Riboproteomic analysis of polypeptides interacting with the internal ribosome‐entry site element of foot‐and‐mouth disease viral RNA

Abstract

Initiation of translation driven by internal ribosome entry site (IRES) elements depends upon the structural organization of this mRNA region. Besides translation initiation factors (eIFs), auxiliary proteins can also affect IRES activity. With the aim to identify proteins interacting with two unrelated IRESs present in the genome of foot-and-mouth disease virus (FMDV) and hepatitis C virus (HCV) we have used a proteomic approach. This procedure allowed the identification of 21 RNA-binding proteins interacting with discrete regions of the FMDV IRES, domains 3 and 5, and 16 interacting with domain III of the HCV IRES. In support of the binding specificity, the factors interacting with domain 3 differed from those interacting with domain 5, and included three poly(rC)-binding protein (PCBP) members, besides proliferation-associated 2G4 (PA2G4) and deleted-azoospermia 1 (DAZ1) protein. Around 71% of the identified factors associated with the FMDV IRES differ from those interacting with the HCV IRES. The group of proteins interacting with the FMDV or the HCV IRES includes eIF4B and 5 subunits of eIF3, respectively, known to interact with each of these RNAs, validating the results of this approach. According to the function of the identified proteins, 55% are involved in translation control, whereas 35% play a role in different aspects of RNA lifespan. Compilation of factors preferentially associated with FMDV or HCV IRES provides a basis for examining the strategies used by IRESs to recruit the translation machinery.

Human G3BP1 interacts with β-F1-ATPase mRNA and inhibits its translation

“…Most of these proteins are known to be involved in virtually all stages of mRNA life cycle and have roles in more than one RNA-processing step, which suggests that they are multifunctional proteins (Huttelmaier et al, 2005;Martin and Ephrussi, 2009;Mongelard and Bouvet, 2007;Moore, 2005). In addition, they are present in other nuclear and cytoplasmic RNP complexes, such as the spliceosome (Chen et al, 2007), the Ago1 complex (Hock et al, 2007), IMP1 granules (Jonson et al, 2007) and FMRP granules (Khandjian et al, 2004), as well as in viral RNPs (Jorba et al, 2008;Mayer et al, 2007;Pacheco et al, 2008). The finding that these proteins built an RNP complex of oxidative phosphorylation highlights for the first time their relevance as post-transcriptional regulators in the biogenesis and function of mitochondria.…”

RNA helicases in infection and disease

“…75 DHX9/RHA interacts with the internal ribosome entry site of FMDV and HCV mRNA, 76 and with FMDV proteins involved in assembly of replication complexes. 75 Recently, a role of DHX9/RHA for the influenza viral life cycle has been demonstrated, 77 where it enhances transcription and replication.…”

Y-Box Binding Protein 1 Stabilizes Hepatitis C Virus NS5A via Phosphorylation-Mediated Interaction with NS5A To Regulate Viral Propagation

“…Given that YB-1 associates with NS5A to sustain the NS5A level (Fig. 10), and that YB-1 has been identified as the HCV 5= and 3=NTR-interacing protein (42,75,76), it is likely that YB-1 regulates the translation-replication switch in the HCV life cycle through the NS5A-YB-1 complex. Interestingly, in the reporter genome assay, the observation that YB-1 moderately inhibits primary translation (Fig.…”