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LitCovid_Glycan-Motif-Structure

LitCovid-PD-FMA-UBERON

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T6","span":{"begin":255,"end":260},"obj":"Body_part"}],"attributes":[{"id":"A6","pred":"uberon_id","subj":"T6","obj":"http://purl.obolibrary.org/obo/UBERON_0000178"}],"text":"5.2. Substrate Diversity of the CoV HEs\nHEs as envelope proteins are found in CoVs, orthomyxoviruses and toroviruses. Coronaviral HEs are involved in virus attachment to SA species. HE protein in β-CoVs binds to Neu5,9Ac2 form SA and agglutinates the red blood cells (RBCs) of rodents [52]. As with SA-O-acetylesterase, HE potentiates viral entry with the S protein and spreading via the mucosal glycans. It contains a carbohydrate-recognizing domain (CRD) known in lectin. The HE glycan-binding domain (GBD) mediates virus attachment to SAs on host cells. HE is the only HA. This indicates that compared to the S glycoprotein, HE is only minor a HA and the S glycoprotein mainly attaches to the cell surface. The HE protein of murine hepatitis virus (MHV), an enveloped CoV, binds to SA-4-acetylester or SA-9-O-acetylester of the carcinoembryonic antigen cell adhesion molecule 1a (CEACAM; known as CD66a) as the key receptor [53]. Murine CoVs HEs acquired by horizontal gene transfer, bind to C9-O-Ac Neu5Ac. However, some murine CoV HEs cannot bind to C4-O-Ac Neu5Ac. The original mouse MHV HE binds to C9-O-Ac Neu5Ac, while the MHV S-strain HE evolutionarily acquired the ability to bind to C4-O-Ac Neu5Ac [12,53,54]. In terms of structure, the C5 N- and C9 O-Ac Neu5Ac-accomodating hydrophobic pocket was shifted to a C5 N- and C4-O-Ac Neu5Ac-accomodating pocket [55].\nType I HE is specific for the 9-O-acetylated SAs (9-O-Ac-SAs). Type II HE is specific for 4-O-Ac-SAs. The SA-binding shift indicates quasi-synchronous adaptations of the SA-recognition sites of the lectin and esterase domains. Type I HE monomers of β-CoV lineage A have a bimodular enzyme–lectin domain similar to cellular glycan/carbohydrate-modifying proteins. Originally, HE homologs are found in various viruses including toroviruses and orthomyxoviruses such as the influenza virus C/D and isavirus, as well as the exceptional case of β-CoV lineage A among CoVs. The HE gene was transmitted to a β-CoV lineage A progenitor via horizontal gene transfer from a 9-O-Ac-Sia–recognizing HEF, as shown in influenza virus C/D. HE acquisition and expansion occurred by cross-species transmission over HE evolution and this phenomenon reflects viral evolutionary adaptation to host SA-containing glycans. Therefore, CoV HE receptor switching precedes virus evolution driven by SA-containing glycan diversity of hosts. For instance, the BcoV HE prefers 7,9-di-O-Ac-SAs, which is also a target of the bovine torovirus HE. For a more outstanding case, such a switching event occurred in the murine CoVs for the β-CoV lineage A type switch toward O-Ac-SA recognition. In the HE specificity of murine CoVs, two different murine CoV subtypes of virus group exist with one subtype possessing the typical 9-O-Ac-SA (type I) attachment factor and the other exclusively 4-O-Ac-SA (type II) attachment virus group [56].\nThe first coronaviral HE proteins identified were from the porcine hemagglutinating encephalomyelitis virus (PHEV), BCoV and HCoV-OC43, which bear SA-9-O-acetylesterases similar to HEF [8]. Rat CoV (RCoV) has SA-4-O-acetylesterases, converting Neu4,5Ac2 to Neu5Ac [53,57,58]. Some murine CoVs prefer 4-O-Ac-SAs and others 9-O-Ac-SAs. HCoV-OC43 and BCoV prefer α2-6-SA 9-O-acetylation by their SA-O-acetyleseterases. The S glycoproteins of BCoV and HCoV-OC43 are Neu5,9Ac2-recognizing lectins and agglutinate murine, rat and chicken erythrocytes due to the enriched 9-O-Ac-SA species [52]. BCoV and HCoV-OC43 adapted to SA receptor determinants of 9-O-Ac-SA receptors [59]. For a second receptor, the binding of S glycoprotein to Neu5,9Ac2 receptor is essential for entry into cells. BCoV-infection is prevented by prior treatment of cells with NA enzyme or with viral SA-O-acetylesterases, blocking the roles of HE and S glycoprotein in SA-dependent entry to host cells."}

