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Association of papillomavirus E6 proteins with either MAML1 or E6AP clusters E6 proteins by structure, function, and evolutionary relatedness

Brimer, Nicole, Drews, Camille M., Vande Pol, Scott B.·2017·PLOS Pathogens
DOI 10.1371/journal.ppat.1006781PMC PMC5760104
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Figures

Fig 1 LXXLL peptide sequences that interact with BPV1 E6 and HPV16 E6. A. LXXLL peptide sequences within the indicated cellular proteins that serve as docking sites for Alpha genus HPV16 E6 (top two peptides, E6AP (NP_000453.2), and IRF3, (NP_001184051.1); and Delta genus BPV1 E6, PXN (XP_010812366.2), HIC5 (NP_001035919), MAML1 (NP_055572.1) and MAML3 (NP_061187.2). Potentially phosphorylated sites (underlined) were identified at PhosphositePlus.org [107], but only PXN pS-273 is confirmed in a publication [108]. Hydrophobic residues are colored blue, and acidic residues are in red. B. The bottom grouping of 14 peptide sequences were selected for BPV1 E6 association from a phage display expression library as detailed in the methods. Amino acids with an associated asterix-encoded a stop codon at that position are suppressed by supE44 suppressor tRNA from amber to glutamine in the E.coli strain used to propagate the M13 phage. At the bottom, a consensus sequence for BPV1 E6 associated LXXLL peptides and the numbering scheme used in this manuscript are shown.
Fig 1 LXXLL peptide sequences that interact with BPV1 E6 and HPV16 E6. A. LXXLL peptide sequences within the indicated cellular proteins that serve as docking sites for Alpha genus HPV16 E6 (top two peptides, E6AP (NP_000453.2), and IRF3, (NP_001184051.1); and Delta genus BPV1 E6, PXN (XP_010812366.2), HIC5 (NP_001035919), MAML1 (NP_055572.1) and MAML3 (NP_061187.2). Potentially phosphorylated sites (underlined) were identified at PhosphositePlus.org [107], but only PXN pS-273 is confirmed in a publication [108]. Hydrophobic residues are colored blue, and acidic residues are in red. B. The bottom grouping of 14 peptide sequences were selected for BPV1 E6 association from a phage display expression library as detailed in the methods. Amino acids with an associated asterix-encoded a stop codon at that position are suppressed by supE44 suppressor tRNA from amber to glutamine in the E.coli strain used to propagate the M13 phage. At the bottom, a consensus sequence for BPV1 E6 associated LXXLL peptides and the numbering scheme used in this manuscript are shown.CC BY · PubMed Central
Fig 2 Contact residues in HPV16 E6 and BPV1 E6 that distinguish between E6AP interaction and MAML1 interaction. A. HPV16 E6 structure (PDB file 4GIZ [41]) showing the amino-terminal zinc structured domain in blue, the connecting helix in yellow and the carboxy-terminal zinc-structured domain in pink) in association with the LXXLL peptide of E6AP (green) where the amino-terminal position -3 is facing the viewer. B. A close-up detail from part A of the HPV16 E6 –E6AP structure showing the interaction between position -3 of the E6AP LXXLL peptide (glutamic acid) with 16E6 amino acids R77 and H78. C. The structure of BPV1 E6 in association with the LXXLL peptide of paxillin (PDB file 3PY7 [41]) in similar orientation to the structure in part A. D. A close-up detail from part C of the BPV1 E6 structure showing the interaction between position -3 of the PXN LXXLL peptide (methionine) with BPV1 E6 amino acids L64 and W65.
Fig 2 Contact residues in HPV16 E6 and BPV1 E6 that distinguish between E6AP interaction and MAML1 interaction. A. HPV16 E6 structure (PDB file 4GIZ [41]) showing the amino-terminal zinc structured domain in blue, the connecting helix in yellow and the carboxy-terminal zinc-structured domain in pink) in association with the LXXLL peptide of E6AP (green) where the amino-terminal position -3 is facing the viewer. B. A close-up detail from part A of the HPV16 E6 –E6AP structure showing the interaction between position -3 of the E6AP LXXLL peptide (glutamic acid) with 16E6 amino acids R77 and H78. C. The structure of BPV1 E6 in association with the LXXLL peptide of paxillin (PDB file 3PY7 [41]) in similar orientation to the structure in part A. D. A close-up detail from part C of the BPV1 E6 structure showing the interaction between position -3 of the PXN LXXLL peptide (methionine) with BPV1 E6 amino acids L64 and W65.CC BY · PubMed Central
Fig 3 Multiple sequence alignment of the studied E6 protein set. A protein multiple sequence alignment was performed using the MUSCLE program [103], and the output then entered into Jalview2 [109] to generate the ClustalX colorized image. The four upward-pointing arrows at the bottom of the alignment indicate the positions of HPV16 E6 amino acids that interact with position -3 of the E6AP LXXLL motif and BPV1 E6 interaction with PXN as shown in Fig 1. The two horizontal arrows on the left denote the positions of BPV1 E6 and HPV16 E6 in the alignment.
