Selective and Nonselective Packaging of Cellular RNAs in Retrovirus Particles

Abstract

Assembly of retrovirus particles normally entails the selective encapsidation of viral genomic RNA. However, in the absence of packageable viral RNA, assembly is still efficient, and the released virus-like particles (termed “Ψ ⁻ ” particles) still contain roughly normal amounts of RNA. We have proposed that cellular mRNAs replace the genome in Ψ ⁻ particles. We have now analyzed the mRNA content of Ψ ⁻ and Ψ ⁺ murine leukemia virus (MLV) particles using both microarray analysis and real-time reverse transcription-PCR. The majority of mRNA species present in the virus-producing cells were also detected in Ψ ⁻ particles. Remarkably, nearly all of them were packaged nonselectively; that is, their representation in the particles was simply proportional to their representation in the cells. However, a small number of low-abundance mRNAs were greatly enriched in the particles. In fact, one mRNA species was enriched to the same degree as Ψ ⁺ genomic RNA. Similar results were obtained with particles formed from the human immunodeficiency virus type 1 (HIV-1) Gag protein, and the same mRNAs were enriched in MLV and HIV-1 particles. The levels of individual cellular mRNAs were ∼5- to 10-fold higher in Ψ ⁻ than in Ψ ⁺ MLV particles, in agreement with the idea that they are replacing viral RNA in the former. In contrast, signal recognition particle RNA was present at the same level in Ψ ⁻ and Ψ ⁺ particles; a minor fraction of this RNA was weakly associated with genomic RNA in Ψ ⁺ MLV particles.