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bionlp-st-ge-2016-reference

bionlp-st-ge-2016-reference-tees

events-check-again

bionlp-st-ge-2016-coref

{"project":"bionlp-st-ge-2016-coref","denotations":[{"id":"T8182","span":{"begin":1232,"end":1239},"obj":"Anaphor"},{"id":"T8183","span":{"begin":1124,"end":1128},"obj":"Antecedent"},{"id":"T8184","span":{"begin":4745,"end":4759},"obj":"Anaphor"},{"id":"T8185","span":{"begin":4558,"end":4563},"obj":"Antecedent"},{"id":"T8186","span":{"begin":4565,"end":4570},"obj":"Antecedent"},{"id":"T8187","span":{"begin":4576,"end":4581},"obj":"Antecedent"},{"id":"T8188","span":{"begin":6805,"end":6815},"obj":"Anaphor"},{"id":"T8189","span":{"begin":6757,"end":6768},"obj":"Antecedent"}],"relations":[{"id":"R6476","pred":"boundBy","subj":"T8182","obj":"T8183"},{"id":"R6478","pred":"boundBy","subj":"T8184","obj":"T8185"},{"id":"R6479","pred":"boundBy","subj":"T8184","obj":"T8186"},{"id":"R6480","pred":"boundBy","subj":"T8184","obj":"T8187"},{"id":"R6482","pred":"boundBy","subj":"T8188","obj":"T8189"}],"namespaces":[{"prefix":"_base","uri":"https://bionlp.dbcls.jp/ontology/ge.owl#"}],"text":"HOIP is necessary for association of the IKK complex with CD40\nThe marked defects in CD40-mediated cell activation and signaling displayed by HOIP-deficient cells suggested that HOIP mediates recruitment of critical components of the CD40 signaling apparatus to the receptor. Previously, we demonstrated that HOIP is recruited to the CD40 signaling complex in a TRAF2-dependent manner, suggesting that HOIP functions downstream of TRAF2 [6]. Studies by others suggest that the TRAF2-associated proteins cIAP1 and cIAP2 play a role in the recruitment of HOIP to TNFR1 and CD40 [14]. Therefore, we determined whether the association of HOIP with CD40 in A20.2J cells was altered by treatment of cells with an inhibitor of cIAP activity, a membrane-permeable peptide derived from the apoptosis regulator SMAC [15]. We found that pretreatment of cells with the SMAC peptide dramatically reduced the amount of cIAP1 associated with the CD40 signaling complex in cells stimulated with anti-CD40 antibody-coated beads (Fig. 5A). SMAC peptide treatment also resulted in a slight but reproducible decrease in the amount of the major HOIP form recovered by CD40 immunoprecipitation, along with an apparent increase in higher molecular weight species recognized by anti-HOIP antibody. In contrast, treatment with the SMAC peptide did not alter the amount or molecular weight of HOIP present in cell lysates. These data suggest that SMAC peptide treatment specifically alters the characteristics of CD40-associated HOIP rather than the entire cellular pool of this protein. Together, these results support the idea that the cIAP proteins influence the recruitment and post-translational modification state of CD40-associated HOIP.\n10.1371/journal.pone.0023061.g005 Figure 5 IKK recruitment to the CD40 signaling complex is defective in HOIP-deficient cells.\n(A) SMAC peptide treatment reduces recruitment of cIAP1 to CD40 and may modify HOIP recruitment. A20.2J cells were incubated for six hours with membrane-permeable SMAC-N7 peptide or 1.5% DMSO (solvent used for the peptide). Following the incubation, cell lysates were prepared, fractionated by SDS-PAGE, and evaluated by Western blot (lanes 1 and 2). Cells incubated with DMSO or SMAC-N7 were also stimulated with magnetic beads coated with anti-CD40 or an isotype control antibody. Immunoprecipitated (IP) material bound to the beads was loaded in lanes 3-5. Samples of the cell lysates after immunoprecipitation appear in lanes 6–8. Western blots were probed with antibodies specific for cIAP1, TRAF2, TRAF3, and HOIP (approximate molecular weights indicated on left). Similar results were obtained in two additional experiments. (B) CD40 was isolated by immunoprecipitation (as in (A)) from A20.2J cells and HOIP-deficient cells transduced with an empty retroviral vector (pMIP) or a retroviral vector encoding