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J. Biol. Chem., Vol. 283, Issue 1, 268-274, January 4, 2008
Structure of the Claudin-binding Domain of Clostridium perfringens Enterotoxin* 1 1
From the
Departments of
Received for publication, September 27, 2007 , and in revised form, October 16, 2007.
Clostridium perfringens enterotoxin is a common cause of food-borne and antibiotic-associated diarrhea. The toxin's receptors on intestinal epithelial cells include claudin-3 and -4, members of a large family of tight junction proteins. Toxin-induced cytolytic pore formation requires residues in the NH2-terminal half, whereas residues near the COOH terminus are required for binding to claudins. The claudin-binding COOH-terminal domain is not toxic and is currently under investigation as a potential drug absorption enhancer. Because claudin-4 is overexpressed on some human cancers, the toxin is also being investigated for targeting chemotherapy. Our aim was to solve the structure of the claudin-binding domain to advance its therapeutic applications. The structure of a 14-kDa fragment containing residues 194 to the native COOH terminus at position 319 was solved by x-ray diffraction to a resolution of 1.75Å. The structure is a nine-strand β sandwich with previously unappreciated similarity to the receptor-binding domains of several other toxins of spore-forming bacteria, including the collagen-binding domain of ColG from Clostridium histolyticum and the large Cry family of toxins (including Cry4Ba) of Bacillus thuringiensis. Correlations with previous studies suggest that the claudin-4 binding site is on a large surface loop between strands β8 and β9 or includes these strands. The sequence that was crystallized (residues 194-319) binds to purified human claudin-4 with a 1:1 stoichiometry and affinity in the submicromolar range similar to that observed for binding of native toxin to cells. Our results provide a structural framework to advance therapeutic applications of the toxin and suggest a common ancestor for several receptor-binding domains of bacterial toxins.
Enterotoxin-positive Clostridium perfringens type A is one of the most common food poisoning agents in the United States; among the several toxins it produces is C. perfringens enterotoxin (CPE).3 CPE has also been implicated in antibiotic-associated diarrhea in humans and is an important cause of gastrointestinal illness in domestic animals (1). CPE binds to human ileal epithelium, where it induces fluid and electrolyte loss along with epithelial cell necrosis (2). CPE cytotoxicity is a multistep process that initiates with CPE binding to an extracellular loop on specific members of the large claudin family of tight junction proteins (3, 4). This is followed by formation of SDS-resistant complexes of 450 and 600 kDa, which contains CPE and claudins; the 600-kDa complex also contains a second tight junction transmembrane protein, occludin (5, 6). These large complexes are thought to represent the cytotoxic pores, which create a hole in the plasma membrane and lead to cell death (7). The structure of CPE remains unknown, and this has slowed a more detailed understanding of its complex pathogenic mechanism.
The 35-kDa CPE toxin lacks primary sequence homology to any identified bacterial proteins, except for limited similarity (of unknown functional significance) between the NH2-terminal two-thirds of CPE and some Clostridium botulinum proteins. CPE has been functionally divided into two major domains, with the NH2-terminal half responsible for toxicity and the COOH-terminal half containing the claudin-binding sequences (8) (Fig. 1A). Exposure to trypsin or chymotrypsin removes a putative prosequence resulting in a 2-3-fold increase in toxicity. The sequences sufficient for binding to cells and to claudins are located within the COOH-terminal 30 residues. Removal of these residues eliminates binding, and a fusion protein containing only these residues can compete for binding with full-length CPE to isolated brush border membranes (9). In other studies, removal of the last 5 amino acids was sufficient to completely abrogate binding (8) (Fig. 1A), although it remains unclear whether these residues contain the binding site or if their removal destabilizes the protein. Although the COOH-terminal half of CPE, C-CPE, is not cytotoxic, it does have distinct effects on the tight junction barrier of epithelia. For example, exposure of cultured Madin-Darby canine kidney cell epithelia monolayers to C-CPE-(184-319) results in a reversible decrease in transepithelial electrical resistance and increase in paracellular permeability for uncharged solutes (4). This is accompanied by a selective loss of claudin-4, whereas the levels and distribution of claudins that do not bind CPE are unaffected. The selective removal of specific claudins from the tight junction appears to be a different mechanism than CPE-induced toxicity, since the former is slow and reversible and does not affect plasma membrane integrity, whereas CPE-induced toxicity is associated with increased cell membrane permeability and is not reversible. This has led to investigation of C-CPE as an agent to enhance transepithelial drug absorption (10). CPE is also being investigated in cancer diagnosis and as a potential cancer chemotherapeutic agent. A large number of recent studies document dramatic up-regulation of the CPE receptors, claudin-3 and/or claudin-4, in many pancreatic ovarian, breast, and uterine cancers (reviewed by Morin (11)). For example, injections of CPE into pancreatic tumors induced in nude mice resulted in tumor necrosis and significant reductions in tumor growth (12). Injection of CPE into the peritoneum of mice seeded with human ovarian cancer cells eliminated the malignant cells (13). In other studies, intracranial CPE administration inhibited tumor growth and increased survival in two murine models of breast cancer brain metastasis (14). In the current study, we determined the structure of the COOH-terminal domain of CPE, residues 194-319, which approximates the C-CPE domain used for functional studies by others and includes the claudin-binding site. The structure of C-CPE-(194-319) is a 9-strand β-sandwich and allows us to rationalize results of the claudin-binding studies. Structural similarity algorithms reveal previously unappreciated structural and sequence homology to the receptor-binding domains located at the COOH termini of several other toxins from spore-forming bacteria, suggesting a common origin. Availability of the structure of C-CPE-(194-319) will accelerate its therapeutic applications in cancer chemotherapy and drug delivery.
