PMC:7105881 / 9904-18333 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7105881","sourcedb":"PMC","sourceid":"7105881","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7105881","text":"Genome of Emerging Human Coronaviruses, as Well as Structure and Function of Their Key Proteins\nThe human CoVs are enveloped viruses with a positive-sense, single-stranded RNA genome. They are 80–160 nm in diameter. Like other CoVs, human CoVs contain the largest viral genome [27–32 kilobase pairs (kb)] among the RNA viruses, and they share similar genome organization (Fehr and Perlman, 2015). Two large overlapping open reading frames (ORFs), ORF 1a and ORF 1b, occupy two-thirds of the genome at the 5′-terminus, and a third of the genome at the 3′-terminus encodes four common structural proteins in the gene order of spike (S), envelope (E), membrane (M), and nucleocapsid (N) (5′–3′) (Fehr and Perlman, 2015). The large ORF 1ab is a replicase gene encoding polyproteins 1a (pp1a) and pp1b/1ab, which can be cleaved into 15–16 non-structural proteins (nsp2-nsp16 or nsp1-nsp16) by 3C-like proteinase (3CLpro, nsp5) and papain-like proteinase (PLpro, nsp3) (Bailey-Elkin et al., 2014; Fehr and Perlman, 2015; Tomar et al., 2015; Snijder et al., 2016). In addition to the genes encoding the above structural proteins, the genes encoding accessory proteins have also been detected in the 3′ region between S–E–M–N (Fehr and Perlman, 2015). Some beta-CoVs, such as HCoV-OC43 and HCoV-HKU1, contain hemagglutinin-esterase (HE) gene located between ORF 1ab and S gene encoding an additional structural protein, HE (De Groot et al., 2011; Desforges et al., 2013; Huang et al., 2015). Similar to other human CoVs, SARS-CoV possesses a ∼29-kb genome, which encodes pp1a and pp1ab, four main structural proteins (S, E, M, and N), and eight accessory proteins, such as 3a, 3b, 6, 7a, 7b, 8a, 8b, and 9b (Figure 2A) (Marra et al., 2003; Snijder et al., 2003). The MERS-CoV genome is about 30 kb in length and encodes pp1a, pp1ab, four structural proteins (S, E, M, and N), and five accessory proteins (3, 4a, 4b, 5, and 8b) (Figure 2A) (van Boheemen et al., 2012). The genomic RNA of SARS-CoV and MERS-CoV is packed inside capsid formed by the N protein, while the M, E, and S proteins form the envelope surrounding the capsid (Figure 2B). Accessory genes may incorporate into virions at low levels (Liu et al., 2014). Nevertheless, neither SARS-CoV nor MERS-CoV appears to contain the HE gene (Rota et al., 2003; Zaki et al., 2012).\nFIGURE 2 Schematic structure of SARS-CoV, MERS-CoV, and 2019-nCoV. (A) Schematic diagram of genomic organization of SARS-CoV, MERS-CoV, and 2019-nCoV. The genomic regions or open-reading frames (ORFs) are compared. Structural proteins, including spike (S), envelope (E), membrane (M) and nucleocapsid (N) proteins, as well as non-structural proteins translated from ORF 1a and ORF 1b and accessory proteins, including 3a, 3b, 6, 7a, 7b, 8a, 8b, and 9b (for SARS-CoV), 3, 4a, 4b, 5, and 8b (for MERS-CoV), and 3a, 6, 7a, 7b, 8, and 10 (for 2019-nCoV) are indicated. 5′-UTR and 3′-UTR, untranslated regions at the N- and C-terminal regions, respectively. Kb, kilobase pair. (B) Schematic structure of virion of SARS-CoV, MERS-CoV, and 2019-nCoV and its major structural proteins. Several proteins of human CoVs are important for viral infection and/or pathogenesis. For example, most nsps participate in viral RNA replication and/or transcription (Snijder et al., 2016). The accessory proteins interact with host cells, potentially helping the viruses to evade the immune system and increase their virulence (Menachery et al., 2017). The HE protein assists in the attachment of virus–host cells, thus playing a key role in the production of infectious virions, as in the case of HCoV-OC43 (Desforges et al., 2013). The M and E proteins are responsible for virus assembly or promote virulence (Scobey et al., 2013; DeDiego et al., 2014). Different from the above proteins, the S protein of human CoVs mediates viral entry into host cells and subsequent membrane fusion, enabling viral infection (Du et al., 2009a; Lu et al., 2014). The S protein is a class I viral protein, which can be cleaved into two functional subunits, an amino-terminal S1 subunit and a carboxyl-terminal S2 subunit. The S1 subunit is