This invention relates to isolated nucleic acid fragments encoding trehalose metabolism enzymes, more specifically, alpha, alpha-trehalase, alpha, alpha-trehalose-phosphate synthase or trehalose-6-phosphate phosphatase. The invention also relates to the construction of a recombinant DNA construct encoding all or a portion of the alpha, alpha-trehalase, alpha, alpha-trehalose-phosphate synthase or trehalose-6-phosphate phosphatase, in sense or antisense orientation, wherein expression of the recombinant DNA construct results in production of altered levels of the alpha, alpha-trehalase, alpha, alpha-trehalose-phosphate synthase or trehalose-6-phosphate phosphatase in a transformed host cell.