HOIP. Material immunoprecipitated with an isotype control antibody (isotype) or anti-CD40 antibody was examined by Western blotting for CD40, TRAF2, TRAF3, cIAP1, HOIP, IKKα/β, and IKKγ (right panels). HOIP expression was required for coprecipitation of IKK proteins with CD40. Cell lysates from unstimulated cells are shown in the left panels. Similar results were obtained in a second experiment and in two experiments with a second HOIP-deficient clone. (C) To further evaluate HOIP-dependent recruitment of IKKγ to CD40, A20.2J cells or HOIP-deficient (HOIP-/-) A20.2J cells were transduced with an empty retroviral vector or a retroviral construct encoding BP epitope-tagged IKKγ (noted in the figure as pMIP and IKKγ, respectively). Lysates (lanes 1–3) and immunoprecipitation (IP) samples (lanes 4–11) from the cell lines were fractionated by SDS-PAGE and evaluated by Western blotting with antibodies to the BP tag (IKKγ, upper panel) and TRAF2. The anti-CD40 IP sample in lane 11 was treated with λ phosphatase; the sample in lane 10 was mock-treated. Protein samples (minus those treated with phosphatase) were also fractionated on a separate gel (lower acrylamide concentration) for the evaluation of TRAF3 and HOIP (bottom two panels). Similar results were obtained in two additional experiments. To test the possibility that HOIP is responsible for the recruitment of other critical signaling proteins to CD40, we immunoprecipitated CD40 signaling complexes from HOIP-deficient and HOIP-reconstituted cells (Fig. 5B). As described previously, CD40 signaling complexes immunoprecipitated from A20.2J cells contained HOIP as well as TRAF2, TRAF3, IKKα/β, and IKKγ [6]. The amounts of TRAF2, TRAF3, and cIAP1 in CD40 immunoprecipitates from HOIP-deficient cells were similar to those from parental A20.2J cells, indicating that HOIP is not required for the association of these proteins with CD40. In contrast, IKKα/β and IKKγ were not detectable in CD40 immunoprecipitates recovered from HOIP-deficient cells (Fig. 5B,C). The amounts of IKKα/β and IKKγ in CD40 immunoprecipitates from HOIP-reconstituted cells were similar to those detected in samples prepared from parental cells, demonstrating that the defects in IKK recruitment we observed were due specifically to the absence of HOIP expression. These data indicate that HOIP is required for recruitment of the NF-κB-activating complex to the CD40 signaling complex.\nAs shown here and in our previous study [6], IKKγ present in CD40 immunoprecipitates appears to have a higher molecular weight than that found in cell lysates. To confirm that this higher molecular weight species was indeed IKKγ, we generated A20.2J cell lines containing a stably integrated retroviral vector that encoded an epitope-tagged version of mouse IKKγ. Cell lysates and CD40 immunoprecipitates prepared from these cells were analyzed by Western blotting for the epitope tag (Fig. 5C). This analysis produced a pattern of bands that was essentially the same as that obtained using an antibody specific for native IKKγ (compare panels B and C in Fig. 5). Moreover, analysis of cells expressing epitope tagged-IKKγ confirmed that recruitment of IKKγ to CD40 requires HOIP. To determine what was responsible for the increased molecular weight of IKKγ in CD40 immunoprecipitates, the protein samples were incubated with lambda phosphatase, which removes phosphates attached to tyrosine, threonine, or serine residues in proteins. This treatment reduced much of CD40-associated IKKγ to an apparent molecular weight similar to that of the protein in cell lysates (Fig. 5C). However, at least one band of significantly higher molecular weight remained after phosphatase treatment, suggesting that CD40-associated IKKγ is subject to at least one other modification in addition to phosphorylation. Overall, these data demonstrate that HOIP is required for the association of IKKγ with CD40, and suggest that this event is coupled to post-translational modifications of IKKγ."}

