Posttranscriptional regulation of retroviral gene expression: primary RNA transcripts play three roles as pre-mRNA, mRNA, and genomic RNA

Abstract

After reverse transcription of the retroviral RNA genome and integration of the DNA provirus into the host genome, host machinery is used for viral gene expression along with viral proteins and RNA regulatory elements. Here, we discuss co-transcriptional and posttranscriptional regulation of retroviral gene expression, comparing simple and complex retroviruses. Cellular RNA polymerase II synthesizes full-length viral primary RNA transcripts that are capped and polyadenylated. All retroviruses generate a singly spliced env mRNA from this primary transcript, which encodes the viral glycoproteins. In addition, complex viral RNAs are alternatively spliced to generate accessory proteins, such as Rev, which is involved in posttranscriptional regulation of HIV-1 RNA. Importantly, the splicing of all retroviruses is incomplete; they must maintain and export a fraction of their primary RNA transcripts. This unspliced RNA functions both as the major mRNA for Gag and Pol proteins and as the packaged genomic RNA. Different retroviruses export their unspliced viral RNA from the nucleus to the cytoplasm by either Tap-dependent or Rev/CRM1-dependent routes. Translation of the unspliced mRNA involves frame-shifting or termination codon suppression so that the Gag proteins, which make up the capsid, are expressed more abundantly than the Pol proteins, which are the viral enzymes. After the viral polyproteins assemble into viral particles and bud from the cell membrane, a viral encoded protease cleaves them. Some retroviruses have evolved mechanisms to protect their unspliced RNA from decay by nonsense-mediated RNA decay and to prevent genome editing by the cellular APOBEC deaminases.

FIGURE 1

Simple retroviruses, such as Rous sarcoma virus, transcribe a 9 kb primary RNA transcript. A fraction of these transcripts are spliced to generate sub-genomic env and src mRNAs (left side), which are exported to the cytoplasm like spliced cellular mRNAs. The remaining primary transcripts are not spliced (right side), due to inhibition by the viral NRS element and by inefficient 3′ splice sites. The viral DR sequences interact with cellular proteins to facilitate export of the unspliced RNA to the cytoplasm. The cytoplasmic translocation of the unspliced viral RNAs through the nuclear pore complex is facilitated by the DEAD box helicase Dbp5. The major translation product of the unspliced mRNA is the Gag protein. In addition, an infrequent −1 frame-shift (*) before the gag termination codon allows translation of the Gag-Pol polyprotein.

FIGURE 2

Complex retroviruses, such as HIV-1, generate 3 classes of mRNA: unspliced (9 kb), singly spliced (4 kb), and completely spliced (2 kb). Early HIV gene expression results in the generation of completely spliced mRNAs (left side), including tat and rev. Following translation, Tat and Rev are imported into the nucleus. Tat binds the TAR RNA element to promote transcriptional elongation, while Rev binds the RRE of singly spliced and unspliced RNAs (right side) to mediate nuclear export of the viral RNA after recruiting the cellular factor CRM1. The cytoplasmic translocation of the partially spliced/unspliced viral RNA through the nuclear pore complex is facilitated by the DEAD box helicase DDX3. Translation of the unspliced HIV-1 RNA is similar to that of RSV shown in Figure 1. * Marks the site of a frame shift from the gag to the pol reading fame.