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LitCovid_Glycan-Motif-Structure

LitCovid-PD-FMA-UBERON

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T6","span":{"begin":2806,"end":2811},"obj":"Body_part"}],"attributes":[{"id":"A6","pred":"uberon_id","subj":"T6","obj":"http://purl.obolibrary.org/obo/UBERON_0000178"}],"text":"5. HE of CoVs\n\n5.1. Evolutionary Origin and Classification of the CoV HE\nCertain viruses use glycoproteins such as HA, HE, S and HEF for host receptor binding or destruction. Coronaviridae, Orthomyxoviridae, Paramyxoviridae and Adenoviridae utilize SAs as binding molecules for attachment and entry. However, only limited human pathogens recognize O-Ac SA.\n\n5.1.1. Influenza Virus A and B Spike Proteins of HA and NA\nInfluenza A and B viruses bear two spikes of receptor-binding HA and NA [45].\n\n5.1.2. Influenza C virus HA-HEF\nHEF is indeed an ancient type of SA-O-acetylesterase. In contrast to A/B, the influenza C virus bears one spike with triple functions of HEF as a homotrimer [46]. Each HEF subunit bears two Neu5,9Ac2-binding sites and binds to the 9-O-acetyl group. In parallel, another modification of O-acetylation is found. Indeed, influenza C virus bears SA-O-acetylesterase [47], which converts 5-N-acetyl-9-O-NeuAc (Neu5,9Ac2) to 5-Neu5Ac. The 9-O-acetyl SA is a unique determinant for the influenza C virus receptor and Neu5,9Ac2 is crucial for receptor activity, but not Neu5Gc or Neu5Ac [48]. Neu5,9Ac2 is an essential determinant for influenza virus C type-specific host cell tropism. NAs cleave the α-ketosidic linkages to the D-Gal or GalNAc. SA-O-acetylesterases cleave different O-acetyl linkages (Figure 5). The OH-group of Tyr224 and the guanidino group of Arg236 interact with the CH3CO-carbonyl oxygen [49]. HEF SA-O-acetylesterase is found in several enveloped (+) ssRNA viruses of influenza C virus and also in certain CoVs and toroviruses [47]. The CoVs are different from the orthomyxoviruses, which hold a segmented (−) ssRNA genome and are instead evolutionary linked to the family Coronaviridae, order Nidovirales [45].\n\n5.1.3. CoV SA-O-Acetylesterase HE\nCoVs and toroviruses of the Coronaviridae family are specific for the O-Ac SA receptors. Their S and HE glycoproteins are similar to influenza C virus HEF. CoVs and all toroviruses bear HE gene form class I envelope membrane proteins of about 400 amino acid residues which bear 7 to 12 N-glycosylation sites [50]. HE multimer forms enter virions. Bovine CoV (BCoV) and HCoV-OC43, similar to influenza C virus, recognize Neu5,9Ac2 and bear SA-9-O-acetylesterase [8]. CoV HEs are all O-acetylesterases. The HE enzymes found in torovirus, CoV and influenza C virus are evolutionarily interspecies-mutated with about 30% homology by heterologous RNA recombination [51] and horizontal gene transfer. Therefore, viral HEs are diverse and widespread over evolution.\n\n5.2. 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

