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J. Biol. Chem., Vol. 279, Issue 30, 31495-31504, July 23, 2004
Hydrophobic Residues of the Autotransporter EspP Linker Domain Are Important for Outer Membrane Translocation of Its Passenger*![]() ![]() ![]() ![]()
From the
Center for Vaccine Development, Departments of
Received for publication, April 21, 2004 , and in revised form, May 17, 2004.
The autotransporter family of proteins is an important class of Gram-negative secreted virulence factors. Their secretion mechanism comprises entry to the periplasm via the Sec apparatus, followed by formation of an outer membrane barrel, which allows the N-terminal passenger domain to pass to the extracellular space. Several groups have identified a region immediately upstream of the domain that is important for outer membrane translocation, the so-called linker region. Here we characterize this region in EspP, a prototype of the serine protease autotransporters of enterobacteriaceae. We hypothesized that the folding of this region would be important in the outer membrane translocation process. We tested this hypothesis using a mutagenesis approach in conjunction with a series of nested deletions and found that in the absence of a complete passenger, mutations to the C-terminal helix, but not the upstream linker, significantly decrease secretion efficiency. However, in the presence of the passenger mutations to the amino-terminal region of the linker decrease secretion efficiency. Moreover, amino acids of hydrophobic character play a crucial role in linker function, suggesting the existence of a hydrophobic core or hydrophobic interaction necessary for outer membrane translocation of autotransporter proteins.
The rapid progress in genomics and widespread availability of genetic information has led to a greater appreciation of the importance of autotransporter proteins. By definition, autotransporters carry all necessary components for translocation through the Gram-negative periplasm and outer membrane within a single protein (14). Inner membrane transit is mediated by a signal sequence, which targets the protein through the Sec apparatus into the periplasmic space (5). The C terminus then creates a barrel in the outer membrane that either as a monomer (2, 3, 6) or in an oligomer with other domains (79), forms an outer membrane pore. The N-terminal passenger domain is thought to traverse this pore, which is estimated by black lipid bilayers (for BrkA (10)) and liposome swelling assays (for IgA protease (9)) to be 20 Å in diameter (2, 611). However, pore formation in planar lipid bilayers and the crystal structure of NalP suggest a diameter between 8.4 and 10 Å (6). Remarkably, a passenger domain over 100 kDa in size can translocate through the outer membrane into the extracellular space utilizing this pore. Recently, however, Oomen et al. (6) have suggested that an accessory protein in the outer membrane may aid the translocation process, perhaps acting with the pore (6, 12). In either case, proper barrel insertion into the outer membrane appears to be crucial, but events taking place in the periplasm and at the outer membrane remain obscure.
Several laboratories have shown that in various autotransporters (namely BrkA (13, 14), Ssp (15), IgA protease (11), and AIDAI (1618)), a region immediately upstream of the
Recognizing the critical importance of and uncertainty regarding the autotransporter linker domain, we here define the linker region of the autotransporter EspP and characterize its properties as they relate to outer membrane translocation. EspP is a member of the serine protease autotransporters of enterobacteriaceae (SPATE)1 subfamily of autotransporters (2). After translocation, it is cleaved away from its
Bacterial StrainsAll genetic manipulations were first transformed into E. coli DH5 (23) and then into HB101 (24) once proper construction was confirmed. Secretion analyses were performed, unless otherwise noted, in HB101. UT5600(OmpT) (25) cells were obtained from New England Biolabs and used for secretion analysis and localization of nonsecreted mutants as indicated below. Linker Deletions and Site-directed MutagenesisMolecular biology techniques were performed according to standard protocols (26) on plasmid PB9-5 (21), which contains the espP gene with its natural promoter in vector pK18 (27). Oligonucleotides used for all PCR and mutagenesis can be found on the World Wide Web at medschool.umaryland.edu/cvd/natarolab.html. All deletions were constructed by inverse PCR (28); primers were designed to flank