We demonstrate that naturally occurring C14 and C16-specific acylacyl carrier protein (ACP) desaturases from plants can complement the unsaturated fatty acid (UFA) auxotrophy of an Escherichia coli fabA͞fadR mutant. Under the same growth conditions, C 18-specific ⌬ 9 -stearoyl (18:0)-ACP desaturases are unable to complement the UFA auxotrophy. This difference most likely results from the presence of sufficient substrate pools of C 14 and C16 acyl-ACPs but a relative lack of C 18 acyl-ACP pools in E. coli to support the activities of the plant fatty acid desaturase. Based on this, a substrate-dependent selection system was devised with the use of the E. coli UFA auxotroph to isolate mutants of the castor ⌬ 9 -18:0-ACP desaturase that display enhanced specificity for C 14 and C16 acyl-ACPs. Using this selection system, a number of desaturase variants with altered substrate specificities were isolated from pools of randomized mutants. These included several G188L mutant isolates, which displayed a 15-fold increase in specific activity with 16:0-ACP relative to the wild-type castor ⌬ 9 -18:0-ACP desaturase. Expression of this mutant in Arabidopsis thaliana resulted in the accumulation of unusual monounsaturated fatty acids to amounts of >25% of the seed oil. The bacterial selection system described here thus provides a rapid means of isolating variant fatty acid desaturase activities for modification of seed oil composition.A cyl-acyl carrier protein (ACP)-desaturases (DES) are a family of soluble enzymes that are associated with the synthesis of monounsaturated fatty acids in plants (1). These enzymes catalyze the insertion of a double bond into saturated fatty acids bound to ACP in the plastids of plant cells, and thus serve as one of the primary determinants of the unsaturated fatty acid content of plant membranes and seed storage oils. The most widely occurring member of this family is the ⌬ 9 -stearoyl (18:0 ‡ )-ACP DES, which introduces the double bond of oleic acid (1). In addition, a number of other acyl-ACP DES have been identified that are associated with the synthesis of unusual monounsaturated fatty acids and have altered substrate and regio-specifities relative to the ⌬ 9 -18:0-ACP DES. Variant acyl-ACP DES identified to date include the ⌬ 4 -palmitoyl (16:0)-ACP DES from Umbelliferae seed (2, 3), the ⌬ 6 -16:0-ACP DES from black-eyed Susan vine (Thunbergia alata) seed (4), the ⌬ 9 -myristoyl (14:0)-ACP DES from geranium (Pelargonium xhortorum) trichomes (5), and ⌬ 9 -16:0-ACP DES from cat's claw (Doxantha unguis-cati) (6) and milkweed (Asclepias syriaca) (7) seeds. These enzymes share Ն60% amino acid sequence identity with the ⌬ 9 -18:0-ACP DES.This collection of structurally related, but functionally diverged, enzymes provides a tool for understanding how acyl-ACP DES recognize the chain length of substrates and position the placement of double bonds. Characterization of these properties also has been greatly aided by information from the crystal structure of the castor ⌬ 9 -18:0-ACP DES (8). From the...