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LitCovid_Glycan-Motif-Structure

LitCovid-PD-FMA-UBERON

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T7","span":{"begin":1637,"end":1642},"obj":"Body_part"},{"id":"T8","span":{"begin":4458,"end":4465},"obj":"Body_part"},{"id":"T9","span":{"begin":4466,"end":4472},"obj":"Body_part"},{"id":"T10","span":{"begin":4772,"end":4778},"obj":"Body_part"},{"id":"T11","span":{"begin":4972,"end":4976},"obj":"Body_part"}],"attributes":[{"id":"A7","pred":"uberon_id","subj":"T7","obj":"http://purl.obolibrary.org/obo/UBERON_0000912"},{"id":"A8","pred":"uberon_id","subj":"T8","obj":"http://purl.obolibrary.org/obo/UBERON_0003126"},{"id":"A9","pred":"uberon_id","subj":"T9","obj":"http://purl.obolibrary.org/obo/UBERON_0000479"},{"id":"A10","pred":"uberon_id","subj":"T10","obj":"http://purl.obolibrary.org/obo/UBERON_0002113"},{"id":"A11","pred":"uberon_id","subj":"T11","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"}],"text":"6.1. CoVs Utilize SAs and SA Linkages as Attachment and Entry Sites to Human Host Cells\nSeveral β-CoV genera such as BCoV bind to O-acetylated SAs and bear an acetylesterase enzyme to act as a host cell RDE. Certain α-CoV and γ-CoV are deficient for the comparable acetylesterase enzyme but have a preference to NeuAc or NeuGc type SA species. Infectious bronchitis virus (IBV) and transmissible gastroenteritis virus are such examples. Additionally, both α-CoV and γ-CoV also include sub-members deficient of any SA-recognizing activity. During evolution, some subtypes of SARS-CoV and HCoV-229E acquired SA-binding capacity. The SA-binding activities of BCoV, transmissible gastroenteritis coronavirus (TGEV) and IBV are well known [60].\n\n6.1.1. α-Coronavirus\nIn α-CoVs such as TGEV, HA-activity is attributed to the SA-recognizing activity to α2,3-NeuGc [61,62]. The SA-binding site is present on the N-terminal region of the S-glycoprotein of TGEV. TGEV has two types with enteric and respiratory tropism. The respiratory TGEV has the porcine aminopeptidase N (pAPN)-binding domain and SA-binding domain. Nucleotide 655 of the S gene is essential for enteric tropism and the S219A mutation of the S glycoprotein confers the enteric to respiratory tropism shift. In addition, a 6-nucleotide insertional mutation at nucleotide 1124, which yields the Y374-T375insND shift of the S glycoprotein, causes enhanced enteric tract tropism. TGEV interacts with SA species on mucin-like glycoprotein (MGP), a highly glycosylated protein, in an SA-dependent manner, on mucin-secreting goblet cells [6]. MGP SA-binding allows virus entry via the mucus layer to the intestinal enterocytes. Different from TGEV, the S glycoprotein of porcine CoV has no hemagglutination activity due to deletion of the SA-binding site of the S glycoprotein [61]. The loss of SA-binding activity is correlated to the non-enteropathogenicity. SAs function as HA-mediated entry determinants for TGEV, causing the enteropathogenic outcome of the virus, and SA-recognition activity is also responsible for virus amplification in cells. SA-binding activity-deficient TGEV can propagate in cells through pAPN, known as CD13, as a receptor [62,63]. The SA-binding activity potentiates infection and is crucial for intestinal infection.