The genes encoding gluconeogenic enzymes in the nonconventional yeast Yarrowia lipolytica were found to be differentially regulated. The expression of Y. lipolytica FBP1 (YlFBP1) encoding the key enzyme fructose-1,6-bisphosphatase was not repressed by glucose in contrast with the situation in other yeasts; however, this sugar markedly repressed the expression of YlPCK1, encoding phosphoenolpyruvate carboxykinase, and YlICL1, encoding isocitrate lyase. We constructed Y. lipolytica strains with two different disrupted versions of YlFBP1 and found that they grew much slower than the wild type in gluconeogenic carbon sources but that growth was not abolished as happens in most microorganisms. We attribute this growth to the existence of an alternative phosphatase with a high K m (2.3 mM) for fructose-1,6-bisphosphate. The gene YlFBP1 restored fructose-1,6-bisphosphatase activity and growth in gluconeogenic carbon sources to a Saccharomyces cerevisiae fbp1 mutant, but the introduction of the FBP1 gene from S. cerevisiae in the Ylfbp1 mutant did not produce fructose-1,6-bisphosphatase activity or growth complementation. Subcellular fractionation revealed the presence of fructose-1,6-bisphosphatase both in the cytoplasm and in the nucleus.The growth of yeasts and other microorganisms in nonsugar carbon sources is dependent on gluconeogenesis. This pathway implicates specific gluconeogenic enzymes, such as fructose-1,6-bisphosphatase (Fbp) and phosphoenolpyruvate carboxykinase (Pck), that bypass the two physiologically irreversible steps in the glycolytic pathway, namely, phosphofructokinase and pyruvate kinase. In addition, under certain growth conditions, the enzymes from the glyoxylate cycle, isocitrate lyase (Icl) and malate synthase, are also required for the function of gluconeogenesis (Fig. 1). Growth in any nonsugar carbon source requires Fbp, which catalyzes the hydrolysis of fructose-1,6-P 2 to fructose-6-phosphate, and therefore, Fbp is a key enzyme in gluconeogenesis. The simultaneous function of specific gluconeogenic enzymes and their glycolytic counterparts would lead to futile cycles, i.e., reactions that waste ATP without yielding a net product (42). Presumably due to evolutionary pressure, a series of control mechanisms have been selected to minimize the functioning of those cycles. In the yeast Saccharomyces cerevisiae, the activities of phosphofructokinase and pyruvate kinase are controlled by a series of activators and inhibitors whose concentrations vary upon growth on sugars or nonsugar carbon sources (12,61,65). The activity of gluconeogenic enzymes is determined by the interplay of a variety of mechanisms. The transcription of the genes encoding them is subjected to catabolite repression, a complex regulatory phenomenon that involves many proteins (13,32,41). In addition, in S. cerevisiae, most of the gluconeogenic enzymes undergo catabolite inactivation (27, 48, 50), a proteolytic degradation that destroys them after glucose addition. Control by metabolites appears to be restricted to Fbp that ...