Structural Basis for the Golgi Association by the Pleckstrin Homology Domain of the Ceramide Trafficking Protein (CERT)

Background: The CERT PH domain is indispensable for the ER-to-Golgi ceramide transport.

Results: The three-dimensional structure and interaction study revealed the Golgi recognition mode of the CERT PH domain.

Conclusion: The basic groove in the CERT PH domain plays a critical role in the Golgi recognition.

Significance: Conservation of the basic groove within lipid transporters uncovers functional significance of the structural motif.

Abstract

Ceramide transport from the endoplasmic reticulum to the Golgi apparatus is crucial in sphingolipid biosynthesis, and the process relies on the ceramide trafficking protein (CERT), which contains pleckstrin homology (PH) and StAR-related lipid transfer domains. The CERT PH domain specifically recognizes phosphatidylinositol 4-monophosphate (PtdIns(4)P), a characteristic phosphoinositide in the Golgi membrane, and is indispensable for the endoplasmic reticulum-to-Golgi transport of ceramide by CERT. In this study, we determined the three-dimensional structure of the CERT PH domain by using solution NMR techniques. The structure revealed the presence of a characteristic basic groove near the canonical PtdIns(4)P recognition site. An extensive interaction study using NMR and other biophysical techniques revealed that the basic groove coordinates the CERT PH domain for efficient PtdIns(4)P recognition and localization in the Golgi apparatus. The notion was also supported by Golgi mislocalization of the CERT mutants in living cells. The distinctive binding modes reflect the functions of PH domains, as the basic groove is conserved only in the PH domains involved with the PtdIns(4)P-dependent lipid transport activity but not in those with the signal transduction activity.

Introduction

Sphingolipids are the major structural element in eukaryotic membranes, and they function as crucial signal mediators in a variety of important biological processes, including apoptosis, inflammation, etc. (1). Sphingolipid synthesis involves multiple steps of metabolic conversion accomplished by a series of enzymes localized in the ER,³ the Golgi apparatus, and the plasma membrane. Therefore, the transportation of sphingolipids from one organelle to others must be highly organized. The interorganelle trafficking of sphingolipids is mediated in either a vesicular or nonvesicular manner (2). For instance, in mammalian cells, a de novo synthesized ceramide in ER membranes is transported to the Golgi in a nonvesicular manner by an ER-to-Golgi specific ceramide transporter (CERT, also known as GPBPΔ26, a splicing variant of Goodpasture antigen-binding protein) (3, 4). The functional impairment of CERT results in the complete loss of the ceramide trafficking activity in cells, indicating its essential role in sphingolipid biogenesis (4).

CERT is a cytoplasmic 68-kDa protein, and it contains two distinct functional domains as follow: the N-terminal pleckstrin homology (PH) domain (∼100 amino acid residues) and the C-terminal StAR-related lipid transfer (START) domain (∼230 amino acid residues) (Fig. 1A) (4). The middle region between the PH and START domains is not predicted to form a globular fold; however, it contains a short peptide motif with the consensus sequence EFFDAXE, named the “two phenylalanines in an acidic trait” (FFAT) motif (Fig. 1A) (5). The FFAT motif interacts with VAMP-associated protein, an ER-resident type II membrane protein, and the interaction is considered to be crucial for association of CERT with the ER membrane (5).

FIGURE 1.

Solution structure of the CERT PH domain, determined by NMR. A, primary structure of CERT; B, backbone superposition of the 20 lowest energy structures; and C, ribbon diagram of the representative structure with the lowest energy. These molecular diagrams were generated with the program MOLMOL (26). D, electrostatic potential surface of the CERT PH domain. Red and blue indicate negative and positive electrostatic surfaces, respectively. The electrostatic potential was calculated using the program MOLMOL (26). The “front view” shows the same side as in B and C. E, ribbon model representation of the CERT PH domain, with magnification of the basic groove. The side chains of the basic and aromatic residues in the basic groove are displayed as blue and green sticks, respectively.

The CERT START domain specifically recognizes and then extracts ceramide from lipid membranes (4). This domain is essential for the activities, as the deletion of the START domain impairs the CERT ceramide transfer activity (4). Recently, the three-dimensional structure of the CERT START domain was determined by x-ray crystallography (6), and the molecular mechanisms for its membrane interaction, and subsequent ceramide extraction, were revealed (7, 8).

Interestingly, however, the CERT START domain alone is not sufficient for the ER-to-Golgi ceramide transport in vivo (4, 5). Indeed, the PH and START domains are both indispensable for the CERT ceramide transport activity, as the impairment of the CERT PH domain also causes the complete loss of the ceramide transport activity (4, 5).

The CERT PH domain specifically recognizes PtdIns(4)P in membranes (4). Because PtdIns(4)P is the most abundant and preferentially distributed phosphoinositide in trans-Golgi membranes, it is assumed that the PH domain is required for efficient association of CERT with the Golgi membrane (4, 5). At present, however, the detailed mechanism, by which the CERT PH domain interacts with PtdIns(4)P in the Golgi membrane to exert the transportation activity, remains unclear.

In this study, we determined the three-dimensional structure of the CERT PH domain by using solution-state NMR techniques. The structure revealed that the CERT PH domain has a characteristic basic groove near the PtdIns(4)P recognition site. Extensive interaction studies using NMR and other biochemical methods indicated that the recognition of the PtdIns(4)P headgroup by the CERT PH domain is weak, but the interaction with PtdIns(4)P in the Golgi membrane is enhanced by an electrostatic interaction between the basic groove and the phospholipid membrane. The Golgi mislocalization of the CERT mutants in living cells supported the functional importance of the basic groove as well as the PtdIns(4)P recognition site. The basic groove might also help to orient the CERT PH domain for an efficient searching for PtdIns(4)P in the Golgi membrane. The membrane-interacting β1/β2 loop also contributes to the Golgi interaction. Furthermore, analyses of the PH domain sequence alignment revealed that the distinctive membrane-binding mode, using the basic groove, is found only among the PH domains involved with the PtdIns(4)P-dependent lipid transport activity and not among those with the signal transduction activity.

EXPERIMENTAL PROCEDURES

All chemicals were purchased from Nacalai Tesque, Inc., unless specifically noted. The diC₄-PtdIns(4)P and inositol (1,4)-bisphosphate were purchased from Echelon Biosciences, Inc.