pmc-enju-pas

2_test

{"project":"2_test","denotations":[{"id":"21829693-20614026-89653769","span":{"begin":438,"end":439},"obj":"20614026"},{"id":"21829693-21455173-89653770","span":{"begin":577,"end":579},"obj":"21455173"},{"id":"21829693-14532003-89653771","span":{"begin":807,"end":809},"obj":"14532003"},{"id":"21829693-20614026-89653772","span":{"begin":4539,"end":4540},"obj":"20614026"},{"id":"21829693-20614026-89653773","span":{"begin":5337,"end":5338},"obj":"20614026"},{"id":"T52587","span":{"begin":438,"end":439},"obj":"20614026"},{"id":"T83759","span":{"begin":577,"end":579},"obj":"21455173"},{"id":"T6761","span":{"begin":807,"end":809},"obj":"14532003"},{"id":"T70732","span":{"begin":4539,"end":4540},"obj":"20614026"},{"id":"T65429","span":{"begin":5337,"end":5338},"obj":"20614026"}],"text":"HOIP is necessary for association of the IKK complex with CD40\nThe marked defects in CD40-mediated cell activation and signaling displayed by HOIP-deficient cells suggested that HOIP mediates recruitment of critical components of the CD40 signaling apparatus to the receptor. Previously, we demonstrated that HOIP is recruited to the CD40 signaling complex in a TRAF2-dependent manner, suggesting that HOIP functions downstream of TRAF2 [6]. Studies by others suggest that the TRAF2-associated proteins cIAP1 and cIAP2 play a role in the recruitment of HOIP to TNFR1 and CD40 [14]. Therefore, we determined whether the association of HOIP with CD40 in A20.2J cells was altered by treatment of cells with an inhibitor of cIAP activity, a membrane-permeable peptide derived from the apoptosis regulator SMAC [15]. We found that pretreatment of cells with the SMAC peptide dramatically reduced the amount of cIAP1 associated with the CD40 signaling complex in cells stimulated with anti-CD40 antibody-coated beads (Fig. 5A). SMAC peptide treatment also resulted in a slight but reproducible decrease in the amount of the major HOIP form recovered by CD40 immunoprecipitation, along with an apparent increase in higher molecular weight species recognized by anti-HOIP antibody. In contrast, treatment with the SMAC peptide did not alter the amount or molecular weight of HOIP present in cell lysates. These data suggest that SMAC peptide treatment specifically alters the characteristics of CD40-associated HOIP rather than the entire cellular pool of this protein. Together, these results support the idea that the cIAP proteins influence the recruitment and post-translational modification state of CD40-associated HOIP.\n10.1371/journal.pone.0023061.g005 Figure 5 IKK recruitment to the CD40 signaling complex is defective in HOIP-deficient cells.\n(A) SMAC peptide treatment reduces recruitment of cIAP1 to CD40 and may modify HOIP recruitment. A20.2J cells were incubated for six hours with membrane-permeable SMAC-N7 peptide or 1.5% DMSO (solvent used for the peptide). Following the incubation, cell lysates were prepared, fractionated by SDS-PAGE, and evaluated by Western blot (lanes 1 and 2). Cells incubated with DMSO or SMAC-N7 were also stimulated with magnetic beads coated with anti-CD40 or an isotype control antibody. Immunoprecipitated (IP) material bound to the beads was loaded in lanes 3-5. Samples of the cell lysates after immunoprecipitation appear in lanes 6–8. Western blots were probed with antibodies specific for cIAP1, TRAF2, TRAF3, and HOIP (approximate molecular weights indicated on left). Similar results were obtained in two additional experiments. (B) CD40 was isolated by immunoprecipitation (as in (A)) from A20.2J cells and HOIP-deficient cells transduced with an empty retroviral vector (pMIP) or a retroviral vector encoding HOIP. Material immunoprecipitated with an isotype control antibody (isotype) or anti-CD40 antibody was examined by Western blotting for CD40, TRAF2, TRAF3, cIAP1, HOIP, IKKα/β, and