The endoplasmic reticulum (ER) is the biggest organelle in most cell types, but its characterization as an organelle with a continuous membrane belies the fact that the ER is actually an assembly of several, distinct membrane domains that execute diverse functions. Almost 20 years ago, an essay by Sitia and Meldolesi first listed what was known at the time about domain formation within the ER. In the time that has passed since, additional ER domains have been discovered and characterized. These include the mitochondria-associated membrane (MAM), the ER quality control compartment (ERQC), where ER-associated degradation (ERAD) occurs, and the plasma membrane-associated membrane (PAM). Insight has been gained into the separation of nuclear envelope proteins from the remainder of the ER. Research has also shown that the biogenesis of peroxisomes and lipid droplets occurs on specialized membranes of the ER. Several studies have shown the existence of specific marker proteins found on all these domains and how they are targeted there. Moreover, a first set of cytosolic ER-associated sorting proteins, including phosphofurin acidic cluster sorting protein 2 (PACS-2) and Rab32 have been identified. Intra-ER targeting mechanisms appear to be superimposed onto ER retention mechanisms and rely on transmembrane and cytosolic sequences. The crucial roles of ER domain formation for cell physiology are highlighted with the specific targeting of the tumor metastasis regulator gp78 to ERAD-mediating membranes or of the promyelocytic leukemia protein to the MAM. Highlights ► This review summarizes mechanisms that lead to the targeting of ER proteins to individual membrane domains (e.g., rough ER). ► Formation of interactions between the Sec61 proteins, ribosomes and mRNAs is critical for rough ER targeting. ► The equilibrium between atlastins, reticulons and DP1/Yop1p determines the formation of smooth ER tubules. ► Targeting to the MAM depends on ER redox and on cytosolic or mitochondrial sorting motifs. ► Targeting to ERES, ERQC, and sites of peroxisome and lipid droplet biogenesis depend on COPI and COPII proteins.