Expression and Purification of the CERT PH Domain

The cDNA containing human CERT was prepared as described previously (4). The cDNA fragment encoding amino acid residues 23–117 from the full-length CERT was amplified by PCR and cloned into the pET28a(+) plasmid (Novagen). The plasmid was transformed into the Escherichia coli BL21(DE3) strain. The uniformly ¹⁵N- and ¹³C/¹⁵N-labeled CERT PH domains were prepared by growing the transformants in M9 media, containing 0.1% (w/v) [¹⁵N]ammonium chloride (99 atom % ¹⁵N) and either 0.2% (w/v) d-glucose or d-[¹³C₆]glucose (98 atom % ¹³C), respectively. Similarly, the uniformly ²H/¹⁵N-labeled protein was prepared by using M9 medium, containing 100% D₂O (99.8 atom % ²H), 0.1% (w/v) [¹⁵N]ammonium chloride, and 0.2% (w/v) d-[²H₇,¹³C₆]glucose (both 98 atom % ²H and ¹³C). The transformants were grown at 37 °C to an A₆₀₀ of 0.6–0.8, and protein expression was induced with 0.5 mm isopropyl 1-thio-β-d-galactopyranoside. The cultivation was continued for an additional 16 h at 25 °C, and the cells were harvested by centrifugation.

The cell pellets were resuspended in lysis buffer, containing 20 mm Tris-HCl (pH 8.0), 300 mm NaCl, and 2.5 mm 2-mercaptoethanol. The suspended cells were lysed by sonication and subjected to centrifugation. The His₆-tagged CERT PH domain was purified from the supernatant of the centrifuged lysate by metal-chelating chromatography, using His-Select^TM nickel affinity gel (Sigma). The His₆ tag was then removed from the purified protein by enzymatic digestion with tobacco etch virus protease (Invitrogen). The digest was passed through His-Select^TM nickel affinity gel, to remove the His₆ tag fragments and the tobacco etch virus protease. The CERT PH domain was further purified by anion exchange column chromatography, using a Mono Q ion exchange column (GE Healthcare).

The recombinant CERT PH domain consists of 96 amino acids, corresponding to Val-24 to Thr-117 in the full-length CERT protein and two glycine residues at the N terminus, which remained after the digestion of the N-terminal purification tag. Site-directed alanine-scanning mutagenesis of the CERT PH domain was performed by QuikChange mutagenesis (Stratagene), according to the manufacturer's protocol. All mutants were expressed and purified in the same manner as the wild type.

Preparation of Liposomes

The phospholipids used in this study (1-palmitoyl-2-oleoylphosphocholine, 1-palmitoyl-2-oleoylphosphoethanolamine, 1-palmitoyl-2-oleoylphosphoserine, and d-myo-phosphatidylinositol 4-monophosphate (PtdIns(4)P)) were purchased from Avanti Polar Lipids or Echelon. For the PtdIns(4)P-embedded liposomes, 1-palmitoyl-2-oleoylphosphocholine/1-palmitoyl-2-oleoylphosphoethanolamine/1-palmitoyl-2-oleoylphosphoserine/PtdIns(4)P = 66.6:24.2:4.2:5.0% (molar ratio) were used. This phospholipid composition used here is similar to that in the Golgi membrane (9), and hereafter, we refer to the corresponding liposome as the “PtdIns(4)P-embedded Golgi-mimetic liposomes.” For the PtdIns(4)P-free liposomes, PtdIns(4)P was exchanged with 1-palmitoyl-2-oleoylphosphocholine. The phospholipid mixture was dissolved in chloroform/methanol (1:1 (v/v)) and was dried under a nitrogen flow to form a thin film. The lipid film was suspended by vortexing with a buffer (10 mm HEPES-NaOH (pH 7.2), 100 mm NaCl, and 5 mm tris(2-carboxyethyl)phosphine-HCl), and small unilamellar vesicles were prepared by using a Mini-Extruder (Avanti Polar Lipids, Inc.), as described previously (8).

NMR Spectroscopy

All NMR experiments were performed on a Bruker Avance 800 spectrometer equipped with a TXI cryogenic probe. All NMR spectra were recorded at 25 °C, using 0.10–0.25 mm CERT PH domain in 10 mm HEPES-NaOH buffer (pH 7.2), containing 100 mm NaCl, 5 mm tris(2-carboxyethyl)phosphine-HCl, and 7% D₂O. For recording two-dimensional ¹H-¹H NOESY, two-dimensional ¹H-¹³C HSQC, two-dimensional (HB)CB(CGCD)HD, two-dimensional (HB)CB(CGCDCE)HE, three-dimensional ¹³C-edited NOESY-HSQC, and three-dimensional HCCH-TOCSY spectra, 100% D₂O buffer was used instead. Site-specific resonance assignments of ¹H, ¹⁵N, ¹³C nuclei of the CERT PH domain were achieved by a standard set of multidimensional triple resonance experiments, such as two-dimensional ¹H-¹⁵N HSQC, two-dimensional ¹H-¹³C CT-HSQC, three-dimensional HNCACB, three-dimensional HN(CO)CACB, three-dimensional HNCO, three-dimensional HN(CA)CO, three-dimensional ¹⁵N-edited NOESY-HSQC, four-dimensional ¹³C,¹⁵N-edited NOESY, and three-dimensional MQ-(H)CCmHm-TOCSY (10–12). All NMR spectra were processed by TopSpin 2.1 (Bruker) or NMRPipe (13) and were analyzed with Sparky (Goddard and Kneller, SPARKY 3-NMR Assignment and Integration Software, University of California, San Francisco). The chemical shift assignments of the CERT PH domain were deposited in the Biological Magnetic Resonance Data Bank under accession number 11473.

In the chemical shift perturbation studies, 0.1 mm of uniformly ¹⁵N-labeled CERT PH domain was titrated with increasing concentrations (0.2–1.6 mm) of diC₄-PtdIns(4)P or Ins(1,4)P₂. The averaged chemical shift changes (Δδ) in the two-dimensional ¹H-¹⁵N HSQC spectra were calculated with the equation Δδ = ((Δδ_H)² + (Δδ_N/5)²)^1/2, where Δδ_H and Δδ_N are the chemical shift changes of the amide protons and ¹⁵N nucleus in parts/million.