LitCovid-PD-CLO

LitCovid-PD-CHEBI

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T46","span":{"begin":1063,"end":1080},"obj":"http://purl.obolibrary.org/obo/GO_0038024"},{"id":"T47","span":{"begin":1197,"end":1204},"obj":"http://purl.obolibrary.org/obo/GO_0009606"},{"id":"T48","span":{"begin":2077,"end":2092},"obj":"http://purl.obolibrary.org/obo/GO_0006487"},{"id":"T49","span":{"begin":2079,"end":2092},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T50","span":{"begin":3407,"end":3429},"obj":"http://purl.obolibrary.org/obo/GO_0098631"},{"id":"T51","span":{"begin":3407,"end":3420},"obj":"http://purl.obolibrary.org/obo/GO_0007155"},{"id":"T52","span":{"begin":6380,"end":6393},"obj":"http://purl.obolibrary.org/obo/GO_0044409"}],"text":"5. HE of CoVs\n\n5.1. Evolutionary Origin and Classification of the CoV HE\nCertain viruses use glycoproteins such as HA, HE, S and HEF for host receptor binding or destruction. Coronaviridae, Orthomyxoviridae, Paramyxoviridae and Adenoviridae utilize SAs as binding molecules for attachment and entry. However, only limited human pathogens recognize O-Ac SA.\n\n5.1.1. Influenza Virus A and B Spike Proteins of HA and NA\nInfluenza A and B viruses bear two spikes of receptor-binding HA and NA [45].\n\n5.1.2. Influenza C virus HA-HEF\nHEF is indeed an ancient type of SA-O-acetylesterase. In contrast to A/B, the influenza C virus bears one spike with triple functions of HEF as a homotrimer [46]. Each HEF subunit bears two Neu5,9Ac2-binding sites and binds to the 9-O-acetyl group. In parallel, another modification of O-acetylation is found. Indeed, influenza C virus bears SA-O-acetylesterase [47], which converts 5-N-acetyl-9-O-NeuAc (Neu5,9Ac2) to 5-Neu5Ac. The 9-O-acetyl SA is a unique determinant for the influenza C virus receptor and Neu5,9Ac2 is crucial for receptor activity, but not Neu5Gc or Neu5Ac [48]. Neu5,9Ac2 is an essential determinant for influenza virus C type-specific host cell tropism. NAs cleave the α-ketosidic linkages to the D-Gal or GalNAc. SA-O-acetylesterases cleave different O-acetyl linkages (Figure 5). The OH-group of Tyr224 and the guanidino group of Arg236 interact with the CH3CO-carbonyl oxygen [49]. HEF SA-O-acetylesterase is found in several enveloped (+) ssRNA viruses of influenza C virus and also in certain CoVs and toroviruses [47]. The CoVs are different from the orthomyxoviruses, which hold a segmented (−) ssRNA genome and are instead evolutionary linked to the family Coronaviridae, order Nidovirales [45].\n\n5.1.3. CoV SA-O-Acetylesterase HE\nCoVs and toroviruses of the Coronaviridae family are specific for the O-Ac SA receptors. Their S and HE glycoproteins are similar to influenza C virus HEF. CoVs and all toroviruses bear HE gene form class I envelope membrane proteins of about 400 amino acid residues which bear 7 to 12 N-glycosylation sites [50]. HE multimer forms enter virions. Bovine CoV (BCoV) and HCoV-OC43, similar to influenza C virus, recognize Neu5,9Ac2 and bear SA-9-O-acetylesterase [8]. CoV HEs are all O-acetylesterases. The HE enzymes found in torovirus, CoV and influenza C virus are evolutionarily interspecies-mutated with about 30% homology by heterologous RNA recombination [51] and horizontal gene transfer. Therefore, viral HEs are diverse and widespread over evolution.\n\n5.2. 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":3286,"end":3295},"obj":"Phenotype"}],"attributes":[{"id":"A9","pred":"hp_id","subj":"T9","obj":"http://purl.obolibrary.org/obo/HP_0012115"}],"text":"5. HE of CoVs\n\n5.1. Evolutionary Origin and Classification of the CoV HE\nCertain viruses use glycoproteins such as HA, HE, S and HEF for host receptor binding or destruction. Coronaviridae, Orthomyxoviridae, Paramyxoviridae and Adenoviridae utilize SAs as binding molecules for attachment and entry. However, only limited human pathogens recognize O-Ac SA.\n\n5.1.1. Influenza Virus A and B Spike Proteins of HA and NA\nInfluenza A and B viruses bear two spikes of receptor-binding HA and NA [45].\n\n5.1.2. Influenza C virus HA-HEF\nHEF is indeed an ancient type of SA-O-acetylesterase. In contrast to A/B, the influenza C virus bears one spike with triple functions of HEF as a homotrimer [46]. Each HEF subunit bears two Neu5,9Ac2-binding sites and binds to the 9-O-acetyl group. In parallel, another modification of O-acetylation is found. Indeed, influenza C virus bears SA-O-acetylesterase [47], which converts 5-N-acetyl-9-O-NeuAc (Neu5,9Ac2) to 5-Neu5Ac. The 9-O-acetyl SA is a unique determinant for the influenza C virus receptor and Neu5,9Ac2 is crucial for receptor activity, but not Neu5Gc or Neu5Ac [48]. Neu5,9Ac2 is an essential determinant for influenza virus C type-specific host cell tropism. NAs cleave the α-ketosidic linkages to the D-Gal or GalNAc. SA-O-acetylesterases cleave different O-acetyl linkages (Figure 5). The OH-group of Tyr224 and the guanidino group of Arg236 interact with the CH3CO-carbonyl oxygen [49]. HEF SA-O-acetylesterase is found in several enveloped (+) ssRNA viruses of influenza C virus and also in certain CoVs and toroviruses [47]. The CoVs are different from the orthomyxoviruses, which hold a segmented (−) ssRNA genome and are instead evolutionary linked to the family Coronaviridae, order Nidovirales [45].\n\n5.1.3. CoV SA-O-Acetylesterase HE\nCoVs and toroviruses of the Coronaviridae family are specific for the O-Ac SA receptors. Their S and HE glycoproteins are similar to influenza C virus HEF. CoVs and all toroviruses bear HE gene form class I envelope membrane proteins of about 400 amino acid residues which bear 7 to 12 N-glycosylation sites [50]. HE multimer forms enter virions. Bovine CoV (BCoV) and HCoV-OC43, similar to influenza C virus, recognize Neu5,9Ac2 and bear SA-9-O-acetylesterase [8]. CoV HEs are all O-acetylesterases. The HE enzymes found in torovirus, CoV and influenza C virus are evolutionarily interspecies-mutated with about 30% homology by heterologous RNA recombination [51] and horizontal gene transfer. Therefore, viral HEs are diverse and widespread over evolution.\n\n5.2. 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 / 26135-32535 JSONTXT

Annnotations TAB JSON ListView MergeView

PMC:7352545 / 26135-32535 JSON TXT