\n\n6.1.2. β-Coronavirus\nIn β-CoV, HE mediates viral attachment to O-Ac-SAs and its function relies on the combined CBD and RDE domains. Most β-CoVs target 9-O-Ac-SAs (type I), but certain strains switched to alternatively targeting 4-O-Ac-SAs (type II). For example, the SA-acetylesterase enzyme in BCoVs and HCoV-OC43 is known to have hemagglutinizing activities as a type of SA-9-O-acetylesterase [8]. The SA-acetylesterase is the HE surface glycoprotein in BCoV. The three-dimensional structure of BCoV HE is similar to other viral esterases [9]. The HE gene is found only in the β-CoV genus. The acetylesterase of murine CoVs differs in its substrate binding specificity from that of BCoV and HCoV-OC43, which is specific for O-acetyl residue release from SA C-9. Murine CoVs prefer to esterize 4-O-acetyl-NeuAc [64]. The β-CoV acetylesterase destroys the receptors and this specificity is similar to that of influenza viruses. Acetylesterase activity can be inhibited by diisopropyl fluorophosphate and this agent decreases viral infection levels [65]. As deduced from the SA acetylesterase of HCoV-OC43 [8], the 9-O-Ac-SA species is a receptor binding determinant for erythrocytes and entry into cells [59]. The BCoV HE protein has dual activity of acetylesterase and HA [9]. BCoV widely agglutinates erythrocytes and purified HE only agglutinates Neu5,9Ac2-enriched erythrocytes of rats and mice. BCoV and HCoV-OC43 can agglutinate chicken erythrocytes, while purified HE cannot. In contrast to the HE protein, purified S glycoprotein can agglutinate chicken erythrocytes [52], indicating that the major HA is the S protein which acts as the major SA-binding protein. However, the role of O-Ac-SAs is not certain to be essential in receptors, and SA-binding activity may be essential only to the HE protein, but not to the S glycoprotein [54].\n\n6.1.3. γ-Coronavirus\nIn γ-CoVs, IBV strains, known as poultry respiratory infectious pathogens, can agglutinate erythrocytes. IBV prefers to recognize α2,3-NeuAc and the SA functions as a host entry receptor for infection [66]. Glycosylation of IBV M41 S1 protein RBD is crucial for interaction with chicken trachea tissue and RBD N-glycosylation confers receptor specificity and enables virus replication. The heavy glycosylated M41 RBD has 10 glycosylation sites. N-glycosylation of IBV determines receptor specificity. However, the host receptor has not yet been found. NA treatment reduces the binding of soluble S to kidney and tracheal epithelial cells. The IBV S protein recognizes epithelial cells in a SA-dependent manner. The SA-binding ability of IBV is necessary for infection of tracheal epithelial cells and lung respiratory epithelial cells [67]. The SA-binding site is located on S1 of the IBV S protein, although the IBV-specific protein receptor is not known. In contrast to BCoV or HCoV-OC43, IBV lacks an RDE. SA binding of IBV is likely more essential than in other viruses such as TGEV.\n\n6.1.4. Torovirus\nIn torovirus, which belongs to the family Coronaviridae, the toroviruses are grouped into the Torovirinae subfamily and the Torovirus genus. The known toroviruses can infect four species of hosts, constituting bovine, equine, porcine and human toroviruses. They mildly infect swine and cattle through the HE protein, which is similar to the β-CoV HE protein [68]. The HE protein is a class I membrane glycoprotein which forms homodimers with a MW of 65 kDa. The RDE protein HE reversibly binds to glycans [15] through binding to SAs. The acetyl-esterase activity disrupts SA binding. HE hemagglutinates mouse erythrocytes and cleaves the acetyl-ester linkage of glycans and acetylated synthetic substrate p-nitrophenyl acetate (pNPA) [69]. Similar to CoV, torovirus HE is an acetylesterase type, which cleaves the O-acetyl group from the SA C-9 position using Neu5,9Ac2 and N-acetyl-7(8),9-O-NeuAc [64]. However, torovirus HE exhibits a restricted specificity for the Neu5,9Ac2 substrate, but not for the Neu5,7(8),9Ac3 substrate, with a unique SA-binding site generated by a single amino acid difference in porcine Thr73 and bovine Ser64 for each HE [70]."}

