Autoinhibition and regulation by phosphoinositides of ATP8B1, a human lipid flippase associated with intrahepatic cholestatic disorders

  1. Thibaud Dieudonné
  2. Sara Abad Herrera
  3. Michelle Juknaviciute Laursen
  4. Maylis Lejeune
  5. Charlott Stock
  6. Kahina Slimani
  7. Christine Jaxel
  8. Joseph A Lyons
  9. Cédric Montigny
  10. Thomas Günther Pomorski  Is a corresponding author
  11. Poul Nissen  Is a corresponding author
  12. Guillaume Lenoir  Is a corresponding author
  1. Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), France
  2. DANDRITE, Nordic EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University, Denmark
  3. Faculty of Chemistry and Biochemistry, Department of Molecular Biochemistry, Ruhr University Bochum, Germany
  4. Department of Molecular Biology and Genetics, Aarhus University, Denmark
  5. Department of Plant and Environmental Sciences, University of Copenhagen, Denmark
10 figures, 5 tables and 1 additional file

Figures

Figure 1 with 1 supplement
Purification and functional assessment of the ATP8B1-CDC50A complex expressed in Saccharomyces cerevisiae.

(A) Predicted topology of ATP8B1-CDC50A with the transmembrane domain of ATP8B1 in tan and the Actuator domain (A), the Nucleotide binding domain (N) and the Phosphorylation domain (P) in yellow, …

Figure 1—figure supplement 1
Strategy for purification of the ATP8B1-CDC50A complex.

(A) Map of the plasmid used for co-expression of BAD-ATP8B1 and His10-CDC50A. Both ATP8B1 and CDC50A genes are cloned into the same expression vector. The cDNA sequence of human CDC50A is fused to a …

Figure 2 with 3 supplements
Overall ATP8B1-CDC50A structure.

(A) Cryo-EM map of ATP8B1-CDC50A in the E2P autoinhibited state. The cytosolic A-, N-, and P-domains of ATP8B1 are colored in yellow, red and blue, respectively. The transmembrane domain of ATP8B1 …

Figure 2—figure supplement 1
Data processing flow chart.

(A) Representative motion-corrected and dose weighted micrograph. (B) Data-processing workflow performed in CryoSparc v3.

Figure 2—figure supplement 2
Cryo-EM density of the ATP8B1-CDC50A complex and its corresponding model.

Map to model FSC curve and cryo-EM densities from different areas of the ATP8B1-CDC50A complex in the E2P autoinhibited state. Cryo-EM map contour levels used are 5–9. TM: transmembrane helical …

Figure 2—figure supplement 3
Structural comparison of P4-ATPases-CDC50A complexes of known structure.

(A) Atomic models of CDC50A in complex with ATP8B1, ATP8A1 (PDB: 6K7L) and ATP11C (6LKN), colored in pink, orange, and blue, respectively. P4-ATPases are colored in gray. (B) Structural alignment of …

Figure 3 with 1 supplement
Detailed interaction of the N- and C-terminal tails with the cytosolic A-, N-, and P-domains of ATP8B1.

(A) Overall view of the cytosolic A-, N-, and P-domains colored in yellow, red and blue, respectively. The transmembrane domain is colored tan. The N- and C-terminal tails of ATP8B1 are colored in …

Figure 3—figure supplement 1
overall and close-up views of the N- and C-terminal extensions of ATP8B1 and their corresponding EM densities.

The cytosolic A-, N-, and P-domains of ATP8B1 are colored in yellow, red, and blue, respectively. The transmembrane domain of ATP8B1 is colored in tan. The N- and C-terminal tails of ATP8B1 and …

Figure 4 with 4 supplements
ATP8B1-CDC50A is autoinhibited by both its N- and C-terminal tails and the presence of lipids is required for its activity.

