Coatomer, the coat protein of coat protein complex (COP)I-vesicles, is a soluble protein complex made up of seven subunits, ␣-, -,  -, ␥-, ␦-, -, and -COP. Higher eukaryotes have two paralogous versions of the ␥-and -subunits, termed ␥1-and ␥2-COP and 1-and 2-COP. Different combinations of these subunits are known to exist within coatomer complexes, and ␥1/ 1-, ␥1/ 2-, and ␥2/ 1-COP represent the major coatomer populations in mammals. The role of COPI vesicles in the early secretory pathway is the subject of considerable debate. To help to resolve this discussion, we used quantitative immunoelectron microscopy and found that significant localization differences for COPI-isoforms do exist, with a preference for ␥1 1-and ␥1 2-coatomer in the early Golgi apparatus and ␥2 1-coatomer in the late Golgi apparatus. These differences suggest distinct functions for coatomer isoforms in a manner similar to clathrin/adaptor vesicles, where different adaptor proteins serve particular transport routes.coat protein complex I ntracellular vesicular transport is mediated by small proteincoated carriers. Various functions are attributed to coated vesicles, which are defined by their constituent coat proteins. Isoforms with different combinations of coat protein complex (COP)II protein paralogs have been found in the COPII coats on vesicles budding from the endoplasmic reticulum (ER) of mammals and yeast (1-3). Because only one direction of travel from the ER to the Golgi apparatus is known for COPII vesicles, these isoforms might reflect differing cargo specificities (4). In the late Golgi/endocytic pathways, a variety of coat proteins are known, including four different tetrameric adaptor complexes, some of which use the clathrin system as an outer shell of their coat (5). Within these pathways, particular transport routes are served by specific coat complexes (for review, see refs. 6 and 7). Thus, for particular pathways, the selection of cargo as well as the direction might be determined by individual coats.Just which pathways are mediated by vesicles bearing the COPI coat is the subject of considerable debate. The COPI coat consists of coatomer, which is a stable cytoplasmic complex of seven subunits, ␣-, -, Ј-, ␥-, ␦-, -, and -COP, and the small GTP-binding protein ADP-ribosylation factor, Arf1. COPI vesicles were found to originate from the Golgi apparatus and are implicated in transport within the Golgi itself in anterograde and retrograde direction, and from the Golgi and the ER-Golgi intermediate compartment (ERGIC) to the ER (8-10). The observation that COPI vesicles participate in several transport directions is difficult to rationalize with just a single isoform of the complex (reviewed in ref. 11). Questions about the function of COPI vesicles are intimately linked to our view of the general mechanisms of transport through the Golgi. Specifically, is transport in both directions, anterograde and retrograde, performed by these carriers, or are COPI vesicles exclusively retrograde carriers within the Golgi and from...