LitCovid-PD-MONDO

LitCovid-PD-CLO

LitCovid-PD-CHEBI

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T53","span":{"begin":1001,"end":1008},"obj":"http://purl.obolibrary.org/obo/GO_0009606"},{"id":"T54","span":{"begin":1163,"end":1170},"obj":"http://purl.obolibrary.org/obo/GO_0009606"},{"id":"T55","span":{"begin":1251,"end":1258},"obj":"http://purl.obolibrary.org/obo/GO_0009606"},{"id":"T56","span":{"begin":1426,"end":1433},"obj":"http://purl.obolibrary.org/obo/GO_0009606"},{"id":"T57","span":{"begin":3327,"end":3342},"obj":"http://purl.obolibrary.org/obo/GO_0016032"},{"id":"T58","span":{"begin":4378,"end":4391},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T59","span":{"begin":4481,"end":4496},"obj":"http://purl.obolibrary.org/obo/GO_0006487"},{"id":"T60","span":{"begin":4483,"end":4496},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T61","span":{"begin":4595,"end":4608},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T62","span":{"begin":4616,"end":4631},"obj":"http://purl.obolibrary.org/obo/GO_0006487"},{"id":"T63","span":{"begin":4618,"end":4631},"obj":"http://purl.obolibrary.org/obo/GO_0070085"}],"text":"6.1. CoVs Utilize SAs and SA Linkages as Attachment and Entry Sites to Human Host Cells\nSeveral β-CoV genera such as BCoV bind to O-acetylated SAs and bear an acetylesterase enzyme to act as a host cell RDE. Certain α-CoV and γ-CoV are deficient for the comparable acetylesterase enzyme but have a preference to NeuAc or NeuGc type SA species. Infectious bronchitis virus (IBV) and transmissible gastroenteritis virus are such examples. Additionally, both α-CoV and γ-CoV also include sub-members deficient of any SA-recognizing activity. During evolution, some subtypes of SARS-CoV and HCoV-229E acquired SA-binding capacity. The SA-binding activities of BCoV, transmissible gastroenteritis coronavirus (TGEV) and IBV are well known [60].\n\n6.1.1. α-Coronavirus\nIn α-CoVs such as TGEV, HA-activity is attributed to the SA-recognizing activity to α2,3-NeuGc [61,62]. The SA-binding site is present on the N-terminal region of the S-glycoprotein of TGEV. TGEV has two types with enteric and respiratory tropism. The respiratory TGEV has the porcine aminopeptidase N (pAPN)-binding domain and SA-binding domain. Nucleotide 655 of the S gene is essential for enteric tropism and the S219A mutation of the S glycoprotein confers the enteric to respiratory tropism shift. In addition, a 6-nucleotide insertional mutation at nucleotide 1124, which yields the Y374-T375insND shift of the S glycoprotein, causes enhanced enteric tract tropism. TGEV interacts with SA species on mucin-like glycoprotein (MGP), a highly glycosylated protein, in an SA-dependent manner, on mucin-secreting goblet cells [6]. MGP SA-binding allows virus entry via the mucus layer to the intestinal enterocytes. Different from TGEV, the S glycoprotein of porcine CoV has no hemagglutination activity due to deletion of the SA-binding site of the S glycoprotein [61]. The loss of SA-binding activity is correlated to the non-enteropathogenicity. SAs function as HA-mediated entry determinants for TGEV, causing the enteropathogenic outcome of the virus, and SA-recognition activity is also responsible for virus amplification in cells. SA-binding activity-deficient TGEV can propagate in cells through pAPN, known as CD13, as a receptor [62,63]. The SA-binding activity potentiates infection and is crucial for intestinal infection.