Oligonucleotides were synthesized by Invitrogen, and DNA was sequenced at the Genome Analysis Core of the University of North Carolina Lineberger Comprehensive Cancer Center. Crystallography and structural studies were performed in the University of North Carolina Biomolecular X-ray and Structural Bioinformatics Cores.
Protein Expression and Purification
Claudin-4—Full-length human claudin-4 with an NH2-terminal His10 tag was expressed in Sf9 baculovirus cells and purified as previously described (16) with the following modifications. Frozen cell pellets were thawed and washed once in phosphate-buffered saline and then resuspended in 10 mM Hepes, pH 7.4, 120 mM NaCl with protease inhibitor tablets (Complete Mini, EDTA-free, Roche Applied Science) and 1 mM phenylmethylsulfonyl fluoride, 20 units/ml DNase I. Cells were sonicated briefly, dodecylmaltoside (Anatrace, Manumee, OH) was added to 2%, and sample was incubated at 90 min at room temperature with gentle mixing. Insoluble material was removed by centrifugation at 30,000 x g for 40 min, and supernatant was incubated with Co2+ resin (Talon) overnight. Resin was washed with 10 mM imidazole, 10 mM Hepes, pH 7.4, 120 mM NaCl, 5 mM dodecylmaltoside, and eluted in the same buffer with 150 mM imidazole. Claudin-4 was further purified by size exclusion chromatography on a Superdex S200 column (1 x 30 cm; GE Healthcare), and peak fractions were
Binding Assays
Crystallization
Data Collection, Phasing, and Refinement The change in unit cell in the NaI-soaked crystal results in completely different packing interfaces and a slight shrinkage (3.6%) in unit cell volume. The NH2 terminus points in a different direction with respect to the main C-CPE fold in the two crystal forms; however, this segment does not have iodide ions bound in the NaI soak, which might have explained the slightly different directions. As expected, there are iodide ions bound to the surface of the protein and participating in packing interactions in the soaked crystal, which could explain the unit cell rearrangement. It is also possible that the two unit cell packing arrangements are present in native crystals, and we happened to select the different form for the NaI quick soak, but it seems more likely that the rearrangement was caused by the soak. We did not collect data from any other native crystals, but since the structure of the protein is the same (except for the first 7 amino acids, which are not part of the COOH-terminal β sandwich) in the two forms, this observation is not biologically relevant. Iodide ion sites were found by SHELXD (19) using data to 2.2 Å (three major sites, SHELXD CC = 40.96 all/22 weak). Solvent-flattened maps created by SHELXE were of excellent quality, such that the ArpWarp (20) automatic chain tracing program could place 112 of 126 of the amino acids of C-CPE-(194-319) correctly. Manual model rebuilding was carried out with COOT (21), and all but the first four amino acids are well ordered (these are at the NH2 terminus of the construct). The model from the iodide soak unit cell was placed into the native unit cell using the molecular replacement program PHASER (22); waters were located, and the model was adjusted with COOT, and then refinement was carried out using Refmac from the CCP4 (23). Final refinement used the native crystal data, because the signal-to-noise ratio was higher in all resolution shells than the iodide-soaked crystal. The final model has good stereochemistry and Rfree of 22.7%.