In the transferred cross-saturation (TCS) experiments (14, 15), the PtdIns(4)P-embedded Golgi-mimetic liposomes were mixed with the 0.20 mm of uniformly ²H/¹⁵N-labeled CERT PH domain. The total lipid concentration in the sample was set to 1.6 mm. The proton content of the solvent was set to 20% (v/v), to suppress the intramolecular spin diffusion in the CERT PH domain (14–17). Saturation of the lipid signals was achieved by a series of Gaussian-shaped pulses with a 3-ms duration and a 1-ms delay between pulses (18, 19). The center of the irradiation frequency was set to 3.2 ppm, which corresponds to the chemical shifts of the lipid headgroups (20). A control spectrum with the irradiation frequency set to −10 ppm was acquired in an interleaved manner. The irradiation time and the pre-scan delay were set to 0.35 and 2.65 s, respectively. The irradiation scheme saturates all of the aliphatic resonances from the phospholipids. The TCS experiment was also performed without liposomes, to estimate the effects of unwanted direct saturations to the protein. In the analyses, the signal intensity reduction ratios obtained with liposomes were normalized by those without liposomes.

Structure Calculation

Proton-proton distance restraints were obtained from two-dimensional ¹H-¹H NOESY (mixing time, 100 ms), three-dimensional ¹³C-edited NOESY-HSQC (mixing time, 150 ms), and three-dimensional ¹⁵N-edited NOESY-HSQC (mixing time, 120 ms) spectra, using the CANDID algorithm of CYANA 2.1 (21). The backbone dihedral angle restraints (58 for ϕ and 56 for ψ angles) were obtained from the program TALOS, using the ¹H_N, ¹⁵N_H, ¹³C^α, ¹³C^β, ¹³C′, and ¹H^α chemical shifts (22). Distance restraints for 32 hydrogen bonds were introduced for sites exhibiting a slow amide proton exchange and an evident secondary structure, in a preliminary structure calculation without hydrogen bond information.

Using the distance and angular restraints obtained from the NMR experiments, structure calculations were performed with a simulated annealing protocol, using the program CYANA 2.1 (21). The 20 final structures with the lowest statistical violations to the experimental data were adopted from 100 independent calculations (23). The ensemble of the 20 structures was further refined by the program CNS with explicit solvent and electrostatics (24). The quality of the 20 final structures was evaluated using the program PROCHECK NMR (25). All structure figures were prepared using the program MOLMOL (26). The structure coordinates have been deposited in the Protein Data Bank, with the accession code 2RSG.

Surface Plasmon Resonance (SPR) Experiments

SPR measurements were performed using a Biacore 2000 instrument (GE Healthcare). The liposomes were immobilized on a sensor chip L1 (GE Healthcare), as described previously (8). The binding assay was performed in running buffer containing 10 mm HEPES-NaOH (pH 7.2), 100 mm NaCl, and 5 mm tris(2-carboxyethyl)phosphine-HCl at 25 °C. Various concentrations of the CERT PH domain (1–16 μm) were injected into the flow cells at a flow rate of 30 μl/min. The binding constants were obtained from the steady-state curve fitting of the SPR sensorgrams, using the BIAevaluation 3.1 software (GE Healthcare).

RESULTS

Characterization of the CERT PH Domain Binding to PtdIns(4)P-embedded Membranes

To clarify the ligand specificities and affinities of the CERT PH domain, the binding constants between the CERT PH domain and phosphoinositide-embedded liposomes were measured by SPR methods. The dissociation constant (K_D) for the PtdIns(4)P-embedded Golgi-mimetic liposomes was ∼3.2 μm (Table 1), which is comparable with the previously reported value (27). Furthermore, the binding affinity for the PtdIns(4)P-embedded liposomes was ∼50-fold higher than for the PtdIns(3)P- and PtdIns(5)P-embedded liposomes, and ∼5-fold higher than for those embedded with PtdIns(4,5)P₂ (Table 1). These results support the proposal that the CERT PH domain specifically recognizes the PtdIns(4)P-containing lipid membrane, as reported previously (4, 27). Unexpectedly, the CERT PH domain showed weak but significant binding (K_D = 220 μm) to the PtdIns(4)P-free liposomes (Table 1). Although the binding was about 70-fold weaker, as compared with that of the PtdIns(4)P-containing liposomes, it suggested that the CERT PH domain also nonspecifically interacts with phospholipid membranes.

TABLE 1.

Dissociation constants (K_D) between the CERT PH domain and phosphoinositide-embedded liposomes

Phosphoinositidesa	KDb	Relative affinityc
	×10−6 m
PtdIns(4)P	3.26 ± 0.23	1.00
PtdIns(3)P	75.4 ± 33	0.05
PtdIns(5)P	64.7 ± 33	0.06
PtdIns(4,5)P2	15.6 ± 1.9	0.21
No phosphoinositides	217 ± 4.1	0.02

^a Phosphoinositides were embedded in liposomes as described under “Experimental Procedures.”

^b The K_D values were measured by the SPR method, as described under “Experimental Procedures.”

^c Relative affinity, as compared with that of the PtdIns(4)P-embedded liposomes, was indicated.

Solution Structure of the CERT PH Domain

To understand the structural basis of the Golgi-specific interaction, the solution structure of the CERT PH domain (residue 23–117) was determined, using standard multidimensional NMR techniques, as described under “Experimental Procedures.” The 20 lowest energy structures of the CERT PH domain were superimposed, as shown in Fig. 1B. The structural statistics of the lowest energy structures are shown in Table 2. The average pairwise root-mean-square differences of all secondary-structure elements indicated were 0.56 ± 0.09 Å for the backbone atoms and 1.20 ± 0.16 Å for all of the non-hydrogen atoms.

TABLE 2.