\n\n6.1.2. β-Coronavirus\nIn β-CoV, HE mediates viral attachment to O-Ac-SAs and its function relies on the combined CBD and RDE domains. Most β-CoVs target 9-O-Ac-SAs (type I), but certain strains switched to alternatively targeting 4-O-Ac-SAs (type II). For example, the SA-acetylesterase enzyme in BCoVs and HCoV-OC43 is known to have hemagglutinizing activities as a type of SA-9-O-acetylesterase [8]. The SA-acetylesterase is the HE surface glycoprotein in BCoV. The three-dimensional structure of BCoV HE is similar to other viral esterases [9]. The HE gene is found only in the β-CoV genus. The acetylesterase of murine CoVs differs in its substrate binding specificity from that of BCoV and HCoV-OC43, which is specific for O-acetyl residue release from SA C-9. Murine CoVs prefer to esterize 4-O-acetyl-NeuAc [64]. The β-CoV acetylesterase destroys the receptors and this specificity is similar to that of influenza viruses. Acetylesterase activity can be inhibited by diisopropyl fluorophosphate and this agent decreases viral infection levels [65]. As deduced from the SA acetylesterase of HCoV-OC43 [8], the 9-O-Ac-SA species is a receptor binding determinant for erythrocytes and entry into cells [59]. The BCoV HE protein has dual activity of acetylesterase and HA [9]. BCoV widely agglutinates erythrocytes and purified HE only agglutinates Neu5,9Ac2-enriched erythrocytes of rats and mice. BCoV and HCoV-OC43 can agglutinate chicken erythrocytes, while purified HE cannot. In contrast to the HE protein, purified S glycoprotein can agglutinate chicken erythrocytes [52], indicating that the major HA is the S protein which acts as the major SA-binding protein. However, the role of O-Ac-SAs is not certain to be essential in receptors, and SA-binding activity may be essential only to the HE protein, but not to the S glycoprotein [54].\n\n6.1.3. γ-Coronavirus\nIn γ-CoVs, IBV strains, known as poultry respiratory infectious pathogens, can agglutinate erythrocytes. IBV prefers to recognize α2,3-NeuAc and the SA functions as a host entry receptor for infection [66]. Glycosylation of IBV M41 S1 protein RBD is crucial for interaction with chicken trachea tissue and RBD N-glycosylation confers receptor specificity and enables virus replication. The heavy glycosylated M41 RBD has 10 glycosylation sites. N-glycosylation of IBV determines receptor specificity. However, the host receptor has not yet been found. NA treatment reduces the binding of soluble S to kidney and tracheal epithelial cells. The IBV S protein recognizes epithelial cells in a SA-dependent manner. The SA-binding ability of IBV is necessary for infection of tracheal epithelial cells and lung respiratory epithelial cells [67]. The SA-binding site is located on S1 of the IBV S protein, although the IBV-specific protein receptor is not known. In contrast to BCoV or HCoV-OC43, IBV lacks an RDE. SA binding of IBV is likely more essential than in other viruses such as TGEV.\n\n6.1.4. Torovirus\nIn torovirus, which belongs to the family Coronaviridae, the toroviruses are grouped into the Torovirinae subfamily and the Torovirus genus. The known toroviruses can infect four species of hosts, constituting bovine, equine, porcine and human toroviruses. They mildly infect swine and cattle through the HE protein, which is similar to the β-CoV HE protein [68]. The HE protein is a class I membrane glycoprotein which forms homodimers with a MW of 65 kDa. The RDE protein HE reversibly binds to glycans [15] through binding to SAs. The acetyl-esterase activity disrupts SA binding. HE hemagglutinates mouse erythrocytes and cleaves the acetyl-ester linkage of glycans and acetylated synthetic substrate p-nitrophenyl acetate (pNPA) [69]. Similar to CoV, torovirus HE is an acetylesterase type, which cleaves the O-acetyl group from the SA C-9 position using Neu5,9Ac2 and N-acetyl-7(8),9-O-NeuAc [64]. However, torovirus HE exhibits a restricted specificity for the Neu5,9Ac2 substrate, but not for the Neu5,7(8),9Ac3 substrate, with a unique SA-binding site generated by a single amino acid difference in porcine Thr73 and bovine Ser64 for each HE [70]."}