Fig 3 Multiple sequence alignment of the studied E6 protein set. A protein multiple sequence alignment was performed using the MUSCLE program [103], and the output then entered into Jalview2 [109] to generate the ClustalX colorized image. The four upward-pointing arrows at the bottom of the alignment indicate the positions of HPV16 E6 amino acids that interact with position -3 of the E6AP LXXLL motif and BPV1 E6 interaction with PXN as shown in Fig 1. The two horizontal arrows on the left denote the positions of BPV1 E6 and HPV16 E6 in the alignment.CC BY · PubMed Central
Fig 4 Preferential physical and functional discrimination between E6AP and MAML1 by E6 proteins. A. Preferential association of E6 proteins for either E6AP or MAML1. HA-tagged E6AP_Ub-, MAML1 and GFP expression plasmids were co-transfected with the indicated FLAG-tagged E6 expression plasmids into 293T cells and harvested 18 hrs. later in 0.5X IPEGAL lysis buffer as described in the methods. Western blots of input samples are clustered at the top and FLAG immune precipitated samples at the bottom, except that lane 1 at the bottom cluster of blots is an input sample, same as lane 2 in the top cluster of blots. Input was 4% of the immune precipitated sample size. E6* is a spliced and truncated E6 variant. B. Alpha genera and selected genus E6 proteins reduce the expression of E6AP upon co-expression. HA-tagged E6AP, HA-GFP and the indicated FLAG-tagged E6 proteins were co-transfected into 293T cells and cells were lysed in SDS sample buffer 18 hrs. later.
Fig 4 Preferential physical and functional discrimination between E6AP and MAML1 by E6 proteins. A. Preferential association of E6 proteins for either E6AP or MAML1. HA-tagged E6AP_Ub-, MAML1 and GFP expression plasmids were co-transfected with the indicated FLAG-tagged E6 expression plasmids into 293T cells and harvested 18 hrs. later in 0.5X IPEGAL lysis buffer as described in the methods. Western blots of input samples are clustered at the top and FLAG immune precipitated samples at the bottom, except that lane 1 at the bottom cluster of blots is an input sample, same as lane 2 in the top cluster of blots. Input was 4% of the immune precipitated sample size. E6* is a spliced and truncated E6 variant. B. Alpha genera and selected genus E6 proteins reduce the expression of E6AP upon co-expression. HA-tagged E6AP, HA-GFP and the indicated FLAG-tagged E6 proteins were co-transfected into 293T cells and cells were lysed in SDS sample buffer 18 hrs. later.CC BY · PubMed Central
Fig 5 E6 proteins discriminate in functional and physical interaction between E6AP_Ub- and MAML1. A. Comparative binding of E6 proteins to MAML1 or E6AP. Quantitation of input HA-tagged E6AP_UB- and HA-tagged MAML1 were immune precipitated by anti-FLAG-E6 proteins as shown in Fig 4 and S5 Fig, and triplicate experiments quantified. Black bars represent MAML1 precipitation and white bars E6AP precipitation. The vertical axis identifies the percentage of input protein precipitated. The averages of three separate experimental replicates with standard deviations is shown. B. HA-E6AP was co-transfected together with the indicated FLAG-tagged E6 proteins and degradation of E6AP quantified relative to vector transfected HA-E6AP, and normalized to a co-transfected HA-GFP to adjust for differences in transfection efficiency. Results are averages with standard deviations from three independent experimental replicates. C. E6 proteins that associate with MAML1 repress GAL4-MAML1 transcriptional activation. GAL4-MAML1, GAL4-luciferase reporter, pCMV-renilla internal transfection control and empty vector or the indicated E6 proteins were co-transfected into 293T cells and harvested for luciferase and renilla assay 18 hrs. later. Results are the average and standard deviation of four independent experiments with duplicate samples in each experiment, and normalized to co-transfected renilla activity.