Statistics for the 20 final NMR structures of the CERT PH domain

NMR distance and dihedral restraints
Distance restraints
NOE upper distance restraints
Short range (|i − j| = 1)	1205
Medium range (1 > |i − j| <5)	178
Long range (|i − j| >5)	521
Hydrogen bonds	32
Total dihedral angle restraints
ϕ	58
ψ	56
Structure statistics
Violations
Distance restraints (>0.5 Å)	0
Dihedral angle restraints (>5°)	0
Ramachandran plota
Most favored region	89.3%
Additionally allowed region	10.3%
Generously allowed region	0.2%
Disallowed regionb	0.1%
Average pairwise r.m.s.d.c
Backbone atoms	0.56 ± 0.09 Å
Non-hydrogen atoms	1.20 ± 0.16 Å

^a Ramachandran analysis was performed for all residues, using the program PROCHECK NMR.

^b The disallowed residue is Gly-64, which is located in the unstructured loop connecting β3 and β4.

^c Pairwise r.m.s.d. was calculated for the ordered secondary structure components (amino acid residues 26–29, 43–47, 52–55, 66–70, 75–77, 85–90, 94–98, and 106–115) of the CERT PH domain.

The CERT PH domain consists of seven β-strands (β1, 26–33; β2, 40–48; β3, 51–55; β4, 67–70; β5, 75–78; β6, 85–90; and β7, 93–98) and one C-terminal α-helix (αC, 106–115) (Fig. 1C). The main chain trace of the CERT PH domain falls in a regular PH domain fold (28, 29). The core structure forms a closely packed “β-sandwich,” with two nearly orthogonal antiparallel β-sheets (β1-β4 and β5-β7). The C-terminal α-helix lies on the top of the β-sandwich, and two loops connecting β1/β2 and β3/β4 are at the “exposed” end of the β-sandwich. The β1/β2 anti-parallel strands are almost twice as long as the β3/β4 anti-parallel strands. This feature makes half of the β1/β2 anti-parallel β-strands and the β1/β2 loop protrude from the core β-sandwich. The β1/β2, β3/β4, and β7/αC loops of the CERT PH domain showed higher deviations, as compared with the other elements. In the two-dimensional ¹H-¹⁵N HSQC spectrum, four backbone amide cross-peaks from the β1/β2 loop (Asn-35, Tyr-36, Ile-37, and Gly-39) and one from the β7/αC loop (Asp-103) were invisible. This might be due to the presence of multiple conformations or solvent exchanges on an intermediate NMR time scale for these sites.

Fig. 1D shows the electrostatic potential surfaces of the CERT PH domain. On the surface of the CERT PH domain, the basic residues are clustered in the middle of the molecule, forming a basic groove around the protruding part of the β1/β2 region. The basic groove stretches from the “exposed end” to the “side surface” of the β-sandwich, and it includes seven basic residues (Lys-32, Arg-43, Lys-56, Arg-66, His-79 Arg-85, and Arg-98) (Fig. 1, C–E). Conversely, the protruding β1/β2 region that is surrounded by the basic groove mainly consists of aromatic and/or hydrophobic residues, such as Trp-33, Tyr-36, Ile-37, and Trp-40 (Fig. 1E).

Determination of the PtdIns(4)P-binding Site on the CERT PH Domain

To identify the PtdIns(4)P-binding site on the CERT PH domain, we performed chemical shift perturbation (CSP) experiments. Fig. 2A shows an overlay of two-dimensional ¹H-¹⁵N HSQC spectra of the [U-¹⁵N]CERT PH domain with various concentrations of water-soluble diC₄-PtdIns(4)P. As exemplified by the backbone amide signals from Trp-33 and Trp-40, as well as the side chain NH₂ signals from Asn-35 (enlarged panels in Fig. 2A), several cross-peaks exhibited significant chemical shift changes upon the addition of diC₄-PtdIns(4)P. Most of the residues exhibited typical “fast-exchanging” CSPs, which indicate rapid binding/unbinding events between the CERT PH domain and diC₄-PtdIns(4)P. The affinity of diC₄-PtdIns(4)P for the CERT PH domain was determined by a global fitting to the titration curves of six different amino acids, and the K_D for diC₄-PtdIns(4)P was 763 ± 13 μm (Fig. 2B). The normalized chemical shift changes caused by the addition of 16 eq (1.6 mm) of diC₄-PtdIns(4)P were summarized in Fig. 2C, and the residues with significant CSPs were mapped onto the tertiary structure of the CERT PH domain (Fig. 2D). The residues on the β1/β2 loop, the C-terminal of the β3 strand, the C-terminal of the β3/β4 loop, as well as the middle of the β7 strand exhibited significant CSPs (Fig. 2C). The mapping of these residues clearly defined a phosphatidylinositol phosphate binding pocket in the CERT PH domain, indicating that the exposed end of the basic groove is the specific PtdIns(4)P-binding site (Fig. 2D). The titration of inositol (1,4)-bisphosphates further supported this notion (supplemental Fig. S1). The side chain of Arg-43 is located in the middle of the binding site (Fig. 2D). However, the side chain Hϵ-Nϵ resonance could not be observed in the two-dimensional ¹H-¹⁵N HSQC spectrum of the CERT PH domain, probably due to the broadening induced by chemical exchange with the water resonance and/or fluctuation among multiple conformations. Nevertheless, the mutation of the residue significantly reduced the binding affinity for the Golgi-mimetic liposomes, as discussed later (Fig. 4). It indicates that the PtdIns(4)P-binding pocket in the CERT PH domain is located in the common phosphatidylinositol phosphate-binding site of the other PH domains (28, 30). We also attempted to determine the tertiary structure of the CERT PH domain bound to diC₄-PtdIns(4)P; however, it was not successful because no intermolecular NOE was observed possibly due to the low binding affinity between the two molecules.

FIGURE 2.