(A) Removal of N- and/or C-terminal extensions of ATP8B1 upon on-column cleavage of streptavidin-bound ATP8B1-CDC50A with both TEV and 3 C proteases assessed by Coomassie blue stained SDS-PAGE. ΔN42 …

Figure 4—figure supplement 1
Sequence alignment of selected P4-ATPases.

Sequences of the human ATP8B1, ATP8B2, ATP8B3, ATP8B4, ATP8A1, ATP8A2, the S. cerevisiae Drs2, the C. elegans tat-1, tat-2, tat-4, the A. thaliana ALA3, the C. neoformans Apt2, the P. falciparum

Figure 4—figure supplement 2
The amount of CDC50A which co-elutes with ATP8B1 upon on-column cleavage with TEV and 3 C proteases is similar for wild-type ATP8B1 (WT) and the 3 C protease cleavage site insertion mutants (ΔN42, ΔC1174, ΔN42/C1174).

The ATP8B1-CDC50A complex recovered from streptavidin beads upon proteolytic cleavage was denatured, treated with EndoH for 1 hr at 37 °C, and analyzed by immunoblotting with a Histidine probe.

Figure 4—figure supplement 3
ATPase activity measurements of streptavidin-purified WT and catalytically-inactive D454N ATP8B1-CDC50A.

(A) ATPase activity of the purified ATP8B1-CDC50A complex determined in DDM/CHS at 30 °C, using an enzyme-coupled assay, where the kinetics of NADH oxidation is monitored continuously. The various …

Figure 4—figure supplement 4
Catalytic properties of the purified ATP8B1-CDC50A complex.

(A) Sensitivity to beryllium fluoride of ATP8B1 turnover rate. ATPase activity of ΔN42/C1174 ATP8B1 was measured at 30 °C in the presence of increasing concentrations of BeFx, with 2 mM DDM, 115 µM …

Figure 4—figure supplement 4—source data 1

GraphPad Prism tables and curve fitting for results displayed in Figure 4—figure supplement 4A, B.

https://cdn.elifesciences.org/articles/75272/elife-75272-fig4-figsupp4-data1-v2.pdf
Figure 5 with 1 supplement
Autoinhibition of ATP8B1 by its N- and C-terminal extensions.

(A) Overall and close-up views of S1223 in the cleft formed by the A- and N-domains. The cytosolic A- and N-domains of ATP8B1 are colored in yellow and red, respectively, and are shown as surface …

Figure 5—source data 1

GraphPad Prism tables and curve fitting for results displayed in Figure 5B.

https://cdn.elifesciences.org/articles/75272/elife-75272-fig5-data1-v2.pdf
Figure 5—source data 2

GraphPad Prism tables and curve fitting for results displayed in Figure 5C.

https://cdn.elifesciences.org/articles/75272/elife-75272-fig5-data2-v2.pdf
Figure 5—source data 3

GraphPad Prism tables for results displayed in Figure 5D.

https://cdn.elifesciences.org/articles/75272/elife-75272-fig5-data3-v2.pdf
Figure 5—source data 4

GraphPad Prism tables and statistical analysis for results displayed in Figure 5E.

https://cdn.elifesciences.org/articles/75272/elife-75272-fig5-data4-v2.pdf
Figure 5—figure supplement 1
Effect of the ATP8B1 C-terminal peptide on the enzyme-coupled assay.

(A) Schematic depicting the principle of the enzyme-coupled assay. PK: pyruvate kinase; LDH: lactate dehydrogenase. For each mole of ATP consumed by the ATP8B1-CDC50A complex, one mole of NADH is …

Figure 6 with 2 supplements
Sensitivity of ATP8B1-CDC50A to phospholipids.

