Biogenesis of photosynthetic membranes depends on galactolipid synthesis, which relies on several cell compartments, notably the ER (endoplasmic reticulum) and the chloroplast envelope. Galactolipid synthesis involves lipid trafficking between both membrane compartments. In Arabidopsis, ALA10, a phospholipid flippase of the P4 type-ATPase family, has a positive effect on leaf development, interestingly counteracting the limitation of monogalactosyldiacylglycerol (MGDG) production. ALA10 locates in distinct domains of the ER depending on the ALIS (ALA interacting subunit) subunit it interacts with: close to the plasma membrane with ALIS1, or next to chloroplasts with ALIS5. It interacts with FAD2 (Fatty acid desaturase 2) and prevents accumulation of linolenic (18:3) containing phosphatidylcholine (PC) stimulating an increase of MGDG synthesis. Here we report that ALA10 interacts with PUB11 (plant U-box type 11), an E3 protein ubiquitin ligase, is ubiquitinated and degraded by the 26S proteasome in a PUB11 independent process.