Identification of the PtdIns(4)P-binding site by CSP experiments, using diC₄-PtdIns(4)P. A, superimposed two-dimensional ¹H-¹⁵N HSQC spectra of 0.1 mm uniformly ¹⁵N-labeled CERT PH domain with increasing concentrations of diC₄-PtdIns(4)P, as shown in the inset: 0 mm (black), 0.1 mm (blue), 0.2 mm (light blue), 0.4 mm (green), 0.8 mm (orange), and 1.6 mm (red). B, determination of the binding constant between the CERT PH domain and diC₄-PtdIns(4)P. CSPs observed for six residues in the CERT PH domain with various concentrations of diC₄-PtdIns(4)P were fitted globally, assuming a single site 1:1 interaction. C, normalized chemical shift changes (Δδ; see “Experimental Procedures”) of individual residues in the CERT PH domain induced by the addition of 1.6 mm diC₄-PtdIns(4)P. Red and orange dashed lines indicate 0.2 and 0.1 ppm normalized chemical shift changes, respectively. Numbers on the horizontal axis indicate the residue number of the backbone amide signals in the CERT PH domain (24–117). For side chains, the names of the resonances are indicated. D, mapping of the residues that were significantly perturbed by the titration of diC₄-PtdIns(4)P on the surface representation of the CERT PH domain structure. Red and orange surfaces indicate the side chains of the residues with Δδ >0.2 and 0.1–0.2 ppm CSP, respectively. The dark gray coloring indicates residues without information from the CSP experiment (Tyr-36, Ile-37, Gly-39, Asn-50, Pro-78, Pro-102, and Asp-103).

FIGURE 4.

Alanine-scanning mutagenesis experiments performed for the CERT PH domain. The dissociation constant (K_D) values of the CERT PH domain mutants for the PtdIns(4)P-embedded liposomes were determined by SPR, and the relative binding affinities, as compared with that of the wild type, were plotted. The absolute K_D values are listed in supplemental Table S2.

The affinity of the CERT PH domain for the soluble form of PtdIns(4)P is quite weak, with a dissociation constant in the millimolar range (Fig. 2B). indicating that the exposed end of the basic groove is the specific PtdIns(4)P-binding site (Fig. 2D). Conversely, the affinity of the CERT PH domain for the PtdIns(4)P-embedded Golgi-mimetic liposomes measured by the SPR method was 3 μm (Table 1). This indicates the presence of additional interactions between the PtdIns(4)P-embedded membrane and the CERT PH domain.

Determination of the Membrane-interacting Site on the CERT PH Domain

To identify the additional membrane-interaction site in the CERT PH domain, we performed TCS experiments (14, 15). As outlined in Fig. 3A, the saturation of the phospholipid resonances in liposomes is transferred to the amide-proton resonances at a membrane interacting surface, which in turn is detected as the attenuation of the CERT PH domain amide signals. It is worth noting that the NMR signals of the bound-state CERT PH domain would not be detected due to the large molecular weight of the liposomes (over a few MDa). However, the rapid exchange between the free and bound states of the CERT PH domain allows us to detect the saturation caused in the bound state as the signal reduction in the free state (15, 17). Under the present experimental conditions, the two-dimensional ¹H-¹⁵N HSQC resonances from the CERT PH domain were almost identical to those in the free state. The fraction of the bound-state CERT PH domain in the NMR sample is estimated to be less than 10%, and the dissociation rate constant between the CERT PH domain and the PtdIns(4)P-embedded Golgi-mimetic liposomes is sufficiently fast (∼1.0 s⁻¹) (supplemental Fig. S2). The bound population and the dissociation rate constants are compatible conditions for a successful TCS experiment, as indicated in the recent theoretical analysis of the TCS method (16). Assuming a 1-μs rotational correlation time, a radio frequency irradiation of 0.3 s would cause >30% signal reductions for protons within 5 Å from the interface (16).

FIGURE 3.

Identification of the membrane interaction site in the CERT PH domain by a TCS experiment using the Golgi-mimetic liposomes. A, schematic representation of the TCS experiment performed in this study. The proton resonances originating from the lipid headgroup were saturated by radiofrequency irradiation, and this saturation was transferred to the residues in the CERT PH domain that was proximal to the PtdIns(4)P-embedded liposome. B, magnified two-dimensional ¹H-¹⁵N HSQC spectra of uniformly ²H/¹⁵N-labeled CERT PH domain in the presence of PtdIns(4)P-embedded liposomes, recorded without (left panel) and with (right panel) radiofrequency irradiation. One-dimensional ¹H cross-sections are also shown for the signals of Asp-92 and Gln-41. C, signal intensity reduction ratios in the TCS experiment. The ratios of the signal intensities with and without saturation were plotted against the residue numbers. Red and orange dashed lines indicate the signal intensity reduction ratios of 0.4 and 0.3, respectively. The bottom axis is the same as in Fig. 2. The error bars were calculated from the root sum square of the S/N ratio in the spectra with and without irradiation. D, mapping of the residues affected by the transferred cross-saturation on the surface of the CERT PH domain. Red and orange surfaces indicate the side chains of the residues with signal intensity reduction ratios of >0.4 and 0.3–0.4, respectively. The dark gray coloring indicates residues without information from the TCS experiment.

The irradiation of the Golgi-mimetic liposome resulted in specific intensity losses in the CERT PH domain resonances (Fig. 3, B and C). The residues that showed over 30% intensity reductions, as compared with the control spectrum, are colored and mapped on the three-dimensional structure of the CERT PH domain (Fig. 3D). Specifically, the protruding part of the β1/β2 sheet, including the β1/β2 loop (main chain H_N resonances of Ser-31, Lys-32, Trp-33, Thr-34, His-38, Trp-40, and Gln-41 and side chain resonances of Trp-33, Asn-35, Trp-40, and Gln-41), the residues in the β5/β6 loop to the β6-β7 sheets (His-79, Cys-84, Arg-85, Phe-86, Asp-87, Ile-88, Ser-93, Trp-95, Tyr-96, and Arg-98), and part of the C-terminal helix (Gln-107, Glu-113, and Gln-114) were strongly affected (Figs. 3B and 6). The mapping of these residues indicates that the membrane interaction surface of the CERT PH domain extends through the entire region of the basic groove, including the PtdIns(4)P-binding site located at the exposed end as well as the basic “side face” of the CERT PH domain (Fig. 3D).

FIGURE 6.

Multiple alignment of the PH domains. The alignment was performed with the program ClustalW2 (52). The specificity of each PH domain is denoted at the end of the aligned sequence (30, 48, 53–55). The secondary structure of the CERT PH domain is indicated above the CERT PH domain sequence. The residues that experienced significant effects in the CSP and TCS experiment are indicated by green and red dots, respectively. The downward-pointing arrowheads indicate the CERT PH domain residues that form the basic groove. The numbers of the conserved basic residues are indicated on the top of the multiple alignments. The β1/β2 loop region is enclosed by a dotted line, and the conserved hydrophobic and hydrophilic residues in the region are highlighted in yellow and light blue, respectively. The residues denoted by a white letter in a blue background are important for the recognition of the 4-phosphate group of phosphoinositide (40).

