Translational control of coronaviruses

Abstract

Coronaviruses represent a large family of enveloped RNA viruses that infect a large spectrum of animals. In humans, the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) is responsible for the current COVID-19 pandemic and is genetically related to SARS-CoV and Middle East respiratory syndrome-related coronavirus (MERS-CoV), which caused outbreaks in 2002 and 2012, respectively. All viruses described to date entirely rely on the protein synthesis machinery of the host cells to produce proteins required for their replication and spread. As such, virus often need to control the cellular translational apparatus to avoid the first line of the cellular defense intended to limit the viral propagation. Thus, coronaviruses have developed remarkable strategies to hijack the host translational machinery in order to favor viral protein production. In this review, we will describe some of these strategies and will highlight the role of viral proteins and RNAs in this process.

Figure 1.

Scheme of the coronaviral replication cycle. After attachment to the cellular receptor, the viral particle is internalized and the gRNA is uncoated and directly translated in the cytoplasm to produce up to 16 nonstructural proteins (nsps) involved in viral proteolytic cleavage, the formation of the viral replication transcription complex (RTC) and in mRNA translational control. Viral genome replication and transcription of the different sgRNAs occur into double membrane vesicles (DMV) that are derived from the endoplasmic reticulum (ER). Some of the sgRNAs are coding for the structural proteins that are mainly expressed through the ER. Viral components (gRNA and viral proteins) assemble at the level of the ERGIC and new virions produced are secreted by exocytosis.

Figure 2.

The cap-dependent translation initiation mechanism. (1) Capped and polyadenylated mRNA is activated by the eIF4F complex, composed of eIF4E, eIF4G and eIF4A, to prepare ribosomal landing. 43S ribosomal complex is formed by the association of eIF1, eIF1A, eIF3, eIF5 and the ternary complex eIF2-GTP-Met-tRNAi with the 40S small ribosomal subunit (see blue square). (2) Attachment of the 43S complex to the mRNA is mediated by multiple protein interactions requiring eIF4E, eIF4G and eIF3. (3) Ribosomal complex scans the 5′UTR with the hydrolysis of GTP into GDP + Pi mediated by eIF5 until it reaches the initiation codon, where its recognition triggers to (4) Pi and eIFs release followed by (5) the association of the 60S and 40S ribosomal subunits to form an 80S ribosome competent for the elongation step. The most known translational controls occur on eIF4E and eIF2. According to the phosphorylation state of 4E-BP, 4E-BP interacts or not with eIF4E and this interaction displaces eIF4E from eIF4F resulting in a decrease of the cap dependent translation efficiency (see violet square). Regeneration of the GDP molecule bound to eIF2 into GTP is catalyzed by the exchange factor eIF2B. Phosphorylation of eIF2α at a serine in position 61 inhibits this regeneration that also induces a strong reduction of global translation (see orange square).

Figure 3.

The translational pathways regulation during CoVs infection. (A) Double strand RNA (dsRNA) accumulation produced during the viral replication is one sensor of the interferon antiviral defense and leads to the phosphorylation and activation of PKR. Viral proteins accumulation in the endoplasmic reticulum (ER) constitutes an ER stress and triggers the unfold protein response (UPR). As a result, PERK is phosphorylated and activated. Both PKR and PERK target the α subunit of eIF2 and its phosphorylation induces a global translational shutdown. The stress-activated phosphorylation of eIF2 can lead to the formation of stress granules (SGs) in which mRNAs stalled in translation initiation step are stored. SGs are connected with P-bodies structures as they share RNA and protein components. (B) Modulation of the p38MAPK and ERK pathways. ERK pathway controlled the phosphorylation state of 4E-BP and promotes the dissociation between 4E-BP and eIF4E that enhances the cap-dependent translation. p38 MAPK pathway targets the MAP kinase-interacting serine/threonine-protein kinase (Mnk) that phosphorylates eIF4E. As a consequence and in the context of CoVs infection, activation of this pathway is associated with a decrease of protein synthesis and viral replication. Viral components modulating the pathway are bolded in red.

Figure 4.

mRNA translation and mRNA decay regulated by SARS-CoV nsp1. A scheme of the 40S ribosomal subunit is showed with the mRNA entry and exit channel and the three tRNA sites: acceptor (A), peptidyl (P) and exit (E). Nsp1 is the first viral protein expressed and is able to interact, through the C-terminal domain, into the mRNA entry channel of the 40S ribosomal subunit. As a result, cellular mRNAs could not be recognized by the ribosome and cellular proteins expression is strongly reduced. In addition, nsp1 promotes endonucleotydic RNA cleavage that conducts the transcript to RNA degradation mediated by Xrn1. In parallel, all SARS-CoV mRNA harbor a common 5′ terminal 72 nt leader sequence with three stem-loop (SL) (labeled in green). SL1 interacts with nsp1 and confers a translational resistance of the viral mRNA to the translation repression mediated by nsp1.