(A) ATPase activity of the ΔN42/C1174 ATP8B1 determined in the presence of various glycerophospholipids, lipid derivatives, and sphingomyelin, at 30 °C. The assay medium contained 1 mM MgATP, 1 mg …

Figure 6—source data 1

GraphPad Prism tables and statistical analysis for results displayed in Figure 6A.

https://cdn.elifesciences.org/articles/75272/elife-75272-fig6-data1-v2.pdf
Figure 6—source data 2

GraphPad Prism tables for results displayed in Figure 6B.

https://cdn.elifesciences.org/articles/75272/elife-75272-fig6-data2-v2.pdf
Figure 6—source data 3

GraphPad Prism tables and curve fitting for results displayed in Figure 6C.

https://cdn.elifesciences.org/articles/75272/elife-75272-fig6-data3-v2.pdf
Figure 6—source data 4

GraphPad Prism tables for results displayed in Figure 6D.

https://cdn.elifesciences.org/articles/75272/elife-75272-fig6-data4-v2.pdf
Figure 6—figure supplement 1
Determination of the kinetic parameters for activation of ATP8B1-CDC50A by PPIns.

Double reciprocal plot of data shown in Figure 6C. Source files related to Figure 6—figure supplement 1 are available in Figure 6—figure supplement 1—source data 1.

Figure 6—figure supplement 1—source data 1

GraphPad Prism tables and curve fitting for results displayed in Figure 6—figure supplement 1.

https://cdn.elifesciences.org/articles/75272/elife-75272-fig6-figsupp1-data1-v2.pdf
Figure 6—figure supplement 2
Quantification of the detergent bound to the transmembrane domain of Drs2-Cdc50.

(A) Size-exclusion chromatography (SEC) on a TSK3000 SW gel filtration column (Tosoh Bioscience) of DDM-purified Drs2-Cdc50 complex. The column was equilibrated with 50 mM MOPS-Tris pH 7, 100 mM …

Figure 7 with 1 supplement
Proposed mechanism for autoinhibition and regulation by phosphoinositides of the ATP8B1-CDC50A complex.

(A) Sequence alignment of select P4-ATPases C-termini, including ATP8B1, ATP8A1 and Drs2, which are all known to be autoinhibited. The shading indicates conservation (blue 0% – red 100%). (B) …

Figure 7—figure supplement 1
Structural comparison of ATP8B1 and Ypk9 autoinhibition mechanism.

(A) Structural alignment of Ypk9 (PDB: 7OP8; yellow) and ATP8B1 (gray), both in the E2P inhibited state. (B) Close-up view of the region where the Ypk9 N-terminal tail (purple) and ATP8B1 N- and …

Structural map of the inherited intrahepatic cholestasis-related mutations.

(A) Mutations found in PFIC1, BRIC1 or ICP1 patients are respectively shown as red, yellow and blue spheres on ATP8B1 E2Pautoinhibited structure (in grey). Mutations indicated in bold are presented …

Author response image 1
Comparison of ATP8B1-CDC50A and Drs2-Cdc50 affinities for phosphoinositides.

The results displayed for ATP8B1-CDC50A correspond to those shown in Figure 6C while the results displayed for Drs2 are adapted from Figure 5B published in Azouaoui et al., (2017) J Biol Chem

Author response image 2
ATPase activity measurements of streptavidin-purified WT ATP8B1-CDC50A.

(A) ATPase activity of the purified ATP8B1-CDC50A complex determined in DDM/CHS at 30°C, using an enzyme-coupled assay, where the kinetics of NADH oxidation is monitored continuously. The various …

Tables

Table 1
Cryo-EM data collection, refinement, and validation statistics.
Data collection and processing
Magnification×130,000
Voltage (kV)300
MicroscopeTitan Krios (Aarhus University)
CameraGatan K3
Physical pixel size (Å/pix)0.66
Electron exposure (e–/Å2)60
Defocus range (μm)0.7–1.8
Number of movies3,918
Initial particle images (no.)470,103
Final particle images (no.)104,643
Symmetry imposedC1
Map resolution (Å)FSC threshold3.10.143
Map resolution range (Å)2.7–4.5
Refinement
Initial model used (PDB code)ATP8B1: I-TASSER homology model based on 6ROHCDC50A: 6K7L
Model resolution (Å)FSC threshold3.30.5
Map sharpening B factor (Å2)–84
Model compositionNon-hydrogen atomsProtein residuesLigands11,8681,4391 MG, 1 BEF, 4 Y01, 4 NAG, 1 BMA
B factors (Å2, min/max/mean)ProteinLigand33.89/136.87/67.0941.58/110.52/60.89
R.m.s. deviationsBond lengths (Å)Bond angles (°)0.0020.492
 Validation MolProbity score Clashscore Poor rotamers (%)1.434.740.08
 Ramachandran plot Favored (%) Allowed (%) Disallowed (%)96.923.080.0
Table 2
Half-maximal inhibitory concentration (IC50) values for the C-terminal peptide, in comparison with its phosphorylated form.

