Function of MGDα, MGDβ, and MGDγ in P. tricornutum cell. The model summarizes all compartmentalization, structural and functional data obtained in this study. FAs are synthesized in the stroma as 16:0-ACP and 16:1-ACP (1), where they can be used for the synthesis of DAG (2a). Alternatively, FAs are exported to extraplastidial membranes where they can serve for the synthesis of DAG (2b) and phospholipids such as PC and PE, or the betaine lipid DGTA (2c). PC and DGTA serve as platforms to produce 20:5 (2c), used inside the plastid (at an unknown membrane site) for the production of 20:5-containing DAG (2d). MGDα is localized at the level of thylakoids, and functional studies reported here are consistent with a utilization of DAG available inside the plastid (3α), to form MGDG species rapidly desaturated (16:1 → 16:4) by plastid desaturases (4α). Based on obtained phenotype of KO and overexpressing lines, MGDG produced by MGDα is likely used by a specific DGD enzyme (5α) to form DGDG. MGDβ is localized at the level of the blob-like structure at the PPM, and functional studies reported here are consistent with a utilization of DAG either produced inside the plastid or with 20:5 acyls imported from the ER by a still uncharacterized Ω-pathway (3β). MGDG produced can be desaturated (16:1 → 16:4) by plastid desaturases (4β). Based on obtained phenotype of KO and overexpressing lines, MGDG produced by MGDβ is likely used by a specific DGD enzyme (5β) to form DGDG. MGDγ is localized at the periphery of the plastid, possibly partitioned between the ER and the EpM. Functional studies are consistent with a utilization of DAG containing FA freshly exported from the plastid (3γ), producing MGDG at a location far from plastid desaturases. Based on obtained phenotype of KO and overexpressing lines, MGDG produced by MGDγ is also likely associated to a specific DGD enzyme (5γ). In nitrogen shortage, MGDα protein level decreases drastically, and MGDG production relies on MGDβ and MGDγ. When 1 MGD is knocked out, compensation mechanisms rely on intact isoforms located in distinct membrane systems, requiring rapid inward and outward trafficking of glycerolipids including MGDG, through the 4 membranes limiting the plastid. KO, knockout; DAG, diacylglycerol; DGTA, diacylglyceryl hydroxymethyltrimethyl-β-alanine; DGD, digalactosyldiacylglycerol synthase; DGDG, digalactosyldiacylglycerol; ER, endoplasmic reticulum; FA; fatty acid; MGD, monogalactosyldiacylglycerol synthase; MGDG, monogalactosyldiacylglycerol; PC, phosphatidylcholine.