LitCovid-sentences

2_test

LitCovid-PD-HP

{"project":"LitCovid-PD-HP","denotations":[{"id":"T10","span":{"begin":355,"end":365},"obj":"Phenotype"}],"attributes":[{"id":"A10","pred":"hp_id","subj":"T10","obj":"http://purl.obolibrary.org/obo/HP_0012387"}],"text":"6.1. CoVs Utilize SAs and SA Linkages as Attachment and Entry Sites to Human Host Cells\nSeveral β-CoV genera such as BCoV bind to O-acetylated SAs and bear an acetylesterase enzyme to act as a host cell RDE. Certain α-CoV and γ-CoV are deficient for the comparable acetylesterase enzyme but have a preference to NeuAc or NeuGc type SA species. Infectious bronchitis virus (IBV) and transmissible gastroenteritis virus are such examples. Additionally, both α-CoV and γ-CoV also include sub-members deficient of any SA-recognizing activity. During evolution, some subtypes of SARS-CoV and HCoV-229E acquired SA-binding capacity. The SA-binding activities of BCoV, transmissible gastroenteritis coronavirus (TGEV) and IBV are well known [60].\n\n6.1.1. α-Coronavirus\nIn α-CoVs such as TGEV, HA-activity is attributed to the SA-recognizing activity to α2,3-NeuGc [61,62]. The SA-binding site is present on the N-terminal region of the S-glycoprotein of TGEV. TGEV has two types with enteric and respiratory tropism. The respiratory TGEV has the porcine aminopeptidase N (pAPN)-binding domain and SA-binding domain. Nucleotide 655 of the S gene is essential for enteric tropism and the S219A mutation of the S glycoprotein confers the enteric to respiratory tropism shift. In addition, a 6-nucleotide insertional mutation at nucleotide 1124, which yields the Y374-T375insND shift of the S glycoprotein, causes enhanced enteric tract tropism. TGEV interacts with SA species on mucin-like glycoprotein (MGP), a highly glycosylated protein, in an SA-dependent manner, on mucin-secreting goblet cells [6]. MGP SA-binding allows virus entry via the mucus layer to the intestinal enterocytes. Different from TGEV, the S glycoprotein of porcine CoV has no hemagglutination activity due to deletion of the SA-binding site of the S glycoprotein [61]. The loss of SA-binding activity is correlated to the non-enteropathogenicity. SAs function as HA-mediated entry determinants for TGEV, causing the enteropathogenic outcome of the virus, and SA-recognition activity is also responsible for virus amplification in cells. SA-binding activity-deficient TGEV can propagate in cells through pAPN, known as CD13, as a receptor [62,63]. The SA-binding activity potentiates infection and is crucial for intestinal infection.\n\n6.1.2. β-Coronavirus\nIn β-CoV, HE mediates viral attachment to O-Ac-SAs and its function relies on the combined CBD and RDE domains. Most β-CoVs target 9-O-Ac-SAs (type I), but certain strains switched to alternatively targeting 4-O-Ac-SAs (type II). For example, the SA-acetylesterase enzyme in BCoVs and HCoV-OC43 is known to have hemagglutinizing activities as a type of SA-9-O-acetylesterase [8]. The SA-acetylesterase is the HE surface glycoprotein in BCoV. The three-dimensional structure of BCoV HE is similar to other viral esterases [9]. The HE gene is found only in the β-CoV genus. The acetylesterase of murine CoVs differs in its substrate binding specificity from that of BCoV and HCoV-OC43, which is specific for O-acetyl residue release from SA C-9. Murine CoVs prefer to esterize 4-O-acetyl-NeuAc [64]. The β-CoV acetylesterase destroys the receptors and this specificity is similar to that of influenza viruses. Acetylesterase activity can be inhibited by diisopropyl fluorophosphate and this agent decreases viral infection levels [65]. As deduced from the SA acetylesterase of HCoV-OC43 [8], the 9-O-Ac-SA species is a receptor binding determinant for erythrocytes and entry into cells [59]. The BCoV HE protein has dual activity of acetylesterase and HA [9]. BCoV widely agglutinates erythrocytes and purified HE only agglutinates Neu5,9Ac2-enriched erythrocytes of rats and mice. BCoV and HCoV-OC43 can agglutinate chicken erythrocytes, while purified HE cannot. In contrast to the HE protein, purified S glycoprotein can agglutinate chicken erythrocytes [52], indicating that the major HA is the S protein which acts as the major SA-binding protein. However, the role of O-Ac-SAs is not certain to be essential in receptors, and SA-binding activity may be essential only to the HE protein, but not to the S glycoprotein [54].\n\n6.1.3. γ-Coronavirus\nIn γ-CoVs, IBV strains, known as poultry respiratory infectious pathogens, can agglutinate erythrocytes. IBV prefers to recognize α2,3-NeuAc and the SA functions as a host entry receptor for infection [66]. Glycosylation of IBV M41 S1 protein RBD is crucial for interaction with chicken trachea tissue and RBD N-glycosylation confers receptor specificity and enables virus replication. The heavy glycosylated M41 RBD has 10 glycosylation sites. N-glycosylation of IBV determines receptor specificity. However, the host receptor has not yet been found. NA treatment reduces the binding of soluble S to kidney and tracheal epithelial cells. The IBV S protein recognizes epithelial cells in a SA-dependent manner. The SA-binding ability of IBV is necessary for infection of tracheal epithelial cells and lung respiratory epithelial cells [67]. The SA-binding site is located on S1 of the IBV S protein, although the IBV-specific protein receptor is not known. In contrast to BCoV or HCoV-OC43, IBV lacks an RDE. SA binding of IBV is likely more essential than in other viruses such as TGEV.\n\n6.1.4. Torovirus\nIn torovirus, which belongs to the family Coronaviridae, the toroviruses are grouped into the Torovirinae subfamily and the Torovirus genus. The known toroviruses can infect four species of hosts, constituting bovine, equine, porcine and human toroviruses. They mildly infect swine and cattle through the HE protein, which is similar to the β-CoV HE protein [68]. The HE protein is a class I membrane glycoprotein which forms homodimers with a MW of 65 kDa. The RDE protein HE reversibly binds to glycans [15] through binding to SAs. The acetyl-esterase activity disrupts SA binding. HE hemagglutinates mouse erythrocytes and cleaves the acetyl-ester linkage of glycans and acetylated synthetic substrate p-nitrophenyl acetate (pNPA) [69]. Similar to CoV, torovirus HE is an acetylesterase type, which cleaves the O-acetyl group from the SA C-9 position using Neu5,9Ac2 and N-acetyl-7(8),9-O-NeuAc [64]. However, torovirus HE exhibits a restricted specificity for the Neu5,9Ac2 substrate, but not for the Neu5,7(8),9Ac3 substrate, with a unique SA-binding site generated by a single amino acid difference in porcine Thr73 and bovine Ser64 for each HE [70]."}

PMC:7352545 / 32571-39004 JSONTXT

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PMC:7352545 / 32571-39004 JSON TXT