C-CPE-(194-319) Binds to Claudin-4 with High Affinity and a 1:1 Stoichiometry—Our long term goal is to understand how CPE and C-CPE interact with their cellular receptors, which are a subset of the large claudin family. The full-length toxin tends to aggregate after purification; consequently, we initially expressed, purified, and attempted to crystallize the previously characterized C-CPE-(168-319) fragment (Fig. 1A). This fragment is known to contain the claudin-binding region within residues 290-319. We found that this fragment is also unstable and oligomerizes upon storage at high concentration. By progressive deletion, we identified a fragment containing residues 194-319, which is highly stable and a monomer as determined by gel exclusion chromatography. In order to determine whether this fragment retained the ability to bind to claudin-4, we performed binding studies using purified His10-tagged human claudin-4 immobilized on Co2+ resin. Binding saturated with a 1:1 stoichiometry and Kd in the submicromolar range (Fig. 1, B and C). This high affinity is similar to that previously reported for C-CPE-(168-319) binding to claudin-expressing cultured cells (24), and we conclude that C-CPE-(194-319) is an appropriate fragment of CPE for structural analysis. Structure of C-CPE-(194-319)—The structure of C-CPE-(194-319) was solved to 1.75 Å resolution using single wavelength anomalous dispersion and the short halide soak derivatization method of Dauter et al. (17). The final model has good stereochemistry and Rfree of 22.7%. A full summary of data collection, phasing, and refinement statistics is included in Table 1.
C-CPE-(194-319) forms a nine-strand β sandwich with a short helical element between strands β1 and β2 (Fig. 2). Adjacent strands within each sheet have antiparallel orientations except for the uncommon parallel alignment of strands β1 and β3 (Figs. 2 and 3). The NH2-terminal seven residues, which are structured, interact with water molecules and not the main β sandwich, suggesting that the minimal C-CPE domain is formed by residues Ala205 through the COOH terminus at Phe319. This should assist future efforts aimed at producing a more solute and stable C-CPE domain for therapeutic application.
The claudin-binding region is known to be within the COOH-terminal 30 residues (25), which corresponds to strands β8 and β9, each positioned in the center of the opposing β sheets, and the intervening surface loop spanning residues Lys304-Tyr312. This region is highlighted in dark blue in Fig. 2. Deletion of the COOH-terminal 30 residues eliminates claudin binding (8). However, given the central position of strands β8 and β9, this manipulation may severely destabilize the overall structure, thus raising concerns about the interpretation of these binding studies. In contrast, a fusion protein encoding the same sequence can compete with native CPE for binding to cells, implicating residues in this region as the claudin-binding site. Furthermore, mutagenesis studies more specifically implicate the large surface loop between β8 and β9 in claudin binding (26). Single mutations of Tyr306, Tyr310, or Tyr312 to Ala all reduce claudin binding, whereas double mutants of Tyr306 with either of the other tyrosines eliminates binding (Fig. 2). Tyr306 and Tyr312 are buried under the loop; we speculate that their mutation will distort presentation of the loop surface but probably not disrupt the overall β sandwich fold or surface residues on strands β8 and β9. Mutation of Tyr306 to phenylalanine, also large and more hydrophobic, did not interfere with claudin binding, whereas mutation to the charged residue lysine eliminated binding (27). Knowledge of the structure suggests very direct mutagenesis studies to define the claudin-binding residues without disrupting the overall domain fold; further identification of these residues and their folding context could lead to development of peptidomimetics with claudin-binding activity. Strands β8 and β9 and especially the large intervening surface loop are attractive sequences for future investigation of claudin-targeting strategies.
