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LitCovid-PD-FMA-UBERON

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T4","span":{"begin":1788,"end":1794},"obj":"Body_part"}],"attributes":[{"id":"A4","pred":"uberon_id","subj":"T4","obj":"http://purl.obolibrary.org/obo/UBERON_0002389"}],"text":"CoVs, like other positive-stranded RNA viruses, induce membranous rearrangements of varying morphologies that are essential for RTCs anchoring [82,83]. The CoV-induced replicative structures consist of double-membrane vesicles (DMVs) and convoluted membranes (CMs), which form a large reticulovesicular network that are critical for viral replication and transcription [84,85,86,87,88,89,90,91,92,93]. Among the CoV nsps, nsp3, nsp4, and nsp6 include the hydrophobic transmembrane domains engaging in anchoring the viral RNA synthesis components to the membranes [94]. For MERS-CoV and SARS-CoV, co-expression of nsp3 and nsp4 is required to induce DMVs [95]. SARS-CoV nsp6 has membrane proliferation ability as well, which also contributes to DMVs formation [96]. The structure and functions of α-CoV nsp3 are largely unknown [97]. Nsp4 is also a marker for CoV-induced membrane structures; some results indicate that the nsp4–10 of pp1a act as a large complex through multidomain structure or scaffold during viral RNA replication progress, before its cleavage into individual products [98]. CoVs nsp5 encodes a 3C-like proteinase (3CLpro). The polyproteins pp1a and pp1ab are processed into individual elements of replicase by 3C-like protease and PLPs [99]. Moreover, PEDV nsp5 plays a crucial role in virus replication and also blocks host innate immune responses [100]. Crystallographic or nuclear magnetic resonance structures have shown that nsp3, nsp5, nsp7, nsp8, nsp9, and nsp10 have the PLprob and the ADP-ribose 1′′-phosphatase (ADRP) activity [101,102,103,104,105,106,107]. The crystal structure of SARS-CoV nsp9 suggests that nsp9 is dimeric and it is able to bind to single-stranded RNA [108]. The crystal structure of SARS CoV nsp10 protein suggests that nsp10 is a zinc-finger protein, which is existent exclusively in CoVs so far [107]. Moreover, nsp7–10 have RNA binding activity and nsp12 encodes a single RNA-dependent RNA polymerase (RdRp). The biochemical characterization and crystallization of SARS CoV nsp7 and nsp8 manifests that eight copies of nsp8 and eight copies of nsp7 form a supercomplex [106]. The complex is supportive for nucleic acid binding and may be associated with the processivity of viral RdRp [102,106]. Recently, structural studies have described that the SARS-CoV nsp12 polymerase binds to the nsp7 and nsp8 complex [109] that may increase the polymerase activity of nsp12 RdRp [110]. CoV nsp13, a NTPase/helicase, is also determined to play essential roles in viral replication [111]. CoV nsp14 is a multifunctional protein with 3′-5′ exoribonuclease activity and N-7-methyltransferase [MTase] activity [112,113]. Nsp14 catalyzes the N7-methylation of Gppp-RNA to form a cap-0 structure. CoV nsp15 encodes an endoribonuclease (EndoU), performing functions through a hexamer in many CoVs [114,115,116]. The endoribonuclease activity of nsp15 is not essential for CoV replication [117,118]. For CoVs, the 5′ end of the viral genomic RNA and subgenomic mRNA (sgmRNA) is supposed to have cap structures: an N-7 methylated guanosine nucleoside (m7GpppN) (cap 0) and a methyl group at the 2′-O-ribose position (cap 1) of the first nucleotide [119]. These cap structures enhance the initiation of translation of viral proteins, protect viral mRNAs against cellular 5′-3′-exoribonuclease and limit the recognition of viral RNA by host innate system [120,121]. Nsp13 is proposed to catalyze the first step of the 5′-capping reaction of viral RNAs [122]. The methylation of the two sites in the 5′ cap are catalyzed by three nsps; nsp14 (the N-7-MTase), nsp16 (the 2′-O-methyltransferase), and nsp10 [112,123,124,125,126]. In addition, the 3′-5′ exoribonuclease activity of nsp14 is involved in a replicative mismatch repair system during RNA synthesis, which improves the replication fidelity of CoV [42]. Although these nsps have been demonstrated to play essential roles in viral replication, transcription and/or post-translational polyprotein processing [127], the nsp12–16 of PEDV and other CoVs are poorly characterized to date, except for SARS-CoV."}