Fig 5 E6 proteins discriminate in functional and physical interaction between E6AP_Ub- and MAML1. A. Comparative binding of E6 proteins to MAML1 or E6AP. Quantitation of input HA-tagged E6AP_UB- and HA-tagged MAML1 were immune precipitated by anti-FLAG-E6 proteins as shown in Fig 4 and S5 Fig, and triplicate experiments quantified. Black bars represent MAML1 precipitation and white bars E6AP precipitation. The vertical axis identifies the percentage of input protein precipitated. The averages of three separate experimental replicates with standard deviations is shown. B. HA-E6AP was co-transfected together with the indicated FLAG-tagged E6 proteins and degradation of E6AP quantified relative to vector transfected HA-E6AP, and normalized to a co-transfected HA-GFP to adjust for differences in transfection efficiency. Results are averages with standard deviations from three independent experimental replicates. C. E6 proteins that associate with MAML1 repress GAL4-MAML1 transcriptional activation. GAL4-MAML1, GAL4-luciferase reporter, pCMV-renilla internal transfection control and empty vector or the indicated E6 proteins were co-transfected into 293T cells and harvested for luciferase and renilla assay 18 hrs. later. Results are the average and standard deviation of four independent experiments with duplicate samples in each experiment, and normalized to co-transfected renilla activity.CC BY · PubMed Central
Fig 6 Preferential association of MAML1 compared to MAML2 or MAML3 with E6 proteins. 293T cells were co-transfected with myc-MAML3, HA-MAML1, HA-MAML2, HA-E6AP_Ub-, HA-GFP, and the indicated FLAG-E6 proteins. 18 hrs. later cells were lysed, an input aliquot of lysate removed, and the remainder of the clarified lysate immune precipitated with FLAG antibody beads as described in the methods. One of two replicated experiments are shown.
Fig 6 Preferential association of MAML1 compared to MAML2 or MAML3 with E6 proteins. 293T cells were co-transfected with myc-MAML3, HA-MAML1, HA-MAML2, HA-E6AP_Ub-, HA-GFP, and the indicated FLAG-E6 proteins. 18 hrs. later cells were lysed, an input aliquot of lysate removed, and the remainder of the clarified lysate immune precipitated with FLAG antibody beads as described in the methods. One of two replicated experiments are shown.CC BY · PubMed Central
Fig 7 E6 proteins that physically and functionally interact with either E6AP or MAML1 cluster phylogenetically. The cladogram is derived from a multiple sequence alignment using the program “MUSCLE” [103], clustering phylogenetically using PhyML [105], and tree rendering with TreeDyn [106]. For physical association by immune precipitation, blue denotes MAML1, red E6AP, and grey denotes neither MAML1 nor E6AP. P denotes the statistical significance of the association as determined from the quantitation of at least three independent experiments of quantified western blot data or four independent Luciferase assays analyzed by Student’s t test (NS, not significant; * <0.05; ** < 0.01; *** < 0.001; **** < 0.0001). For some samples, low-level MAML1 was consistently observed upon co-immune precipitation and so colored, even though statistical significance was not reached. For MAML1 repression, blue denotes repression of GAL4-MAML1, and grey no repression. E6-induced E6AP degradation is shown in red color, and lack of degradation in grey. E6 expression level is from a representative experiment and is normalized to the expression of BPV1 E6, set at 100.