IKKγ (right panels). HOIP expression was required for coprecipitation of IKK proteins with CD40. Cell lysates from unstimulated cells are shown in the left panels. Similar results were obtained in a second experiment and in two experiments with a second HOIP-deficient clone. (C) To further evaluate HOIP-dependent recruitment of IKKγ to CD40, A20.2J cells or HOIP-deficient (HOIP-/-) A20.2J cells were transduced with an empty retroviral vector or a retroviral construct encoding BP epitope-tagged IKKγ (noted in the figure as pMIP and IKKγ, respectively). Lysates (lanes 1–3) and immunoprecipitation (IP) samples (lanes 4–11) from the cell lines were fractionated by SDS-PAGE and evaluated by Western blotting with antibodies to the BP tag (IKKγ, upper panel) and TRAF2. The anti-CD40 IP sample in lane 11 was treated with λ phosphatase; the sample in lane 10 was mock-treated. Protein samples (minus those treated with phosphatase) were also fractionated on a separate gel (lower acrylamide concentration) for the evaluation of TRAF3 and HOIP (bottom two panels). Similar results were obtained in two additional experiments. To test the possibility that HOIP is responsible for the recruitment of other critical signaling proteins to CD40, we immunoprecipitated CD40 signaling complexes from HOIP-deficient and HOIP-reconstituted cells (Fig. 5B). As described previously, CD40 signaling complexes immunoprecipitated from A20.2J cells contained HOIP as well as TRAF2, TRAF3, IKKα/β, and IKKγ [6]. The amounts of TRAF2, TRAF3, and cIAP1 in CD40 immunoprecipitates from HOIP-deficient cells were similar to those from parental A20.2J cells, indicating that HOIP is not required for the association of these proteins with CD40. In contrast, IKKα/β and IKKγ were not detectable in CD40 immunoprecipitates recovered from HOIP-deficient cells (Fig. 5B,C). The amounts of IKKα/β and IKKγ in CD40 immunoprecipitates from HOIP-reconstituted cells were similar to those detected in samples prepared from parental cells, demonstrating that the defects in IKK recruitment we observed were due specifically to the absence of HOIP expression. These data indicate that HOIP is required for recruitment of the NF-κB-activating complex to the CD40 signaling complex.\nAs shown here and in our previous study [6], IKKγ present in CD40 immunoprecipitates appears to have a higher molecular weight than that found in cell lysates. To confirm that this higher molecular weight species was indeed IKKγ, we generated A20.2J cell lines containing a stably integrated retroviral vector that encoded an epitope-tagged version of mouse IKKγ. Cell lysates and CD40 immunoprecipitates prepared from these cells were analyzed by Western blotting for the epitope tag (Fig. 5C). This analysis produced a pattern of bands that was essentially the same as that obtained using an antibody specific for native IKKγ (compare panels B and C in Fig. 5). Moreover, analysis of cells expressing epitope tagged-IKKγ confirmed that recruitment of IKKγ to CD40 requires HOIP. To determine what was responsible for the increased molecular weight of IKKγ in CD40 immunoprecipitates, the protein samples were incubated with lambda phosphatase, which removes phosphates attached to tyrosine, threonine, or serine residues in proteins. This treatment reduced much of CD40-associated IKKγ to an apparent molecular weight similar to that of the protein in cell lysates (Fig. 5C). However, at least one band of significantly higher molecular weight remained after phosphatase treatment, suggesting that CD40-associated IKKγ is subject to at least one other modification in addition to phosphorylation. Overall, these data demonstrate that HOIP is required for the association of IKKγ with CD40, and suggest that this event is coupled to post-translational modifications of IKKγ."}