responsible for virus–host cell receptor binding, whereas the S2 subunit is involved in virus–host membrane fusion (Li et al., 2005a; Lu et al., 2014). The S1 contains two major domains, an N-terminal domain (NTD) and a C-terminal domain (CTD). In general, NTDs mediate sugar binding (Li, 2016; Li et al., 2017; Ou et al., 2017; Hulswit et al., 2019; Tortorici et al., 2019), whereas CTDs facilitate protein receptor recognition (Wong et al., 2004; Hofmann et al., 2006; Lu et al., 2013). The NTDs and CTDs of the S1 subunit can bind host receptors or function as receptor-binding domains (RBDs) (Lu et al., 2013; Hulswit et al., 2019). The entry of human CoVs relies on the interaction between viral and cellular membrane proteins. Recognition of S1 subunit with a receptor and/or sugar on the cell surface initiates the infection (Li, 2015). After the initial recognition and binding, the S protein undergoes conformational changes, followed by membrane fusion through the S2 region (Li, 2015, 2016; Du et al., 2017). Consequently, the viral genetic materials are delivered into the host cell through the fusion core (Du et al., 2009a).\nSimilar to HCoV-NL63 (Hofmann et al., 2005; Li, 2015), SARS-CoV recognizes, through the RBD in the CTD region of its S1 subunit, angiotensin-converting enzyme 2 (ACE2) as the receptor on the target cell (Li et al., 2003). The RBD (CTD) in two states (standing or lying) has been observed in the trimeric S protein. ACE2 binds to standing RBD, specifically in the receptor-binding motif (RBM), keeping the RBD in the “standing” state (Yuan et al., 2017). In addition to human ACE2, SARS-CoV S protein could also bind to palm civet and mouse ACE2s (Li et al., 2004; Li, 2008). Mutations in the RBD of S1 subunit are required for cross-species transmission of SARS-CoV (Li et al., 2005c; Li, 2008, 2016). Several bat SARSr-CoVs have been identified, and these CoVs can utilize human ACE2 as their receptor to bind the target cells (Ge et al., 2013; Hu et al., 2017). The structure of SARS-CoV S trimer and RBD binding to the ACE2 receptor is shown in Supplementary Figures S1A,B.\nMERS-CoV RBD shares a structure similar to that of the homology domain of SARS-CoV (Wang et al., 2013). However, antibodies induced by SARS-CoV RBD have no cross-reactivity and/or cross-neutralizing activity to MERS-CoV (Du et al., 2013b). Moreover, MERS-CoV utilizes dipeptidyl peptidase 4 (DPP4) as a receptor through the RBD (CTD) region (Raj et al., 2013), which is distinct from the SARS-CoV receptor ACE2. Although the core regions of SARS-CoV and MERS-CoV RBDs are similar, their RBM regions are significantly different, which explains why they recognize different receptors (Li, 2015). MERS-CoV S trimer also maintains a structure similar to that of SARS-CoV S trimer. Both standing and lying states can be detected in the MERS-CoV RBDs, whereas DPP4 only binds to the standing RBD (Pallesen et al., 2017; Yuan et al., 2017). MERS-CoV is clustered with Ty-BatCoV HKU4 and Pi-BatCoV HKU5 in the subgenus Merbecovirus. Ty-BatCoV HKU4, but not Pi-BatCoV HKU5, could use human DPP4 as a receptor (Yang et al., 2014b). Recently, some MERS-related CoVs (MERSr-CoVs) have been discovered from bats that can enter human DPP4-expressing cells (Lau et al., 2018; Luo et al., 2018a). These findings suggest that the emergence of MERSr-CoV may threaten human health owing to their potential for cross-species transmission. The MERS-CoV S protein and RBD and their complexes, along with the DPP4 receptor, are shown in Supplementary Figures S1C,D.\nRecent studies have found that the new human CoV, 2019-nCoV, which belongs to the species of SARSr-CoV, shares high sequence identify (about 79.5%) to SARS-CoV (Zhou et al., 2020). The genome of 2019-nCoV encodes pp1ab (translated from ORF 1ab), four structural proteins (S, E, M, and N), and six accessory proteins (3a, 6, 7a, 7b, 8, and 10) (Figure 2A). Same as SARS-CoV and MERS-CoV, 2019-nCoV appears to have no HE gene. The virion of 2019-nCoV consists of similar structure as SARS-CoV and MERS-CoV (Figure 2B). Like SARS-CoV, 2019-nCoV also uses ACE2 as its cellular receptor to enter host cells (Zhou et al., 2020). Currently, the structure of 2019-nCoV RBD and/or its binding with the viral receptor has not yet been 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