Focus on Translation Initiation of the HIV-1 mRNAs

Abstract

To replicate and disseminate, viruses need to manipulate and modify the cellular machinery for their own benefit. We are interested in translation, which is one of the key steps of gene expression and viruses that have developed several strategies to hijack the ribosomal complex. The type 1 human immunodeficiency virus is a good paradigm to understand the great diversity of translational control. Indeed, scanning, leaky scanning, internal ribosome entry sites, and adenosine methylation are used by ribosomes to translate spliced and unspliced HIV-1 mRNAs, and some require specific cellular factors, such as the DDX3 helicase, that mediate mRNA export and translation. In addition, some viral and cellular proteins, including the HIV-1 Tat protein, also regulate protein synthesis through targeting the protein kinase PKR, which once activated, is able to phosphorylate the eukaryotic translation initiation factor eIF2α, which results in the inhibition of cellular mRNAs translation. Finally, the infection alters the integrity of several cellular proteins, including initiation factors, that directly or indirectly regulates translation events. In this review, we will provide a global overview of the current situation of how the HIV-1 mRNAs interact with the host cellular environment to produce viral proteins.

Keywords: HIV-1; IRES; RNA helicases; translation initiation; unspliced mRNA.

Figure 1

Model for cap-dependent and -independent ribosome recruitment on mRNAs. Interaction of the ternary complex to the 40S ribosome is enhanced in the presence of eIFs to form the 43S pre-initiation complex (PIC). 43S PIC can be recruited on activated mRNAs by the eIF4F complex composed of the eIF4E cap binding protein, the eIF4G scaffold protein, and the eIF4A helicase. 43S PIC bound to the mRNA scans the 5′ untranslated region (UTR) to initiate translation at the AUG initiation codon. This is the cap-dependent translation initiation mechanism. Cap-independent ribosome attachment is largely mediated by IRESes in which components of the 43S PIC can interact directly with some RNA structures. The requirement of eIFs to promote ribosome attachment depends of the type of the IRES: briefly, type 1 and 2 IRESes require all eIFs except eIF4E, type 3 IRESes do not need any of the eIF4F complex components, and type 4 IRESes do not rely on any eIFs nor Met-tRNAi. Finally, the 43S PIC can bind m⁶A located into the 5′ UTR.

Figure 2

Schematic representation of the HIV-1 genome. The different colored boxes indicate the HIV-1 ORFs located between the two LTRs. Position of the conserved donor (D1 to D4) and acceptor (A1 to A7) sites are shown. The HIV-1 primary transcript serves as both mRNA that encodes for the Gag and Gag-Pol polyproteins and as genomic RNA. The red RRE box corresponds to the binding site of Rev, which is required for the nuclear export of partially spliced and unspliced RNA transcripts. The exons of the partially and fully spliced mRNAs are shown in black boxes. The first exon is a noncoding exon (exon 1) present in all HIV-1 transcripts. Either both or one of the small noncoding exons 2 and 3 (grey boxes) are included in a fraction of the corresponding mRNA species leading to the diversity of the HIV-1 mRNAs.

Figure 3

Translation initiation of the HIV-1 unspliced mRNA. Scheme of the RNA structures of the first ≈800 nt, which includes the 5′ UTR composed of the TAR, poly(A), PBS, DIS, SD, and Psi element required for viral replication, and the beginning of the Gag-coding region. The cap structure is at position +1 and the Gag-p55 and Gag-p40 initiation codons are located at positions 336 and 759, respectively. Cap-dependent translation is inhibited by the presence of the TAR element and needs the TAR interacting proteins (such as TRBP, La, Staufen1, RNA helicase A (RHA), and DEAD-box polypeptide 3 (DDX3)) to certainly promote RNA unwinding and ribosomal recruitment at the 5′ end of the mRNA. Two complexes composed of DDX3, eIF4G, eIF4A, and eIF3 on the one hand, and cap binding protein 80 (CBP80), Rev, and eIF4A on the other hand exist and could drive ribosome recruitment on the mRNA independently of eIF4E. The 5′ UTR IRES is depicted inside the blue line, and ribosome attachment can be promoted via hnRNPA1 and S25 proteins and is enhanced during cell cycle arrest in the G2 phase, which is induced by Vpr and induces the sequestration of eIF4E by 4E-BP. The two internal ribosome binding sites of the Gag-coding region are indicated inside the red lines and they drive expression of Gag p55 and Gag p40. The PCE and IRENE regions are also indicated.