Molecularly distinct sets of SNARE proteins localize to specific intracellular compartments and catalyze membrane fusion events. Although their central role in membrane fusion is appreciated, little is known about the mechanisms by which individual SNARE proteins are targeted to specific organelles. Here we investigated functional domains in Sec22p that direct this SNARE protein to the endoplasmic reticulum (ER), to Golgi membranes, and into SNARE complexes with Bet1p, Bos1p, and Sed5p. A series of Sec22p deletion mutants were monitored in COPII budding assays, subcellular fractionation gradients, and SNARE complex immunoprecipitations. We found that the N-terminal "profilinlike" domain of Sec22p was required but not sufficient for COPII-dependent export of Sec22p from the ER. Interestingly, versions of Sec22p that lacked the N-terminal domain were assembled into ER/Golgi SNARE complexes. Analyses of Sec22p SNARE domain mutants revealed a second signal within the SNARE motif (between layers ؊4 and ؊1) that was required for efficient ER export. Other SNARE domain mutants that contained this signal were efficiently packaged into COPII vesicles but failed to assemble into SNARE complexes. Together these results indicated that SNARE complex formation is neither required nor sufficient for Sec22p packaging into COPII transport vesicles and subsequent targeting to the Golgi complex. We propose that the COPII budding machinery has a preference for unassembled ER/Golgi SNARE proteins.In eukaryotic cells, most intracellular membrane fusion processes are mediated by a related family of small proteins, called SNARE 1 (soluble NSF attachment protein receptors) proteins (1, 2). SNAREs share a conserved heptad repeat coiled coil sequence, called the SNARE domain, that is typically adjacent to a C-terminal-membrane bound region (3). Specific sets of SNARE domains assemble into parallel four-helix bundles forming the stable core of a SNARE protein complex (4 -6). Current membrane fusion models theorize that cognate sets of SNARE proteins provided from opposing membranes assemble into "trans" SNARE complexes and drive membrane bilayers together during fusion (2, 7).The assembly of cognate SNAREs has also been proposed to define the compartmental specificity of membrane fusion based on experiments showing that only specific combinations of SNARE proteins catalyze in vitro fusion when reconstituted into synthetic proteoliposomes (8 -10). However, this proposal remains debated given the promiscuity of SNARE interactions in vitro (11-13), functional redundancy in vivo (14, 15), and requirements for individual SNARE proteins in multiple intracellular membrane fusion steps (16). These and other observations suggest that additional spatial and temporal determinants in SNARE proteins contribute to the specificity of the membrane fusion (2). The N-terminal domains of SNARE proteins display significant diversity and appear to govern SNARE protein activity and distribution. For example, the N-terminal domain of the syntaxin-like SNARE prot...