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T112","span":{"begin":735,"end":744},"obj":"Disease"},{"id":"T113","span":{"begin":1845,"end":1854},"obj":"Disease"},{"id":"T114","span":{"begin":2078,"end":2087},"obj":"Disease"},{"id":"T115","span":{"begin":2963,"end":2980},"obj":"Disease"},{"id":"T116","span":{"begin":3667,"end":3676},"obj":"Disease"}],"attributes":[{"id":"A112","pred":"mondo_id","subj":"T112","obj":"http://purl.obolibrary.org/obo/MONDO_0002251"},{"id":"A113","pred":"mondo_id","subj":"T113","obj":"http://purl.obolibrary.org/obo/MONDO_0005812"},{"id":"A114","pred":"mondo_id","subj":"T114","obj":"http://purl.obolibrary.org/obo/MONDO_0005812"},{"id":"A115","pred":"mondo_id","subj":"T115","obj":"http://purl.obolibrary.org/obo/MONDO_0005156"},{"id":"A116","pred":"mondo_id","subj":"T116","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"}],"text":"5.2. Substrate Diversity of the CoV HEs\nHEs as envelope proteins are found in CoVs, orthomyxoviruses and toroviruses. Coronaviral HEs are involved in virus attachment to SA species. HE protein in β-CoVs binds to Neu5,9Ac2 form SA and agglutinates the red blood cells (RBCs) of rodents [52]. As with SA-O-acetylesterase, HE potentiates viral entry with the S protein and spreading via the mucosal glycans. It contains a carbohydrate-recognizing domain (CRD) known in lectin. The HE glycan-binding domain (GBD) mediates virus attachment to SAs on host cells. HE is the only HA. This indicates that compared to the S glycoprotein, HE is only minor a HA and the S glycoprotein mainly attaches to the cell surface. The HE protein of murine hepatitis virus (MHV), an enveloped CoV, binds to SA-4-acetylester or SA-9-O-acetylester of the carcinoembryonic antigen cell adhesion molecule 1a (CEACAM; known as CD66a) as the key receptor [53]. Murine CoVs HEs acquired by horizontal gene transfer, bind to C9-O-Ac Neu5Ac. However, some murine CoV HEs cannot bind to C4-O-Ac Neu5Ac. The original mouse MHV HE binds to C9-O-Ac Neu5Ac, while the MHV S-strain HE evolutionarily acquired the ability to bind to C4-O-Ac Neu5Ac [12,53,54]. In terms of structure, the C5 N- and C9 O-Ac Neu5Ac-accomodating hydrophobic pocket was shifted to a C5 N- and C4-O-Ac Neu5Ac-accomodating pocket [55].