D-6-fatty acid desaturase (FADS2) is the key enzyme in the biosynthesis of polyunsaturated fatty acids (PUFAs), the essential structural determinants of mammalian membrane lipid-bilayers. We developed the auxotrophic fads2 À/À mouse mutant to assess the enigmatic role of x3-and x6-PUFAs in lipid homeostasis, membrane structure and function. Obesity resistance is another major phenotype of the fads2 À/À mutant, the molecular basis of which is unknown. Phospholipidomic profiling of membrane systems of fads2 À/À mice revealed diacylglycerol-structures, deprived of PUFAs but substituted with surrogate eicosa-5,11,14-trienoic acid. x6-Arachidonic (AA) and x3-docosahexaenoic acid (DHA) supplemented diets transformed fads2 À/À into AA-fads2 À/À and DHA-fads2 À/À mutants. Severely altered phospholipid-bilayer structures of subcellular membranes of fads2 À/À liver specifically interfered with maturation of transcription factor sterol-regulatory-element-binding protein, the key regulator of lipogenesis and lipid homeostasis. This study strengthens the concept that specific PUFA-substituted membrane phospholipid species are critical constituents of the structural platform operative in lipid homeostasis in normal and disease conditions.