bionlp-st-ge-2016-spacy-parsed

GO-BP

GO-MF

{"project":"GO-MF","denotations":[{"id":"T8305","span":{"begin":5090,"end":5093},"obj":"http://purl.obolibrary.org/obo/GO_0008384"},{"id":"T8306","span":{"begin":989,"end":997},"obj":"http://purl.obolibrary.org/obo/GO_0003823"},{"id":"T8307","span":{"begin":1264,"end":1272},"obj":"http://purl.obolibrary.org/obo/GO_0003823"},{"id":"T8308","span":{"begin":5890,"end":5898},"obj":"http://purl.obolibrary.org/obo/GO_0003823"},{"id":"T8309","span":{"begin":6229,"end":6240},"obj":"http://purl.obolibrary.org/obo/GO_0016791"},{"id":"T8310","span":{"begin":6557,"end":6568},"obj":"http://purl.obolibrary.org/obo/GO_0016791"},{"id":"T17753","span":{"begin":1763,"end":1766},"obj":"http://purl.obolibrary.org/obo/GO_0008384"},{"id":"T17754","span":{"begin":3115,"end":3118},"obj":"http://purl.obolibrary.org/obo/GO_0008384"},{"id":"T17755","span":{"begin":2320,"end":2328},"obj":"http://purl.obolibrary.org/obo/GO_0003823"},{"id":"T17756","span":{"begin":2919,"end":2927},"obj":"http://purl.obolibrary.org/obo/GO_0003823"},{"id":"T17757","span":{"begin":2951,"end":2959},"obj":"http://purl.obolibrary.org/obo/GO_0003823"},{"id":"T17758","span":{"begin":3759,"end":3769},"obj":"http://purl.obolibrary.org/obo/GO_0003823"},{"id":"T17759","span":{"begin":3869,"end":3880},"obj":"http://purl.obolibrary.org/obo/GO_0016791"},{"id":"T17760","span":{"begin":3964,"end":3975},"obj":"http://purl.obolibrary.org/obo/GO_0016791"}],"text":"HOIP is necessary for association of the IKK complex with CD40\nThe marked defects in CD40-mediated cell activation and signaling displayed by HOIP-deficient cells suggested that HOIP mediates recruitment of critical components of the CD40 signaling apparatus to the receptor. Previously, we demonstrated that HOIP is recruited to the CD40 signaling complex in a TRAF2-dependent manner, suggesting that HOIP functions downstream of TRAF2 [6]. Studies by others suggest that the TRAF2-associated proteins cIAP1 and cIAP2 play a role in the recruitment of HOIP to TNFR1 and CD40 [14]. Therefore, we determined whether the association of HOIP with CD40 in A20.2J cells was altered by treatment of cells with an inhibitor of cIAP activity, a membrane-permeable peptide derived from the apoptosis regulator SMAC [15]. We found that pretreatment of cells with the SMAC peptide dramatically reduced the amount of cIAP1 associated with the CD40 signaling complex in cells stimulated with anti-CD40 antibody-coated beads (Fig. 5A). SMAC peptide treatment also resulted in a slight but reproducible decrease in the amount of the major HOIP form recovered by CD40 immunoprecipitation, along with an apparent increase in higher molecular weight species recognized by anti-HOIP antibody. In contrast, treatment with the SMAC peptide did not alter the amount or molecular weight of HOIP present in cell lysates. These data suggest that SMAC peptide treatment specifically alters the characteristics of CD40-associated HOIP rather than the entire cellular pool of this protein. Together, these results support the idea that the cIAP proteins influence the recruitment and post-translational modification state of CD40-associated HOIP.\n10.1371/journal.pone.0023061.g005 Figure 5 IKK recruitment to the CD40 signaling complex is defective in HOIP-deficient cells.\n(A) SMAC peptide treatment reduces recruitment of cIAP1 to CD40 and may modify HOIP recruitment. A20.2J cells were incubated for six hours with membrane-permeable SMAC-N7 peptide or 1.5% DMSO (solvent used for the peptide). Following the incubation, cell lysates were prepared, fractionated by SDS-PAGE, and evaluated by Western blot (lanes 1 and 2). Cells incubated with DMSO or SMAC-N7 were also stimulated with magnetic beads coated with anti-CD40 or an isotype control antibody. Immunoprecipitated (IP) material bound to the beads was loaded in lanes 3-5. Samples of the cell lysates after immunoprecipitation appear in lanes 6–8. Western blots were probed with antibodies specific for cIAP1, TRAF2, TRAF3, and HOIP (approximate molecular weights indicated on left). Similar results were obtained in two additional experiments. (B) CD40 was isolated by immunoprecipitation (as in (A)) from A20.2J cells and HOIP-deficient cells