The values indicated in the table were deduced from dose-response curves displayed in Figure 5B and C. The number of data points used to calculate the IC50 is indicated in parenthesis. IC50 values …

ATP8B1-CDC50AInhibitory peptideIC50 (µM)
ΔN42/C1174(n = 33)C-terminal22.1 ± 1.2
ΔN42/C1174(n = 35)PhosphorylatedC-terminal377.4 ± 227
ΔC1174 (n = 34)C-terminal0.081 ± 0.014
ΔC1174 (n = 47)PhosphorylatedC-terminal1.96 ± 0.35
Key resources table
Reagent type (species) or resourceDesignationSource or referenceIdentifiersAdditional information
Strain, strain background (Saccharomyces cerevisiae, MATα)W303.1b/Δpep4López-Marqués laboratoryStrain deficient for the main vacuolar protease
Strain, strain background (Saccharomyces cerevisiae, MATα)W303.1b/GAL4-2Pompon LaboratoryAdditional copy of the GAL4 gene in the yeast chromosome
AntibodyFIC1 (H-91) rabbit polyclonal anti-ATP8B1 antibodySanta-Cruz BiotechnologyCat#sc-134967(1:10000)This product has been discontinued
AntibodyGoat anti-rabbit HRP-coupled polyclonal IgG antibodyBioradCat#1706515(1:2000)
Recombinant DNA reagentATP8B1 cDNAJoost Holthuis laboratoryUniprot: O43520
Recombinant DNA reagentCDC50 cDNAJoost Holthuis laboratoryUniprot: Q9NV96
Peptide, recombinant proteinATP8B1 C-terminal peptideBiomatik Company
Peptide, recombinant proteinATP8B1 phosphorylated C-terminal peptideBiomatik CompanyPhosphorylated on S1223
Peptide, recombinant proteinHRV 3 C proteaseThis studyExpressed (pGEX-4T-2) and purified in Lenoir laboratory. The purification procedure of N-terminally tagged HRV 3 C protease can be found in the Materials and methods section
Peptide, recombinant proteinTEV proteaseThis studyExpressed (pRK793) and purified in Lenoir laboratory. The purification procedure of N-terminally tagged TEV protease can be found in the Materials and methods section
Commercial assay or kitNucleoSpin Plasmid, Mini kit for Plasmid DNAMacherey-NagelCat#740588.250
Commercial assay or kitQuickChange II XL site-directed mutagenesis kitAgilent technologiesCat#200,521
Commercial assay or kitAmicon 100 kDa cutoffEMD MilliporeCat#UFC510024For volume ≤0.5 ml
Commercial assay or kitVivaspin 500SartoriusCat#VS0142For volumes from 0.5 to 0.005 ml
Commercial assay or kitVivaspin 6SartoriusCat#VS0641For volumes from 0.5 to 6 ml
Commercial assay or kitVivaspin 20SartoriusCat#VS2041For volumes from 2 to 20 ml
Commercial assay or kitSuperose 6 Increase 10/300 GLGE Healthcare/CytivaCat#29091596
Commercial assay or kitTSK3000-SWTosoh BioscienceCat#08541
Commercial assay or kitStreptavidin-sepharose resinGE Healthcare/CytivaCat#17511301
Chemical compound, drugn-dodecyl-β-D-maltopyranoside, AnagradeAnatraceCat#D310
Chemical compound, drugCholesteryl hemisuccinateSigmaCat#C6013