The TCS experiments were also performed with PtdIns(4)P-free liposomes (supplemental Fig. S3). As expected from the lower binding affinity to the PtdIns(4)P-free liposomes (K_D ∼220 μm), the absolute values of the signal intensity reductions were smaller than those obtained from the experiments with the PtdIns(4)P-embedded liposomes. In this experiment, the side face of the CERT PH domain was preferentially saturated (supplemental Fig. S3). This suggests that the side face forms a nonspecific membrane interaction surface, besides the specific PtdIns(4)P-binding site at the exposed end of the CERT PH domain.

Alanine-scanning Mutageneses

To confirm the importance of the basic groove in the interaction with the Golgi membrane, we performed a series of alanine-scanning mutageneses. Single alanine substitutions were introduced for 18 amino acids in the basic groove of the CERT PH domain (Lys-32, Trp-33, Thr-34, Asn-35, Tyr-36, Ile-37, His-38, Gly-39, Trp-40, Gln-41, Arg-43, Lys-56, Arg-66, His-78, Arg-85, Ser-93, Tyr-96, and Arg-98), and their binding constants for the PtdIns(4)P-embedded Golgi-mimetic liposomes were measured by SPR experiments (Fig. 4 and supplemental Table S1). We could not test three of the mutants (W40A, H79A, and R85A), because they were not expressed in the soluble fraction. As judged from the two-dimensional ¹H-¹⁵N HSQC spectra, the overall structures of the mutants expressed in the soluble fractions were not affected by the substitutions (data not shown). As expected, most of the mutants (K32A, W33A, T34A, N35A, Y36A, R43A, R66A, and Y96A) showed decreased affinities for the Golgi-mimetic liposomes, by more than 10-fold, as compared with that of the wild-type CERT PH domain (Fig. 4 and supplemental Table S1), indicating that these residues energetically contribute to the binding. In particular, the affinities of the K32A, W33A, Y36A, and R43A mutants were reduced nearly 100-fold, as compared with that of the wild type (Fig. 4 and supplemental Table S1). However, the affinities of the G39A, Q41A, K56A, S93A, and R98A mutants did not change significantly. Those mutations are localized on the edge of the Golgi-binding interface and thus do not show significant energetic contributions to the binding.

Intracellular Localization of CERT Mutants

To confirm our new finding in the CERT PH domain-Golgi membrane interaction, we performed immunofluorescence microscopy experiments using living HeLa cells and verified intracellular localization of the CERT mutants, K32A, W33A, and R43A, which consist of the PtdIns(4)P-binding pocket, and R66A and R98A, which participate in nonspecific charged interactions. The HeLa transfectants were stained with rat anti-HA antibodies and mouse anti-GM130 (Golgi apparatus marker), followed by Alexa Fluor 488 anti-rat IgG (green) and Alexa Fluor 594 (red) anti-mouse IgG (supplemental Fig. S4). Both types of mutations led Golgi mislocalization of CERT, which is comparable with the result of the in vitro mutagenesis analyses. Thus, both the PtdIns(4)P-specific site and the nonspecific basic groove are responsible for the Golgi localization of CERT.

Structural Dynamics in the β1/β2 Loops

The FAPP1 PH domain also recognizes PtdIns(4)P (36). A comparison of the tertiary structures between the CERT PH domain and the FAPP1 PH domain suggested that the dynamic nature of the β1/β2 loop region could be different (supplemental Fig. S5A). In the case of the FAPP1 PH domain, the signals from the β1/β2 loop region were observed, and the loop was structurally well defined. In contrast, the backbone NMR signals from Asn-35, Tyr-36, Ile-37, and Gly-39 of the CERT PH domain were broadened beyond the detection limit. The amide resonances of Thr-34 and His-38, as well as the side chain NH₂ signals of Asn-35, were observed but severely broadened, suggesting that the β1/β2 loop undergoes a chemical exchange process. The severely broadened NMR signals of the β1/β2 loop region remain invisible with saturated amount of diC₄-PtdIns(4)P.

Although the amino acid sequences of the β1/β2 loop itself is highly conserved between these two PH domains, a pair of residues in the neck of the β1/β2 loop, corresponding to Ser-31 and Asp-42 in the CERT PH domain, are different. In the FAPP1 PH domain, these residues are substituted with tyrosine and proline, respectively (supplemental Fig. S5A). Because the β1/β2 loop of the CERT PH domain does not interact with the other parts of the proteins, we assumed that the two amino acids might be responsible for the difference in the dynamic nature of the β1/β2 loops.

To test this notion, structural dynamics of the β1/β2 loop of the CERT PH domain, we introduced the S31Y/D42P mutations to the CERT PH domain. The mutations mimic the structural character of the FAPP PH domain. As a result, the backbone amide signals of Ile-37 and Gly-39, which are severely broadened, became detectable in the two-dimensional ¹H-¹⁵N HSQC spectrum of the S31Y/D42P mutant (supplemental Fig. S5B). Furthermore, ¹⁵N R₂ relaxation dispersion experiments revealed that the structural fluctuation on the microsecond to millisecond time scale in the β1/β2 loop region of the CERT PH domain was largely suppressed by the S31Y/D42P mutation (supplemental Fig. S5C). These data suggest that the structural dynamics of the β1/β2 loop is at least partially regulated by the two amino acid residues located in the neck of the loop.

DISCUSSION

The PH domain in the CERT protein plays a central role in the ER-to-Golgi transport of ceramide, which bound to the parental protein (4). To elucidate the structural basis of the PH domain-dependent Golgi association of the CERT protein, we utilized SPR along with solution state NMR analyses.