\nType I HE is specific for the 9-O-acetylated SAs (9-O-Ac-SAs). Type II HE is specific for 4-O-Ac-SAs. The SA-binding shift indicates quasi-synchronous adaptations of the SA-recognition sites of the lectin and esterase domains. Type I HE monomers of β-CoV lineage A have a bimodular enzyme–lectin domain similar to cellular glycan/carbohydrate-modifying proteins. Originally, HE homologs are found in various viruses including toroviruses and orthomyxoviruses such as the influenza virus C/D and isavirus, as well as the exceptional case of β-CoV lineage A among CoVs. The HE gene was transmitted to a β-CoV lineage A progenitor via horizontal gene transfer from a 9-O-Ac-Sia–recognizing HEF, as shown in influenza virus C/D. HE acquisition and expansion occurred by cross-species transmission over HE evolution and this phenomenon reflects viral evolutionary adaptation to host SA-containing glycans. Therefore, CoV HE receptor switching precedes virus evolution driven by SA-containing glycan diversity of hosts. For instance, the BcoV HE prefers 7,9-di-O-Ac-SAs, which is also a target of the bovine torovirus HE. For a more outstanding case, such a switching event occurred in the murine CoVs for the β-CoV lineage A type switch toward O-Ac-SA recognition. In the HE specificity of murine CoVs, two different murine CoV subtypes of virus group exist with one subtype possessing the typical 9-O-Ac-SA (type I) attachment factor and the other exclusively 4-O-Ac-SA (type II) attachment virus group [56].\nThe first coronaviral HE proteins identified were from the porcine hemagglutinating encephalomyelitis virus (PHEV), BCoV and HCoV-OC43, which bear SA-9-O-acetylesterases similar to HEF [8]. Rat CoV (RCoV) has SA-4-O-acetylesterases, converting Neu4,5Ac2 to Neu5Ac [53,57,58]. Some murine CoVs prefer 4-O-Ac-SAs and others 9-O-Ac-SAs. HCoV-OC43 and BCoV prefer α2-6-SA 9-O-acetylation by their SA-O-acetyleseterases. The S glycoproteins of BCoV and HCoV-OC43 are Neu5,9Ac2-recognizing lectins and agglutinate murine, rat and chicken erythrocytes due to the enriched 9-O-Ac-SA species [52]. BCoV and HCoV-OC43 adapted to SA receptor determinants of 9-O-Ac-SA receptors [59]. For a second receptor, the binding of S glycoprotein to Neu5,9Ac2 receptor is essential for entry into cells. BCoV-infection is prevented by prior treatment of cells with NA enzyme or with viral SA-O-acetylesterases, blocking the roles of HE and S glycoprotein in SA-dependent entry to host cells."}

