides with molecular masses of 56, 102 and 123 kDa. We have cloned the genes TSSl and TSLl coding for the 56-and 123-kDa subunits, respectively. These genes are located on chromosomes I1 (TSSI) and XI11 (TSLI). The TSSl gene was found to be identical with ClFl, a gene required for normal growth on glucose. The product of the entire TSSl gene exibits 37% identity with a 502-amino-acid stretch from the middle of the TSLl product. Disruption of the TSSl gene in yeast eliminates both trehalose 6-phosphate synthase (Tre6P synthase) and trehalose 6-phosphate phosphatase (Tre6Pase) activities, and reintroduction of this gene restores these activities. Transformation of Escherichia coli with TSSl increases its Tre6P synthase activity. Specific proteolytic degradation of the 123-kDa polypeptide from the N-terminus greatly influences the Tre6P synthase activity, decreasing its inhibition by phosphate and activatability by fructose 6-phosphate but has little effect on the Tre6Pase activity. These results suggest that this N-terminal part confers regulatory properties upon the Tre6P synthase activity.Trehalose, a non-reducing disaccharide of glucose, occurs in Saccharomyces cerevisiae during periods of reduced growth, such as during starvation of cells for nitrogen, phosphate or sulfur, as well as during the stationary phase after growth on glucose (Lillie and Pringle, 1980). It is also accumulated in cells exposed to extremes of temperature, dehydration or hazardous chemicals (Attfield, 1987 ;Hottiger et al., 1987;Hino et al., 1990). Experiments using mutants producing varying amounts of trehalose and the increases in intracellular trehalose concentration caused by heat-shock treatment, have shown that heat tolerance, as well as desiccation tolerance, are closely related to the trehalose content of the yeast cell (Hottiger et al., 1987).The formation of trehalose is catalysed by the sequential action of trehalose-6-phosphate synthase (Tre6P synthase) and trehalose-6-phosphate phosphatase (Tre6Pase) activities. These activities co-elute through several chromatographic procedures, suggesting that they are part of a single bifunctional protein (Vandercammen et al., 1989 ;Londesborough and Vuorio, 1991). A protein complex, called trehalose synthase, has been purified in a specifically proteolysed form (Londesborough and Vuorio, 1991) and an apparently intact form (Vuorio et al