RNA-Binding Proteins as Regulators of Internal Initiation of Viral mRNA Translation

Figure 1. Cap-dependent translation initiation and viral strategies for ribosomal recruitment. (A) Schematic representation of a eukaryotic mRNA, including the 5′ cap structure, the 5′ untranslated region (UTR), the open reading frame (ORF), followed by the 3′ UTR and the Poly(A) at the 3′ end. The initiation codon (red) is also highlighted as part of the optimal context. (B) Schematic representation of canonical cap-dependent translation initiation summarized in 6 steps. Circularization of the mRNA is omitted. The eIF4F complex, 43S-preinitiation complex (PIC), and ternary complex (TC) are shown. The presence of the cap structure at the 5′ end of the mRNA allows for the recruitment of the eIF4F complex (1) and the 43S PIC (2). After these complexes scan the mRNA, they travel in an ATP-dependent, 5′ to 3′ direction (3). During scanning, eIF4A, in association with cofactor eIF4B, unwinds the secondary structure of the 5′ UTR. Scanning ends when the initiation codon is recognized (4). The factor eIF1 and eIF1A help avoid non-initiation codon interaction with the tRNAMeti placed in the P-site of the 40S subunit. Codon:anticodon interaction allows for the hydrolysis of eIF2-GTP and triggers…

Figure 2. Nuclear and Cytoplasmic RBPs act as ITAFs. (A,B) IRES-transacting factors (ITAFs) are cytoplasmic or nucleus–cytoplasmic shuttling RNA-binding proteins (RBPs) [82,222]. (C) These ITAF–RNA and ITAF–ITAF interactions depend on cellular conditions such as stress, proliferation, or viral infection, which may trigger specific ITAF PTMs, that reduce or enhance the RBPs affinity for its target RNA. (D) ITAFs assist in RNA structuring by establishing multiple contacts with the same RNA molecules and other RBP [82,95,96,147,168,223]. Thus, RBPs induce RNA conformations or RNP complexes with differential affinities for the translation machinery.

Figure 3. Model of IRES translational control mediated by RNA protein binding. (A) Some vRNAs do not require ITAFs to assemble (ON state). However, the association of different RBPs regulates the rate of translation initiation. ITAFs can also suffer PTMs, impacting their function over the IRES, further stimulating (green arrow) or reducing (red arrow) its activity [225]. (B) Some vRNAs (OFF state) require RBPs to assemble a functional IRES (ON state) [68,198]. ITAF PTMs can impact the ITAF localization, RNA affinity, or affinity for other RBPs impacting IRES function [81,225].

Figure 4. HnRNPA1: a model ITAF for the HIV-1 IRES. (A) In HIV-1 replicating cells, hnRNPA1 associates with the HIV-1 vRNA in the nucleus as part of the HIV-1 RNP [212,367]. (B) The HIV-1 RNP export is mediated by the viral protein Rev (reviewed in [367,373,374]). (C) HnRNPA1 stimulates (green arrow) HIV-1 IRES-mediated translation initiation [212,225]. (D) In cells, HIV-1 replication increases hnRNPA1 expression [212]. Cytoplasmic hnRNP A1 is re-imported into the nucleus by bound Trn-1, which interacts with the core member of the nuclear pore complex Nup62. However, in cells replicating HIV-1, Nup62 is downregulated, leading to the cytoplasmic retention of hnRNPA1. Cytoplasmic accumulation of hnRNPA1 further increases HIV-1 IRES activity [212]. (E) Post-translational modifications (PTMs) of hnRNPA1, including Mnk-mediated phosphorylation and PRMT5-induced symmetrical di-methylation of arginine residues, further promote HIV-1 IRES activity [212,225].