LitCovid-PD-CLO

LitCovid-PD-CHEBI

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T50","span":{"begin":856,"end":878},"obj":"http://purl.obolibrary.org/obo/GO_0098631"},{"id":"T51","span":{"begin":856,"end":869},"obj":"http://purl.obolibrary.org/obo/GO_0007155"},{"id":"T52","span":{"begin":3829,"end":3842},"obj":"http://purl.obolibrary.org/obo/GO_0044409"}],"text":"5.2. Substrate Diversity of the CoV HEs\nHEs as envelope proteins are found in CoVs, orthomyxoviruses and toroviruses. Coronaviral HEs are involved in virus attachment to SA species. HE protein in β-CoVs binds to Neu5,9Ac2 form SA and agglutinates the red blood cells (RBCs) of rodents [52]. As with SA-O-acetylesterase, HE potentiates viral entry with the S protein and spreading via the mucosal glycans. It contains a carbohydrate-recognizing domain (CRD) known in lectin. The HE glycan-binding domain (GBD) mediates virus attachment to SAs on host cells. HE is the only HA. This indicates that compared to the S glycoprotein, HE is only minor a HA and the S glycoprotein mainly attaches to the cell surface. The HE protein of murine hepatitis virus (MHV), an enveloped CoV, binds to SA-4-acetylester or SA-9-O-acetylester of the carcinoembryonic antigen cell adhesion molecule 1a (CEACAM; known as CD66a) as the key receptor [53]. Murine CoVs HEs acquired by horizontal gene transfer, bind to C9-O-Ac Neu5Ac. However, some murine CoV HEs cannot bind to C4-O-Ac Neu5Ac. The original mouse MHV HE binds to C9-O-Ac Neu5Ac, while the MHV S-strain HE evolutionarily acquired the ability to bind to C4-O-Ac Neu5Ac [12,53,54]. In terms of structure, the C5 N- and C9 O-Ac Neu5Ac-accomodating hydrophobic pocket was shifted to a C5 N- and C4-O-Ac Neu5Ac-accomodating pocket [55].\nType I HE is specific for the 9-O-acetylated SAs (9-O-Ac-SAs). Type II HE is specific for 4-O-Ac-SAs. The SA-binding shift indicates quasi-synchronous adaptations of the SA-recognition sites of the lectin and esterase domains. Type I HE monomers of β-CoV lineage A have a bimodular enzyme–lectin domain similar to cellular glycan/carbohydrate-modifying proteins. Originally, HE homologs are found in various viruses including toroviruses and orthomyxoviruses such as the influenza virus C/D and isavirus, as well as the exceptional case of β-CoV lineage A among CoVs. The HE gene was transmitted to a β-CoV lineage A progenitor via horizontal gene transfer from a 9-O-Ac-Sia–recognizing HEF, as shown in influenza virus C/D. HE acquisition and expansion occurred by cross-species transmission over HE evolution and this phenomenon reflects viral evolutionary adaptation to host SA-containing glycans. Therefore, CoV HE receptor switching precedes virus evolution driven by SA-containing glycan diversity of hosts. For instance, the BcoV HE prefers 7,9-di-O-Ac-SAs, which is also a target of the bovine torovirus HE. For a more outstanding case, such a switching event occurred in the murine CoVs for the β-CoV lineage A type switch toward O-Ac-SA recognition. In the HE specificity of murine CoVs, two different murine CoV subtypes of virus group exist with one subtype possessing the typical 9-O-Ac-SA (type I) attachment factor and the other exclusively 4-O-Ac-SA (type II) attachment virus group [56].\nThe first coronaviral HE proteins identified were from the porcine hemagglutinating encephalomyelitis virus (PHEV), BCoV and HCoV-OC43, which bear SA-9-O-acetylesterases similar to HEF [8]. Rat CoV (RCoV) has SA-4-O-acetylesterases, converting Neu4,5Ac2 to Neu5Ac [53,57,58]. Some murine CoVs prefer 4-O-Ac-SAs and others 9-O-Ac-SAs. HCoV-OC43 and BCoV prefer α2-6-SA 9-O-acetylation by their SA-O-acetyleseterases. The S glycoproteins of BCoV and HCoV-OC43 are Neu5,9Ac2-recognizing lectins and agglutinate murine, rat and chicken erythrocytes due to the enriched 9-O-Ac-SA species [52]. BCoV and HCoV-OC43 adapted to SA receptor determinants of 9-O-Ac-SA receptors [59]. For a second receptor, the binding of S glycoprotein to Neu5,9Ac2 receptor is essential for entry into cells. BCoV-infection is prevented by prior treatment of cells with NA enzyme or with viral SA-O-acetylesterases, blocking the roles of HE and S glycoprotein in SA-dependent entry to host cells."}

