How retroviruses select their genomes

Abstract

All retroviruses — except spumaretroviruses — efficiently select and package two copies of their full-length RNA genomes as they assemble in infected cells. The nucleocapsid (NC) domains of the assembling retroviral Gag polyproteins are primarily responsible for genome selection. Upstream regions of the viral genomes, primarily located within 5′-untranslated regions (5′-UTRs), are essential for genome packaging and can independently direct the packaging of heterologous RNAs. In some cases, relatively small fragments of the UTRs can direct genome packaging, although not as efficiently as larger fragments or intact genomes. Regions of retroviral genomes that promote genome packaging often overlap with segments that promote RNA dimerization, and there is mounting evidence that dimerization and packaging events are intimately coupled. Except for the spumaretroviruses, all retroviral NC proteins contain one or two copies of a conserved zinc-knuckle motif that is crucial for packaging. The zinc knuckles generally contain a hydrophobic surface cleft, and in structurally characterized NC–RNA complexes the cleft serves as a binding site for exposed guanosine bases. Structural studies of large portions of some retroviral UTRs, primarily using chemical and enzymatic protection experiments and phylogenetic analyses, indicate that RNA structural changes occur upon dimerization. It has been suggested that such changes may regulate translation and/or packaging. High-resolution structural studies confirmed that fragments of the Moloney murine leukemia virus 5′-UTR undergo dimerization-dependent structural changes that regulate NC binding, consistent with the above proposal. It is currently unclear if other retroviruses, such as HIV, use similar mechanisms to selectively package a diploid genome. Although good progress has been made over the past two decades to identify protein and RNA elements important for genome packaging, additional studies, possibly using combinations of high- and low-resolution technologies, are needed to determine how multiple elements interact to cooperatively promote genome packaging.