The SPR analyses, using the phosphoinositide-embedded liposomes, confirmed that the CERT PH domain specifically recognizes the PtdIns(4)P-embedded Golgi-mimetic liposome with a few micromolar affinity, while showing considerably lower affinities for the liposomes, containing either PtdIns(3)P, PtdIns(5)P or PtdIns(4,5)P₂ (Table 1). Considering the localization of PtdIns(4)P in the Golgi membrane, a specific PtdIns(4)P recognition by the CERT PH domain would be reasonable to allow the molecule to associate with the Golgi membrane. The dissociation rate of the CERT PH domain from the PtdIns(4)P-embedded liposomes was rather fast, on the order of s⁻¹, as indicated by the box-shaped SPR sensorgram (supplemental Fig. S5D). Thus, the average dwell time of the CERT protein on the Golgi membrane is intrinsically short unless the interaction of the other domain or elements in the CERT protein, such as the START domain, enhances the binding to the Golgi membrane.

Interestingly, the titration of the water-soluble analog of PtdIns(4)P, diC₄-PtdIns(4)P, revealed that the affinity between the CERT PH domain and the headgroup of PtdIns(4)P is quite weak (Fig. 2B). This is markedly different from the typical phosphoinositide recognition by other PH domains, in which most of the binding energy is derived from the specific interaction with the headgroup (31). In supplemental Fig. S6, tertiary structures of the CERT PH domain were compared side-by-side as well as by superimposition with other PH domains from Grp1 and DAPP1. The CERT PH domain only have two basic residues, Lys-32 and Arg-43, in the PtdInsP binding pocket, which is significantly less compared with Grp1 and DAPP1 PH domain. This might be one of the reasons for the weak headgroup recognition by the CERT PH domain. Assuming that the structure of the CERT PH domain would not change significantly upon the binding to PtdIns(4)P and that the position of PtdIns(4)P in the complex is structurally similar to the other PH domains, both basic residues in the CERT PH domain seem to be directed to the phosphate group of PtdIns(4)P. The residue corresponding to Arg-43 recognizes phosphate in the third position (P3) in other PH domains; however, the difference in the relative position between Arg-43 and Tyr-54 force Arg-43 toward P4. This also seems to make the binding to P3 hindered by the steric clash between the side chain of Arg-43 and P3 in the CERT PH domain. As for the other residues that recognize P1 and P5 in the other PH domains, there is no corresponding residue in the CERT PH domain. These may explain the PtdIns(4)P specificity of the CERT PH domain. The difference in the affinities between the PtdIns(4)P-embedded liposome and diC₄-PtdIns(4)P strongly indicates that additional interactions are required for the full binding affinity of the CERT PH domain.

To understand the details of this characteristic interaction between the CERT PH domain and the Golgi-mimetic membrane, we determined the tertiary structure of the CERT PH domain by solution NMR techniques (Fig. 1, B and C). The structural determination revealed that the main chain trace of the CERT PH domain resembles a typical PH domain fold (Fig. 1, B and C) and that the basic residues are clustered in the middle of the molecule in the CERT PH domain, forming a characteristic basic groove that encircles the protruding part of the β1/β2 region (Fig. 1, D and E).

The NMR binding experiments suggested that the entire basic groove is responsible for the interaction with the PtdIns(4)P-embedded liposomes (Fig. 3). Although the specific PtdIns(4)P-binding site was successfully mapped to the exposed end (Fig. 2), the side face of the basic groove mainly contributes to the nonspecific phospholipid membrane interaction (supplemental Fig. S3). This indicates that the two regions in the basic groove play rather distinct roles. Interestingly, the specific PtdIns(4)P binding and nonspecific phospholipid membrane interactions contribute almost equally to the binding of the CERT PH domain to PtdIns(4)P-embedded liposomes. The dissociation constant of the CERT PH domain to the soluble form of the PtdIns(4)P determined in this study was 760 μm, which is weaker than the binding to the liposome without PtdIns(4)P (220 μm). The functional role of the nonspecific electrostatic interaction has also been proposed for other PH domains (31). However, the contributions of those nonspecific interactions are less prominent, as compared with that of the CERT PH domain (32, 33). For example, in the case of the GRP1 PH domain, the K_D to PtdIns(3,4,5)P₃-embedded liposomes is 50 ± 10 nm, and the affinity was reduced by only 12-fold when the acidic lipid components were eliminated from the liposome (34).

The basic groove is composed of seven basic residues and one aromatic residue (Tyr-96) (Fig. 1E). In addition, there is the hydrophobic/aromatic β1/β2 loop protruding from the middle of the basic groove. It is well known that basic residues contribute to the interaction with the anionic surface of phospholipid membranes by electrostatic attraction (31), and that aromatic residues, such as Trp and Tyr, are usually located at the lipid-water interface in membrane proteins or membrane-associating proteins (35). Thus, the basic groove of the CERT PH domain is suitable to interact with the anionic surface of the Golgi membrane. The interaction between the basic groove and the membrane would orient the β1/β2 loop toward the membrane interior (Fig. 5). The interaction of the basic groove does not seem to be selective for particular anionic phospholipids in the Golgi membrane. The CERT PH domain binds to both Golgi-mimetic PtdIns(4)P-free liposomes, which containing 5% of PS, and the PA-containing liposomes, which replace PS in the PtdIns(4)P-free liposomes with PA. Response induced by 16 μm of the CERT PH domain in SPR analysis was 230 and 311 resonance units for phosphatidylserine and phosphatidic acid-containing liposomes, respectively. Stronger binding to PA-embedded liposome was somewhat unexpected; however, the exposed phosphate groups in PA can be the reason for the higher affinity.

FIGURE 5.

Proposed mechanism of the PH domain-mediated CERT translocation to the Golgi apparatus. A, unbound state of the CERT PH domain. B, weakly bound CERT PH domain. The nonspecific electrostatic interaction was between the basic groove in the CERT PH domain and the surface of the phospholipid membrane. C, orientation of the CERT PH domain for high affinity interaction. The specific high affinity interaction with the PtdIns(4)P-embedded membrane is shown.