LitCovid-sentences

2_test

LitCovid-PD-HP

{"project":"LitCovid-PD-HP","denotations":[{"id":"T9","span":{"begin":735,"end":744},"obj":"Phenotype"}],"attributes":[{"id":"A9","pred":"hp_id","subj":"T9","obj":"http://purl.obolibrary.org/obo/HP_0012115"}],"text":"5.2. Substrate Diversity of the CoV HEs\nHEs as envelope proteins are found in CoVs, orthomyxoviruses and toroviruses. Coronaviral HEs are involved in virus attachment to SA species. HE protein in β-CoVs binds to Neu5,9Ac2 form SA and agglutinates the red blood cells (RBCs) of rodents [52]. As with SA-O-acetylesterase, HE potentiates viral entry with the S protein and spreading via the mucosal glycans. It contains a carbohydrate-recognizing domain (CRD) known in lectin. The HE glycan-binding domain (GBD) mediates virus attachment to SAs on host cells. HE is the only HA. This indicates that compared to the S glycoprotein, HE is only minor a HA and the S glycoprotein mainly attaches to the cell surface. The HE protein of murine hepatitis virus (MHV), an enveloped CoV, binds to SA-4-acetylester or SA-9-O-acetylester of the carcinoembryonic antigen cell adhesion molecule 1a (CEACAM; known as CD66a) as the key receptor [53]. Murine CoVs HEs acquired by horizontal gene transfer, bind to C9-O-Ac Neu5Ac. However, some murine CoV HEs cannot bind to C4-O-Ac Neu5Ac. The original mouse MHV HE binds to C9-O-Ac Neu5Ac, while the MHV S-strain HE evolutionarily acquired the ability to bind to C4-O-Ac Neu5Ac [12,53,54]. In terms of structure, the C5 N- and C9 O-Ac Neu5Ac-accomodating hydrophobic pocket was shifted to a C5 N- and C4-O-Ac Neu5Ac-accomodating pocket [55].\nType I HE is specific for the 9-O-acetylated SAs (9-O-Ac-SAs). Type II HE is specific for 4-O-Ac-SAs. The SA-binding shift indicates quasi-synchronous adaptations of the SA-recognition sites of the lectin and esterase domains. Type I HE monomers of β-CoV lineage A have a bimodular enzyme–lectin domain similar to cellular glycan/carbohydrate-modifying proteins. Originally, HE homologs are found in various viruses including toroviruses and orthomyxoviruses such as the influenza virus C/D and isavirus, as well as the exceptional case of β-CoV lineage A among CoVs. The HE gene was transmitted to a β-CoV lineage A progenitor via horizontal gene transfer from a 9-O-Ac-Sia–recognizing HEF, as shown in influenza virus C/D. HE acquisition and expansion occurred by cross-species transmission over HE evolution and this phenomenon reflects viral evolutionary adaptation to host SA-containing glycans. Therefore, CoV HE receptor switching precedes virus evolution driven by SA-containing glycan diversity of hosts. For instance, the BcoV HE prefers 7,9-di-O-Ac-SAs, which is also a target of the bovine torovirus HE. For a more outstanding case, such a switching event occurred in the murine CoVs for the β-CoV lineage A type switch toward O-Ac-SA recognition. In the HE specificity of murine CoVs, two different murine CoV subtypes of virus group exist with one subtype possessing the typical 9-O-Ac-SA (type I) attachment factor and the other exclusively 4-O-Ac-SA (type II) attachment virus group [56].\nThe first coronaviral HE proteins identified were from the porcine hemagglutinating encephalomyelitis virus (PHEV), BCoV and HCoV-OC43, which bear SA-9-O-acetylesterases similar to HEF [8]. Rat CoV (RCoV) has SA-4-O-acetylesterases, converting Neu4,5Ac2 to Neu5Ac [53,57,58]. Some murine CoVs prefer 4-O-Ac-SAs and others 9-O-Ac-SAs. HCoV-OC43 and BCoV prefer α2-6-SA 9-O-acetylation by their SA-O-acetyleseterases. The S glycoproteins of BCoV and HCoV-OC43 are Neu5,9Ac2-recognizing lectins and agglutinate murine, rat and chicken erythrocytes due to the enriched 9-O-Ac-SA species [52]. BCoV and HCoV-OC43 adapted to SA receptor determinants of 9-O-Ac-SA receptors [59]. For a second receptor, the binding of S glycoprotein to Neu5,9Ac2 receptor is essential for entry into cells. BCoV-infection is prevented by prior treatment of cells with NA enzyme or with viral SA-O-acetylesterases, blocking the roles of HE and S glycoprotein in SA-dependent entry to host cells."}

PMC:7352545 / 28686-32535 JSONTXT

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PMC:7352545 / 28686-32535 JSON TXT