transduced with an empty retroviral vector (pMIP) or a retroviral vector encoding HOIP. Material immunoprecipitated with an isotype control antibody (isotype) or anti-CD40 antibody was examined by Western blotting for CD40, TRAF2, TRAF3, cIAP1, HOIP, IKKα/β, and IKKγ (right panels). HOIP expression was required for coprecipitation of IKK proteins with CD40. Cell lysates from unstimulated cells are shown in the left panels. Similar results were obtained in a second experiment and in two experiments with a second HOIP-deficient clone. (C) To further evaluate HOIP-dependent recruitment of IKKγ to CD40, A20.2J cells or HOIP-deficient (HOIP-/-) A20.2J cells were transduced with an empty retroviral vector or a retroviral construct encoding BP epitope-tagged IKKγ (noted in the figure as pMIP and IKKγ, respectively). Lysates (lanes 1–3) and immunoprecipitation (IP) samples (lanes 4–11) from the cell lines were fractionated by SDS-PAGE and evaluated by Western blotting with antibodies to the BP tag (IKKγ, upper panel) and TRAF2. The anti-CD40 IP sample in lane 11 was treated with λ phosphatase; the sample in lane 10 was mock-treated. Protein samples (minus those treated with phosphatase) were also fractionated on a separate gel (lower acrylamide concentration) for the evaluation of TRAF3 and HOIP (bottom two panels). Similar results were obtained in two additional experiments. To test the possibility that HOIP is responsible for the recruitment of other critical signaling proteins to CD40, we immunoprecipitated CD40 signaling complexes from HOIP-deficient and HOIP-reconstituted cells (Fig. 5B). As described previously, CD40 signaling complexes immunoprecipitated from A20.2J cells contained HOIP as well as TRAF2, TRAF3, IKKα/β, and IKKγ [6]. The amounts of TRAF2, TRAF3, and cIAP1 in CD40 immunoprecipitates from HOIP-deficient cells were similar to those from parental A20.2J cells, indicating that HOIP is not required for the association of these proteins with CD40. In contrast, IKKα/β and IKKγ were not detectable in CD40 immunoprecipitates recovered from HOIP-deficient cells (Fig. 5B,C). The amounts of IKKα/β and IKKγ in CD40 immunoprecipitates from HOIP-reconstituted cells were similar to those detected in samples prepared from parental cells, demonstrating that the defects in IKK recruitment we observed were due specifically to the absence of HOIP expression. These data indicate that HOIP is required for recruitment of the NF-κB-activating complex to the CD40 signaling complex.\nAs shown here and in our previous study [6], IKKγ present in CD40 immunoprecipitates appears to have a higher molecular weight than that found in cell lysates. To confirm that this higher molecular weight species was indeed IKKγ, we generated A20.2J cell lines containing a stably integrated retroviral vector that encoded an epitope-tagged version of mouse IKKγ. Cell lysates and CD40 immunoprecipitates prepared from these cells were analyzed by Western blotting for the epitope tag (Fig. 5C). This analysis produced a pattern of bands that was essentially the same as that obtained using an antibody specific for native IKKγ (compare panels B and C in Fig. 5). Moreover, analysis of cells expressing epitope tagged-IKKγ confirmed that recruitment of IKKγ to CD40 requires HOIP. To determine what was responsible for the increased molecular weight of IKKγ in CD40 immunoprecipitates, the protein samples were incubated with lambda phosphatase, which removes phosphates attached to tyrosine, threonine, or serine residues in proteins. This treatment reduced much of CD40-associated IKKγ to an apparent molecular weight similar to that of the protein in cell lysates (Fig. 5C). However, at least one band of significantly higher molecular weight remained after phosphatase treatment, suggesting that CD40-associated IKKγ is subject to at least one other modification in addition to phosphorylation. Overall, these data demonstrate that HOIP is required for the association of IKKγ with CD40, and suggest that this event is coupled to post-translational modifications of IKKγ."}

GO-CC

sentences

bionlp-st-ge-2016-uniprot

test2

PMC:3148254 / 15212-22083 JSONTXT

Annnotations TAB JSON ListView MergeView

PMC:3148254 / 15212-22083 JSON TXT