Based on these observations, we proposed a model that describes the PH domain-mediated Golgi association of the CERT protein. The initial membrane association of the CERT PH domain might be driven by a nonspecific electrostatic interaction between the basic groove and the phospholipid membrane (Fig. 5B). The interaction using the basic groove with the aromatic residues would orient the β1/β2 loop of the CERT PH domain toward the membrane, and the binding mode would be suitable for the efficient recognition of PtdIns(4)P in the membrane (Fig. 5C). The site-specific mutagenesis analyses further support this binding mode, as they revealed that most of the basic and hydrophobic residues in the basic groove and the β1/β2 loop play critical roles in binding to the PtdIns(4)P-embedded membrane (Fig. 4). The proposed CERT PH domain-Golgi membrane binding mode was confirmed by immunofluorescence microscopy experiments using HeLa cells, which verified Golgi mislocalization of the CERT with mutation in the PtdIns(4)P-binding pocket or the nonspecific basic groove (supplemental Fig. S4). It has been shown that the PH domain is the essential determinant for the Golgi localization of CERT, and its START domain has little contribution to Golgi association (4). The result of the immunofluorescence microscopy using living HeLa cells (supplemental Fig. S4) in this study supports this notion by directly showing that both PtdIns(4)P-specific sites and the nonspecific basic groove are responsible for the Golgi localization of CERT.

The FAPP1 PH domain also recognizes PtdIns(4)P (36). The β1/β2 loop of the PH domain reportedly penetrates into the membrane (36). The binding mode of the FAPP1 PH domain is consistent with our binding model, as the β1/β2 loop of the CERT PH domain should be buried in the membrane (Fig. 5). However, a comparison of the tertiary structures between the CERT and the FAPP1 PH domain as well as the NMR relaxation properties of the CERT PH domain suggested that there is enhanced dynamics in the β1/β2 loop region of the CERT PH domain (supplemental Fig. S5A). Sequence comparison and NMR dynamics analysis using a chimeric mutant of the CERT PH domain suggested that the difference in the pair of residues in the neck of the β1/β2 loop, corresponding to Ser-31 and Asp-42 in the CERT PH domain, would at least partially regulate the dynamics of the difference in the dynamic nature of the β1/β2 loops (supplemental Fig. S5). In the FAPP1 PH domain, these residues are substituted with tyrosine and proline, respectively (supplemental Fig. S5A), whereas other residues in the β1/β2 loop is highly conserved between these two PH domains.

The difference in the dynamics might also be reflected in the biological functions of the CERT and FAPP1 PH domains. The FAPP1 and FAPP2 PH domains initiate membrane tubule formation in a PtdIns(4)P-dependent manner and are required for Golgi-to-plasma membrane vesicular transport (36–39). The rigid β1/β2 loop of the FAPP1 PH domain is considered to “wedge” into the Golgi and to reshape the lipid bilayer into a tubule form by increased membrane surface pressure (36). However, the CERT PH domain binding reportedly has no effect on the membrane structure. The structurally disordered β1/β2 loop in the CERT PH domain is clearly not appropriate to wedge into the membrane, but it might “lasso” the lipids without affecting the membrane structure. Therefore, it would be interesting to investigate the dynamics of the β1/β2 loops of PH domains, to see if the dynamics of the region coincide with certain functions of the PH domains.

As we mentioned above, the basic groove, composed of Lys-32, Arg-43, Lys-56, Arg-66, His-79, Arg-85, and Arg-98, seems to be primarily important for the recognition of PtdIns(4)P in the Golgi membrane. Among the basic residues in the basic groove, the residues corresponding to Lys-32 and Arg-43 in the CERT PH domain are highly conserved within most of the PH domains, as indicated in the multiple sequence alignment shown in Fig. 6. These residues specifically recognize the phosphate group of phosphatidylinositol (40, 41), and thus the conservation throughout the PH domains would be reasonable. Moreover, the rest of the basic amino acids except for Lys-56, which was proved to be nonessential in the CERT PH domain, are conserved only among the specific types of PH domains that were classified in the top four rows of the sequence alignments. The four PH domains are referred to as the COFs (acronym for CERT, OSBP, and FAPPs) family (Fig. 6) (42, 43). All of the COFs family proteins specifically recognize PtdIns(4)P and target the Golgi in a PtdIns(4)P-dependent manner (4, 27, 39, 40, 44–46). In addition, the binding mode of all of the COFs family PH domains are similar to that of the CERT PH domain, as characterized the weak affinities to the headgroup of PtdIns(4)P (the K_D values are millimolar range or even undetected) and significant affinities to the PtdIns(4)P-embedded Golgi-mimetic liposomes (the K_D values are 0.3∼3 μm) (27, 36, 45). Furthermore, all of the COFs family proteins are known to mainly function in the lipid transport to the organelle, and thus the characteristic binding mode might be suitable to perform this role. The PH domains that recognize bi- or tri-phosphate forms of phosphoinositides (41) lack the basic residues that we proposed to be conserved within the COFs family proteins (Fig. 6). Interestingly, these PH domains have distinct functions, as compared with those of the COFs family PH domains, and contribute to specific signal transduction. This indicates that the interaction modes shared within the subsets of PH domains, including the CERT PH domain, are closely related to their functional characteristics.

In summary, we determined the solution structure of the CERT PH domain, and we identified the PtdIns(4)P-binding site and the membrane-binding interface by solution NMR techniques. The results were supported by SPR-binding experiments, combined with site-specific mutagenesis analyses in vitro and in living cells. Based on the observations, we proposed a model in which the rather nonspecific electrostatic interaction between the basic groove and the phospholipid membrane would additionally contribute to the specific interaction with PtdIns(4)P.

The primary sequence alignment indicated that most of the residues located on the basic groove identified in this study are highly conserved within the COFs family but not in other PH domains. Therefore, the nonspecific membrane binding by the basic groove might be a unique characteristic of the COFs family PH domains.

In addition, most of the COFs family proteins are lipid transport proteins that are associated with the Golgi in a PtdIns(4)P-dependent manner (36, 37, 47). However, the proteins involved in signaling are usually specific to the di- or triphosphate forms of phosphoinositides (48–51). The signaling proteins require higher specificity and stability. For this purpose, relying on the specific interaction with a multiphosphorylated inositide might be preferred. In contrast, the low affinity recognition of the mono-phosphoinositide headgroup might be favored by lipid transport proteins, because the rather nonspecific scanning of the intracellular membrane is more important for these molecules. The initial membrane binding phase might effectively reduce the effective volume of the space, allowing the lipid transport proteins to find PtdIns(4)P more efficiently on the membrane surface.