Although alphaviruses dramatically alter cellular function within hours of infection, interactions between alphaviruses and specific host cellular proteins are poorly understood. Although the alphavirus nonstructural protein 2 (nsP2) is an essential component of the viral replication complex, it also has critical auxiliary functions that determine the outcome of infection in the host. To gain a better understanding of nsP2 function, we sought to identify cellular proteins with which Venezuelan equine encephalitis virus nsP2 interacted. We demonstrate here that nsP2 associates with ribosomal protein S6 (RpS6) and that nsP2 is present in the ribosome-containing fractions of a polysome gradient, suggesting that nsP2 associates with RpS6 in the context of the whole ribosome. This result was noteworthy, since viral replicase proteins have seldom been described in direct association with components of the ribosome. The association of RpS6 with nsP2 was detected throughout the course of infection, and neither the synthesis of the viral structural proteins nor the presence of the other nonstructural proteins was required for RpS6 interaction with nsP2. nsP1 also was associated with RpS6, but other nonstructural proteins were not. RpS6 phosphorylation was dramatically diminished within hours after infection with alphaviruses. Furthermore, a reduction in the level of RpS6 protein expression led to diminished expression from alphavirus subgenomic messages, whereas no dramatic diminution in cellular translation was observed. Taken together, these data suggest that alphaviruses alter the ribosome during infection and that this alteration may contribute to differential translation of host and viral messages.The Alphavirus genus contains over 25 recognized viruses with a wide geographic distribution. Venezuelan equine encephalitis virus (VEE) is a New World alphavirus that is maintained in nature by cycling between a mosquito vector and susceptible vertebrate hosts. VEE is responsible for periodic outbreaks of disease in humans and equines and is classified as a select agent, making it a prominent pathogen among the alphaviruses.Alphaviruses possess a genome of single-stranded messagesense RNA that is approximately 11.5 kb in length. The alphavirus genome is organized such that the 5Ј two-thirds of the genome encodes four nonstructural proteins (nsP1 through nsP4), whereas the 3Ј one-third encodes three mature structural proteins (capsid, E2, and E1) that are expressed at high levels after transcription from an internal 26S subgenomic mRNA promoter. The viral genome appears to be similar to cellular mRNAs, since it contains 5Ј and 3Ј untranslated regions, with a 5Ј-terminal methylguanylate cap and a 3Ј-terminal polyadenylate tail. Upon release into a host cell, the viral genomic RNA is directly translated by the cellular translation machinery. The nonstructural proteins are synthesized as two polyproteins, termed P123 and P1234. P123 results when translation terminates at an opal termination codon between nsP3 and nsP4. When t...