The cyanobacterium Synechocystis PCC6803 was fed heptanoic acid to study the substrate specificities of desaturases and acyltransferases in lipid synthesis. This aliphatic acid was elongated to C15, C17, and C19 fatty acids, which were incorporated into polar glycerolipids and desaturated. The double bonds were located at the [delta]6, [delta]9, [delta]12, and [omega]3 positions of the fatty acids. This suggests that the [delta]9 desaturase counts the carbon number from the carboxy terminus, whereas the so-called [delta]15 desaturase counts from the methyl terminus. The counting mechanisms of the [delta]6 and [delta]12 desaturases are not fully understood. In the distribution of fatty acids at the sn positions of the glycerol moiety, the C17, C18, and C19 fatty acids were located at the sn-1 position, whereas the C15 and C16 fatty acids were located at the sn-2 position. This suggests that glycerol-3-phosphate acyltransferase specifically transfers heptadecanoic, octadecanoic, and nonadecanoic acids, whereas 1-acylglycerol-3-phosphate acyltransferase specifically transfers pentadecanoic and hexadecanoic acids.