Hepatitis C virus (HCV) nonstructural protein 4B (NS4B) is an integral membrane protein, which plays an important role in the organization and function of the HCV replication complex (RC). Although much is understood about its amphipathic N-terminal and C-terminal domains, we know very little about the role of the transmembrane domains (TMDs) in NS4B function. We hypothesized that in addition to anchoring NS4B into host membranes, the TMDs are engaged in intra-and intermolecular interactions required for NS4B structure/ function. To test this hypothesis, we have engineered a chimeric JFH1 genome containing the Con1 NS4B TMD region. The resulting virus titers were greatly reduced from those of JFH1, and further analysis indicated a defect in genome replication. We have mapped this incompatibility to NS4B TMD1 and TMD2 sequences, and we have defined putative TMD dimerization motifs (GXXXG in TMD2 and TMD3; the S/T cluster in TMD1) as key structural/functional determinants. Mutations in each of the putative motifs led to significant decreases in JFH1 replication. Like most of the NS4B chimeras, mutant proteins had no negative impact on NS4B membrane association. However, some mutations led to disruption of NS4B foci, implying that the TMDs play a role in HCV RC formation. Further examination indicated that the loss of NS4B foci correlates with the destabilization of NS4B protein. Finally, we have identified an adaptive mutation in the NS4B TMD2 sequence that has compensatory effects on JFH1 chimera replication. Taken together, these data underscore the functional importance of NS4B TMDs in the HCV life cycle.Hepatitis C virus (HCV) is an enveloped, positive-sense RNA virus responsible for 170 million cases of chronic infections worldwide. HCV is the only member of the genus Hepacivirus in the family Flaviviridae (51, 63), which includes other human pathogens, such as West Nile virus and dengue virus. Translation of the virus genome yields at least three structural proteins (core, E1, and E2), the highly hydrophobic p7 peptide, and six nonstructural (NS) proteins (NS2, NS3, NS4A, NS4B, NS5A, and NS5B). The NS proteins, including NS3 to NS5B, are sufficient to promote HCV replication in vitro (10,43). However, with the advent of the HCV cell culture system, many of the NS proteins (NS2, NS3, and NS5A) have been reported to play an active role in HCV assembly (5,46,50,69,73), further supporting the idea that the NS proteins in general have multiple functions in the HCV life cycle.NS3 is illustrative of multifunctionality. Its N-terminal serine protease activity is responsible for processing the NS proteins into their mature forms, whereas the C-terminal helicase activity may be required for the unwinding of HCV RNA (35,66). Similarly, NS4A is a cofactor of NS3 serine protease; it also assists NS3 in binding to host membranes (72) and facilitates the association of NS3 with the HCV replication complex (RC). NS5A may have multiple functions, including inhibition of the interferon response to virus infection and HCV RNA ...