Chemical compound, drugLauryl maltose neopentyl glycolAnatraceCat#NG310
Chemical compound, drugSodium chlorideROTHCat#3957.2
Chemical compound, drugPotassium chlorideSigma-AldrichCat#P9541
Chemical compound, drugMagnesium chlorideSigma-AldrichCat#M2670
Chemical compound, drugMOPSSigma-AldrichCat#M1254
Chemical compound, drugATPSigma-AldrichCat#A2383
Chemical compound, drugPhospho(enol)pyruvic acidSigma-AldrichCat#860,077
Chemical compound, drugβ-nicotinamide adenine dinucleotide, reduced disodium
salt hydrate (NADH) Grade I, disodium salt
RocheCat#10107730001
Chemical compound, drugGlycerolVWR ChemicalsCat#24387.292
Chemical compound, drugD-glucoseBecton DickinsonCat#215,530
Chemical compound, drugD-galactoseSigma AldrichCat#G5388
Chemical compound, drugSIGMAFAST EDTA-free protease inhibitor cocktailSigmaCat#S8830
Chemical compound, drugBrain phosphatidylinositol-4-phosphate (PI4P)Avanti Polar Lipids, IncCat#840045 P
Chemical compound, drugBrain phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2)Avanti Polar Lipids, IncCat#840046 P
Chemical compound, drug1,2-dioleoyl-sn-glycero-3-phospho-(1'-myo-inositol-3'-phosphate) (PI(3)P)Avanti Polar Lipids, IncCat#850150 P
Chemical compound, drug1,2-dioleoyl-sn-glycero-3-phospho-(1'-myo-inositol-5'-phosphate) (PI(5)P)Avanti Polar Lipids, IncCat#850152 P
Chemical compound, drug1,2-dioleoyl-sn-glycero-3-phospho-(1'-myo-inositol-3',4'-bisphosphate) (PI(3,4)P2)Avanti Polar Lipids, IncCat#850153 P
Chemical compound, drug1,2-dioleoyl-sn-glycero-3-phospho-(1'-myo-inositol-3',5'-bisphosphate) (PI(3,5)P2)Avanti Polar Lipids, IncCat#850154 P
Chemical compound, drug1,2-dioleoyl-sn-glycero-3-phospho-(1'-myo-inositol-3',4',5'-trisphosphate) (PI(3,4,5)P3)Avanti Polar Lipids, IncCat#850156 P
Chemical compound, drugBrain phosphatidylserine (PS)Avanti Polar Lipids, IncCat#840032 P
Chemical compound, drug1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)Avanti Polar Lipids, IncCat#850457 P
Chemical compound, drug1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE)Avanti Polar Lipids, IncCat#850757 P
Chemical compound, drug1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoserine (POPS)Avanti Polar Lipids, IncCat#840034 P
Chemical compound, drugBovine heart cardiolipin (CL)Avanti Polar Lipids, IncCat#840012 P
Chemical compound, drugegg chicken sphingomyelin (SM)Avanti Polar Lipids, IncCat#860061 P
Chemical compound, drugedelfosineAvanti Polar Lipids, IncCat#999995 P
Chemical compound, drugMiltefosine(Fos-Choline-16)AnatraceCat#F316
Chemical compound, drug1-stearoyl-2-hydroxy-sn-glycero-3-phosphocholine (Lyso-PC)SigmaCat#L2131
Chemical compound, drugPyruvate kinaseSigmaCat#P7768
