RNA-Binding Proteins at the Host-Pathogen Interface Targeting Viral Regulatory Elements

Figure 1. Diagram of the genomic RNA of flavivirus, picornavirus, alphavirus, and calicivirus. The regulatory elements targeted by host RNA-binding proteins (RBPs) described in this review are depicted. The RNA length of the genome is approximately drawn to scale (flavivirus 10–11 kb, picornavirus 7.5–9 kb, alphavirus 12 kb, calicivirus 7.4–8.3 kb). In all cases the open reading frame (ORF) encodes a polyprotein, which is processed into the mature viral proteins. Stem-loops on the 5′ and 3′UTRs of the viral RNA, as well as the downstream stem-loop (DLP) of alphavirus, are schematically represented by hairpins. A black circle depicts the m7GTP residue at the 5′ end of the mRNA in flavivirus (Dengue virus (DENV), West Nile virus (WNV), Zika Virus (ZIKV)) and alphavirus (Sindbis virus (SINV), Semliki forest virus (SFV), Chikungunya (CHKV)); the violet and orange circles depict the viral protein (VPg) covalently linked to the 5′ end in picornavirus (Poliovirus (PV), encephalomyocarditis virus (EMCV), foot-and-mouth disease virus (FMDV)) and calicivirus (FCV) RNA, respectively, while (A)n denotes the poly(A) tail at the 3′ end of the RNA in picornavirus, alphavirus, and calicivirus. The…

Figure 2. Schematic representation of main events in picornavirus infected cells. Following attachment of the virus to the receptor on the cell surface, internalization, and uncoating leads to release of the viral RNA into the cytoplasm of the host cell. The virus life cycle then proceeds to translation of the polyprotein precursor encoded in the viral genome through interaction with the host translation machinery (green oval). Processing of the polyprotein by viral encoded proteases renders the mature viral proteins required for virus multiplication. Viral RNA replication takes place in viral RNA replication organelles within reorganized cell membranes. Following assembly of viral capsids, the viral RNA is packaged into virions. Viral infection also alters host gene expression through activation of signaling pathways, and modification and/or proteolysis of host factors (eukaryotic initiation factors (eIFs) and RBPs) by viral proteases, inducing cap-dependent shutoff, nucleus-cytoplasm redistribution, trafficking stress, and antiviral response (yellow oval).

Figure 3. Pathways leading to the assembly of stress granules (SGs) in RNA virus infected cells and outcome in gene expression regulation. Early infection events trigger the interferon (IFN) signaling, concomitant to protein kinase R (PKR) activation via dsRNA and eIF2α phosphorylation, leading to SGs assembly, generating a cascade of pathways that impact on host gene expression, viral gene regulation, and antiviral response. Blue letters denote main components of SGs.

Figure 4. Host factors interacting with domain 3 of the FMDV IRES element. RNA structure model of the IRES element based on RNA Selective 2′ Hydroxyl Acylation analyzed by Primer Extension (SHAPE) probing (33) (top). The central domain (3) is colored in green. The functional association of proteins identified using the tRNA-scaffold methodology (123), interacting with domain 3 of the IRES, related to ER-Golgi vesicles trafficking was generated with STRING software (https://string-db.org). Factors involved in the anterograde (COPII) or retrograde (COPI) transport are marked by orange and blue shadow, respectively. Proteins are represented by circles and colored based on their functional grouping.

Figure 5. Diagram of m6A RNA modification enzymes. The proteins known as writers, readers, and erasers are depicted. The image on the right shows the interaction of YTH N6-methyladenosine RNA binding protein 1 (YTHDF1) protein with labeled domain 3 the FMDV IRES in RNA retarded gel shift assay.