The C-CPE-(194-319) Structure Reveals Unexpected Similarity to the Receptor-binding Domains of Other Bacterial Toxins—C-CPE-(194-319) lacks convincing primary sequence homology to domains of any other bacterial toxin when subjected to standard BLAST searching and is thought to be biologically unique. However, a search for similar three-dimensional structures using the DALI (Z-score) and root mean square (DRMS) similarity algorithms (28) revealed structural similarity with domains of more than 10 bacterial toxins. We highlight two examples that have striking biological analogy to C-CPE-(194-319) despite the initial absence of obvious sequence homology, namely domains within the ColG collagenase of Clostridium histolyticum (29) (Z-score = 9.1, DRMS = 2.9) and the Cry4Ba toxin of Bacillus thuringiensis (30) (Z-score = 6.5, DRMS = 3.8). In both cases, the similarity is with the 14-kDa COOH-terminal domain of the toxin/enzyme, which, like C-CPE-(194-319), functions in receptor binding by these toxins. Both are β sandwiches that share a similar secondary structure topology with C-CPE-(194-319). This includes the same relationship amongβ strands in each sheet, 6-5-8-3-1 on one side and 2-9-4-7 on the other, and the unusual parallel orientation of strands β1 and β3, noted in Fig. 3. Ribbon models of the three domains are oriented in Fig. 3 to optimize alignment of the secondary structure elements. Primary sequence homology can be identified within the corresponding β strands after first aligning residues that are located at analogous three-dimensional positions, using the Insight II algorithm (Accelrys Software Inc.). Alignment of homologous positions within the three sequences is presented in Fig. 4 with residues within each strand colored blue. Interestingly, when ClustalW is used to search for sequence homology among the three sequences, it aligns (boxed regions of Fig. 4) some but not all of the analogous three-dimensional positions. For example, ClustalW will align β4 of C-CPE and Cry4Ba but not ColG, despite ColG having chemically homologous residues at the analogous three-dimensional positions along the strand. Sequence homology is found at analogous positions within strands 3, 4, 5, 7, 8, and 9. Strands 1, 2, and 6, which are on the periphery of the sheets, are not as clearly related, perhaps suggesting conservation of interactions within but not at the edges of the sandwich. We speculate that these receptor-binding domains share an evolutionary origin because of their similar folds, sequence homology at corresponding structural positions, and biological activities. Others have noted that β sandwich domains are common in receptor-binding domains for both microbial and eukaryotic proteins (31, 32). C. histolyticum is an anaerobic spore-forming bacterium that causes gas gangrene and produces collagenases that lead to extensive tissue destruction. The mature enzyme class I collagenase from C. histolyticum is composed of an NH2-terminal metalloprotease domain, a spacer domain, and two collagen binding domains. The COOH-terminal binding domain not only shows structural similarity to C-CPE-(194-319), but mutational analysis of selected amino acids demonstrates that, like CPE, several tyrosines near the extreme COOH terminus are critical for collagen binding (29). However, these are not analogous residues, since they are exposed to the solvent and present on strand β8 and not buried on the loop between β8 and β9 like in CPE. B. thuringiensis is also a spore-forming Gram-positive bacterium. It produces a large number of insecticidal toxins stored as crystalline (Cry) protoxins (33). In an analogous fashion to CPE, following ingestion and activation by gut proteases, the Cry4Ba toxin binds to specific receptors on insect gut epithelial cells. Binding is followed by a conformational change that leads to the formation of membrane pores in the epithelial cells and cell lysis (33). The Cry toxins have three domains, the first of which is the toxic/pore-forming domain, and the second two domains, II and to a lesser extent domain III, are involved in receptor binding (30, 34). Domain III, which has structural similarity to C-CPE, resembles a number of carbohydrate binding domains that are found in microbial hydrolases and esterases (35), but specific residues known to be critical for carbohydrate binding are not generally conserved in the domain III of Cry toxins. Thus, the receptor binding surfaces on Cry proteins and CPE do not appear to be analogous. C-CPE has been reported to interact with the second extracellular domain of claudins (24). However, although we could demonstrate high affinity interactions with full-length claudin-3 (not shown) and claudin-4, we were unable to demonstrate binding of purified C-CPE to either synthetic peptides or fusion proteins comprising the second extracellular domain of claudin-3 or claudin-4. Future investigations will focus on the region of claudin-4 that interacts with C-CPE. In summary, the availability of a structure for C-CPE-(194-319) suggests an unsuspected shared origin for the receptor-binding domains of several bacterial toxins and should allow rational modifications of the protein for future therapeutic applications.
The atomic coordinates and structure factors (code 2QUO) have been deposited in the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers University, New Brunswick, NJ (http://www.rcsb.org/).
* This work was supported by grants from the National Institutes of Health, including a Pilot Feasibility project from P30 DK 034987 (to C. M. V. I.), R01 DK45134 (to J. M. A.), and R37 AI19844 (to B. A. M.).
1 Both authors contributed equally to this work. 2 To whom correspondence should be addressed: Cell and Molecular Physiology, University of North Carolina at Chapel Hill, 6314 MBRB, CB#7545, 103 Mason Farm Rd., Chapel Hill, NC 27599-7545. Fax: 919-966-6413; E-mail: jandersn{at}med.unc.edu.
3 The abbreviations used are: CPE, C. perfringens enterotoxin; C-CPE, COOH-terminal domain of CPE; N-CPE, NH2-terminal domain of CPE.
We thank Dr. Brenda Temple (University of North Carolina) for assistance with bioinformatics methods and Drs. Alan Fanning (University of North Carolina) and Arnon Lavie (University of Illinois, Chicago) for helpful suggestions.
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