Chemical compound, drugLactate dehydrogenaseSigmaCat#L1006
Chemical compound, drug[γ-32P]ATPPerkin-ElmerCat#BLU002A
Chemical compound, drugHis-probe-HRPThermo ScientificCat#15,165
Software, algorithmEPU v 2.3Thermo Fisherhttps://www.thermofisher.com/it/en/home/electron-microscopy/products/software-em-3d-vis/epu-software.html
Software, algorithmcryoSPARC v3Punjani et al., 2017,Structura Biotechnology Inchttps://www.nature.com/articles/nmeth.4169
Software, algorithmChimeraX 1.4Goddard et al., 2018https://www.cgl.ucsf.edu/chimerax/
Software, algorithmI-TASSERYang et al., 2015https://zhanggroup.org/I-TASSER/
Software, algorithmCoot 0.9.6Emsley et al., 2010https://doi.org/10.1107/S0907444904019158https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/
Software, algorithmPhenix 1.19.2Liebschner et al., 2019https://doi.org/10.1107/S2059798318006551http://phenix-online.org/
Software, algorithmMolprobity 4.5.1Williams et al., 2018https://doi.org/10.1002/pro.3330http://molprobity.biochem.duke.edu
Software, algorithmImageJSchneider et al., 2012https://imagej.nih.gov/ij/
Software, algorithmPrism 9GraphPadhttps://www.graphpad.com/scientific-software/prism/
OtherC-Flat 1.2/1.3 Cryo-EM Grid - Copper (400 Grid Mesh, 20 nm Carbon Thickness)Molecular DimensionsCF-1.2/1.3-4CU-50Support film for biological samples in cryo-EM techniques -20 nm C-flat carbon film with 1.2 μm hole size and 1.3 μm hole spacing
Table 3
Primers used in this study.
Primers
FwBadATP8B15’- ACAGTTTAAACGGTGGTGAGAATCTTTATTTT
CAGGGCGGTGGTGGTGGTATGAGTACAGAAAGAGACTCAG - 3’
RevBadATP8B15’- AGCATGGAGCTCTCAGCTGTCCCCGGTGCGCCTGTA - 3’
FwHisCDC50A5’ – CACAGAATTCTAGTATGCATCATCATCATCATCATCAT
CATCATCACCTAGGTGGTATGGCGATGAACTATAACGCG – 3’
RevHisCDC50A5’ – CACAGAGCTCCTAAATGGTAATGTCAGCTGTATTAC - 3’
FwdD454N5’- GATCCATTATATCTTCTCTAATAAGACGGGGACACTCACAC –3’
RevD454N5’- GTGTGAGTGTCCCCGTCTTATTAGAGAAGATATAATGGATC –3’
Fwd3 C-P435’ – CTGGAGGTGCTGTTCCAGGGCCCGG
AACAAAACCGAGTCAACAGGGAAGC – 3’
Rev3 C-P435’ – CGGGCCCTGGAACAGCACCTCCAGTG
GTTCAACAGCAGACCCCTGGTCATCAAG – 3’
Fwd3C-E11745’ – CTGGAGGTGCTGTTCCAGGGCCCGAGTGATAAGATCCAGAAGCATC – 3’
Rev3C-E11745’ – CGGGCCCTGGAACAGCACCTCCAGTTCTGATGGCCAGATGGTCAT– 3’
Table 4
Plasmids used in this study.
PlasmidsReferences
pYeDP60_BAD-TevS-ATP8B1 (WT) / His10CDC50AThis study
pYeDP60_BAD-TevS-ATP8B1 (D454N) / His10CDC50AThis study
pYeDP60_BAD-TevS-ATP8B1 (P42-3CS) / His10CDC50AThis study
pYeDP60_BAD-TevS-ATP8B1 (P42-3CS) / His10CDC50AThis study
pYeDP60_BAD-TevS-ATP8B1 (E1174-3CS) / His10CDC50AThis study
pYeDP60_BAD-TevS-ATP8B1 (P43 +E1174-3 CS) / His10CDC50AThis study
pRK793 MBP-Tevsite-His7-TEVS219V-Arg5Kapust et al., 2001
pGEX-4T-2 His6-Arg8-GST-3C

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