HIV-1 and two avian retroviral 5′ untranslated regions bind orthologous human and chicken RNA binding proteins

•Cellular proteins are responsible for activity of retroviral 5′ cis-responsive sequences.•Comprehensive inventory of high affinity cellular partners of retroviral RNA is needed.•Retroviral RNA affinity-coupled-human/avian proteomics is comprehensive and unbiased.•Higher-order structure of HIV-1 and SNV 5′ UTRs are similar, RSV is distinct.•Nonreciprocal DXH9-5′ UTR binding explains human restriction of avian sarcoma virus.

Essential host cofactors in retrovirus replication bind cis-acting sequences in the 5′untranslated region (UTR). Although host RBPs are crucial to all aspects of virus biology, elucidating their roles in replication remains a challenge to the field. Here RNA affinity-coupled-proteomics generated a comprehensive, unbiased inventory of human and avian RNA binding proteins (RBPs) co-isolating with 5′UTRs of HIV-1, spleen necrosis virus and Rous sarcoma virus. Applying stringent biochemical and statistical criteria, we identified 185 RBP; 122 were previously implicated in retrovirus biology and 63 are new to the 5′UTR proteome. RNA electrophoretic mobility assays investigated paralogs present in the common ancestor of vertebrates and one hnRNP was identified as a central node to the biological process-anchored networks of HIV-1, SNV, and RSV 5′ UTR-proteomes. This comprehensive view of the host constituents of retroviral RNPs is broadly applicable to investigation of viral replication and antiviral response in both human and avian cell lineages.