Fig 7 E6 proteins that physically and functionally interact with either E6AP or MAML1 cluster phylogenetically. The cladogram is derived from a multiple sequence alignment using the program “MUSCLE” [103], clustering phylogenetically using PhyML [105], and tree rendering with TreeDyn [106]. For physical association by immune precipitation, blue denotes MAML1, red E6AP, and grey denotes neither MAML1 nor E6AP. P denotes the statistical significance of the association as determined from the quantitation of at least three independent experiments of quantified western blot data or four independent Luciferase assays analyzed by Student’s t test (NS, not significant; * <0.05; ** < 0.01; *** < 0.001; **** < 0.0001). For some samples, low-level MAML1 was consistently observed upon co-immune precipitation and so colored, even though statistical significance was not reached. For MAML1 repression, blue denotes repression of GAL4-MAML1, and grey no repression. E6-induced E6AP degradation is shown in red color, and lack of degradation in grey. E6 expression level is from a representative experiment and is normalized to the expression of BPV1 E6, set at 100.CC BY · PubMed Central
Fig 8 Binding of Delta or Gamma genera E6 proteins to E6AP is not sufficient to initiate E6AP degradation. (A) HA-E6AP_Ub- or HA-E6AP_Ub- LDDLL (E6AP where the LXXLL motif was mutated to the MAML1 LXXLL amino acid sequence) were co-transfected with the indicated E6 protein and HA-GFP in 293T cells. Cells were lysed 18 hours post-transfection in 0.5X IPEGAL lysis buffer. E6AP_Ub- does not immunoprecipitate with Delta or Gamma E6 proteins (BPV1, HPV112, HPV4, and HPV131) but E6AP_Ub- LDDLL immunoprecipitates with both Delta and Gamma genera E6 proteins. Alpha genera HPV16 E6 immunoprecipitates both E6AP_Ub- and E6AP_Ub- LDDLL, but significantly less of the MAML-like E6AP. Vertical black line indicates removal of an irrelevant sample. Quantification normalized to HPV16 E6 sample (= 100%). n = 4, * < 0.05; ** < 0.01; **** < 0.0001 by Student’s t-test. (B) Binding of E6 to LXXLL of E6AP is insufficient to stimulate E6AP degradation. Although Alpha, Gamma, and Delta E6 proteins bind to E6AP LDDLL (panel A), only Alpha E6 stimulates E6AP degradation. 293T cells were transfected with indicated E6 protein, HA-GFP, and either HA-E6AP or HA-E6AP LDDLL. 18 hours post-transfection, cells were lysed in 1X SDS sample buffer and E6AP expression determined by western blot. Vertical black line indicates removal of an irrelevant sample. Quantified samples normalized to HA-GFP and vector transfected cells. n = 4, * < 0.05; *** < 0.001; **** < 0.0001 by Student’s t-test.
Fig 8 Binding of Delta or Gamma genera E6 proteins to E6AP is not sufficient to initiate E6AP degradation. (A) HA-E6AP_Ub- or HA-E6AP_Ub- LDDLL (E6AP where the LXXLL motif was mutated to the MAML1 LXXLL amino acid sequence) were co-transfected with the indicated E6 protein and HA-GFP in 293T cells. Cells were lysed 18 hours post-transfection in 0.5X IPEGAL lysis buffer. E6AP_Ub- does not immunoprecipitate with Delta or Gamma E6 proteins (BPV1, HPV112, HPV4, and HPV131) but E6AP_Ub- LDDLL immunoprecipitates with both Delta and Gamma genera E6 proteins. Alpha genera HPV16 E6 immunoprecipitates both E6AP_Ub- and E6AP_Ub- LDDLL, but significantly less of the MAML-like E6AP. Vertical black line indicates removal of an irrelevant sample. Quantification normalized to HPV16 E6 sample (= 100%). n = 4, * < 0.05; ** < 0.01; **** < 0.0001 by Student’s t-test. (B) Binding of E6 to LXXLL of E6AP is insufficient to stimulate E6AP degradation. Although Alpha, Gamma, and Delta E6 proteins bind to E6AP LDDLL (panel A), only Alpha E6 stimulates E6AP degradation. 293T cells were transfected with indicated E6 protein, HA-GFP, and either HA-E6AP or HA-E6AP LDDLL. 18 hours post-transfection, cells were lysed in 1X SDS sample buffer and E6AP expression determined by western blot. Vertical black line indicates removal of an irrelevant sample. Quantified samples normalized to HA-GFP and vector transfected cells. n = 4, * < 0.05; *** < 0.001; **** < 0.0001 by Student’s t-test.CC BY · PubMed Central

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Cited by

Metadata

Authors
Brimer, N., Drews, C. M., & Vande Pol, S. B.
Venue
PLOS Pathogens
Publisher
Public Library of Science (PLoS)
Published
2017-12-27
Volume
13
Issue
12
Pages
e1006781
ISSN
1553-7374
DOI
10.1371/journal.ppat.1006781
PMC
PMC5760104
Cited by
52
References
4
Language
en
Update notices
new_version (2018-01-09)
Licence
creativecommons.org/licenses/by/4.0/ (vor)
Funders
National Cancer Institute (CA120352 and CA08093, T32 CA 009109)

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