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T43","span":{"begin":586,"end":594},"obj":"Disease"},{"id":"T44","span":{"begin":660,"end":668},"obj":"Disease"},{"id":"T45","span":{"begin":1613,"end":1621},"obj":"Disease"},{"id":"T46","span":{"begin":1735,"end":1739},"obj":"Disease"},{"id":"T47","span":{"begin":2020,"end":2024},"obj":"Disease"},{"id":"T48","span":{"begin":2304,"end":2312},"obj":"Disease"},{"id":"T49","span":{"begin":4087,"end":4095},"obj":"Disease"}],"attributes":[{"id":"A43","pred":"mondo_id","subj":"T43","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A44","pred":"mondo_id","subj":"T44","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A45","pred":"mondo_id","subj":"T45","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A46","pred":"mondo_id","subj":"T46","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A47","pred":"mondo_id","subj":"T47","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A48","pred":"mondo_id","subj":"T48","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A49","pred":"mondo_id","subj":"T49","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"CoVs, like other positive-stranded RNA viruses, induce membranous rearrangements of varying morphologies that are essential for RTCs anchoring [82,83]. The CoV-induced replicative structures consist of double-membrane vesicles (DMVs) and convoluted membranes (CMs), which form a large reticulovesicular network that are critical for viral replication and transcription [84,85,86,87,88,89,90,91,92,93]. Among the CoV nsps, nsp3, nsp4, and nsp6 include the hydrophobic transmembrane domains engaging in anchoring the viral RNA synthesis components to the membranes [94]. For MERS-CoV and SARS-CoV, co-expression of nsp3 and nsp4 is required to induce DMVs [95]. SARS-CoV nsp6 has membrane proliferation ability as well, which also contributes to DMVs formation [96]. The structure and functions of α-CoV nsp3 are largely unknown [97]. Nsp4 is also a marker for CoV-induced membrane structures; some results indicate that the nsp4–10 of pp1a act as a large complex through multidomain structure or scaffold during viral RNA replication progress, before its cleavage into individual products [98]. CoVs nsp5 encodes a 3C-like proteinase (3CLpro). The polyproteins pp1a and pp1ab are processed into individual elements of replicase by 3C-like protease and PLPs [99]. Moreover, PEDV nsp5 plays a crucial role in virus replication and also blocks host innate immune responses [100]. Crystallographic or nuclear magnetic resonance structures have shown that nsp3, nsp5, nsp7, nsp8, nsp9, and nsp10 have the PLprob and the ADP-ribose 1′′-phosphatase (ADRP) activity [101,102,103,104,105,106,107]. The crystal structure of SARS-CoV nsp9 suggests that nsp9 is dimeric and it is able to bind to single-stranded RNA [108]. The crystal structure of SARS CoV nsp10 protein suggests that nsp10 is a zinc-finger protein, which is existent exclusively in CoVs so far [107]. Moreover, nsp7–10 have RNA binding activity and nsp12 encodes a single RNA-dependent RNA polymerase (RdRp). The biochemical characterization and crystallization of SARS CoV nsp7 and nsp8 manifests that eight copies of nsp8 and eight copies of nsp7 form a supercomplex [106]. The complex is supportive for nucleic acid binding and may be associated with the processivity of viral RdRp [102,106]. Recently, structural studies have described that the SARS-CoV nsp12 polymerase binds to the nsp7 and nsp8 complex [109] that may increase the polymerase activity of nsp12 RdRp [110]. CoV nsp13, a NTPase/helicase, is also determined to play essential roles in viral replication [111]. CoV nsp14 is a multifunctional protein with 3′-5′ exoribonuclease activity and N-7-methyltransferase [MTase] activity [112,113]. Nsp14 catalyzes the N7-methylation of Gppp-RNA to form a cap-0 structure. CoV nsp15 encodes an endoribonuclease (EndoU), performing functions through a hexamer in many CoVs [114,115,116]. The endoribonuclease activity of nsp15 is not essential for CoV replication [117,118]. For CoVs, the 5′ end of the viral genomic RNA and subgenomic mRNA (sgmRNA) is supposed to have cap structures: an N-7 methylated guanosine nucleoside (m7GpppN) (cap 0) and a methyl group at the 2′-O-ribose position (cap 1) of the first nucleotide [119]. These cap structures enhance the initiation of translation of viral proteins, protect viral mRNAs against cellular 5′-3′-exoribonuclease and limit the recognition of viral RNA by host innate system [120,121]. Nsp13 is proposed to catalyze the first step of the 5′-capping reaction of viral RNAs [122]. The methylation of the two sites in the 5′ cap are catalyzed by three nsps; nsp14 (the N-7-MTase), nsp16 (the 2′-O-methyltransferase), and nsp10 [112,123,124,125,126]. In addition, the 3′-5′ exoribonuclease activity of nsp14 is involved in a replicative mismatch repair system during RNA synthesis, which improves the replication fidelity of CoV [42]. Although these nsps have been demonstrated to play essential roles in viral replication, transcription and/or post-translational polyprotein processing [127], the nsp12–16 of PEDV and other CoVs are poorly characterized to date, except for SARS-CoV."}

LitCovid-PD-CLO

LitCovid-PD-CHEBI

LitCovid-PD-GO-BP

LitCovid-sentences

2_test

LitCovid-PubTator

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