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The plasma membrane has a complex organization that includes the polarized distribution of membrane proteins as well as lipids. Glycosylphosphatidylinositol-anchored proteins (GPI-AP) are ubiquitously expressed in eukaryotes and represent a functionally diverse group of proteins some of which are critical for the organization and function of the plasma membrane. Here we investigated how the plasma membrane of yeast cells responded to the accumulation of GPI-APs in which phosphoethanolamine (EtNP) had not been removed from mannose 2 (Man2) of the GPI moiety. The persistence of EtNP on Man2 prevented cleavage of a subset of GPI-APs, but the proteins were not endocytosed. Man2 unremodeled GPI-APs increased lipid disorder and generated a stress response whereby abnormal ubiquitin- and clathrin-dependent endocytosis was triggered. The resulting stress-induced endocytosis disrupted the trafficking repertoire of a subset of plasma membrane proteins. These proteins were redirected, via the multivesicular body, to numerous small vacuoles for degradation. Our findings highlight the critical importance GPI-AP Man2 remodeling for maintaining the integrity and homeostasis of the plasma membrane.