the regions to be deleted. PCR was performed according to standard protocols utilizing a high fidelity polymerase (Platinum Pfx; Invitrogen) at an extension temperature of 68 °C for 2 min per kilobase of amplified DNA. 200 ng of plasmid PB9-5 was used as template with 10 pmol of each primer in a 50-µl reaction. MgCl2 concentrations were kept between 1.5 and 2 mM. The primers were designed to introduce NotI sites at both ends of the resulting PCR product, which was then NotI-digested and ligated. The result was a plasmid with a deletion of the region flanked by the primers and a new NotI restriction site at the deletion site. To follow secretion, we introduced an epitope containing the Myc epitope, His epitope, and TEV protease recognition sequence (29) (MHT) by PCR. The Myc-His epitope was amplified from plasmid PBAD/Myc-His (Invitrogen) using Platinum Pfx (Invitrogen) utilizing a primer that introduced the TEV protease site at the C terminus of the PCR product. NotI restriction sites were also introduced at both ends of the primers. This epitope was inserted by digesting it and the modified plasmids with NotI, incubating the linear plasmids with calf intestinal phosphatase, and ligating the MHT epitope into the plasmid. Proper insertion was detected by anti-His6 immunoblot analysis of bacterial supernatants. All linker deletions were sequenced for accuracy over the entire length of the passenger domain. All nested deletions were sequenced over the deletion site. Site-directed mutagenesis was performed with the QuikChangeTM (Stratagene) protocol with PfuTurbo (Stratagene), a high fidelity polymerase. Template was used at 2550 ng per reaction with 10 pmol each of complementary primers. Reactions were carried out according to the manufacturer's protocol. All constructs were sequenced at the University of Maryland, Baltimore, Biopolymer Core Facility.
ELISA Quantitation of EspP SecretionMutant and wild-type EspP linker constructs and deletions, transformed into chemically competent (26) HB101 or UT5600, were grown in 5-ml LB cultures supplemented with 50 µg/ml kanamycin overnight. Once the cells reached stationary phase, they were centrifuged (10,000 x g at 4 °C), washed twice, and resuspended to an A600 = 4.0 in 1 ml of LB with kanamycin. Cultures were then placed at 37 °C shaking at 250 rpm and allowed to express for a total of 3 h; they were subsequently centrifuged at 10,000 x g in a refrigerated centrifuge for 20 min. 200 µl of supernatant, filtered through a 0.45-µm filter, was serially diluted 2-fold down a column to a final 1:128 dilution in a 96-well plate. All dilutions were performed in triplicate. Secreted protein was allowed to bind in the wells at 4 °C overnight. ELISAs were performed according to standard protocol (30) with 0.40.5 µg/ml mouse anti-Myc IgG as a primary antibody and 0.2 µg/ml phosphatase labeled goat anti-mouse IgG as secondary antibody. Results were developed for an appropriate amount of time (30 min for ImmunoblottingAll immunoblot analyses were done according to standard protocols (30). Samples were separated by 12.5% (w/v) acrylamide SDS-PAGE and transferred overnight at 34 V in Towbin's buffer (31) onto polyvinylidene difluoride. Membranes were blocked with 5% skim milk in phosphate-buffered saline/Tween. Primary anti-His6 antibody (Qiagen) was used at a concentration of 200 ng/ml; primary anti-EspP antiserum was used at a 1:5000 dilution; and primary MBP antiserum (New England Biolabs) was used at a 1:17,000 dilution. Secondary anti-mouse antibody (KPL) for the anti-His6 immunoblots was used at a concentration of 40 ng/ml, and secondary anti-rabbit antibody (KPL) for the EspP and MBP immunoblots was used at a concentration of 28.6 ng/ml. Results were visualized with ECL+ (Amersham Biosciences) and after exposure to Kodak autoradiography film for an appropriate time. Outer Membrane Preparations and SDS-PAGE AnalysisAll HB101 and UT5600 strains expressing nonsecreting mutants were grown to log phase and their optical density measured. Outer membranes from equal cell densities were isolated by differential Triton X-100 solubility, as previously described (32, 33). Bacteria were lysed in a French press and the inner membrane was solubilized in 2% Triton X-100, 5 mM MgCl2, 8 mM Tris, pH 8.0, and separated by centrifugation (13,000 x g for 30 min at 4 °C) from the outer membrane. The outer membrane was then resuspended in Laemmli buffer containing 1 mM EDTA. 30 µl of this sample was analyzed by one-dimensional SDS-PAGE at an acrylamide concentration (w/v) of 15% according to standard protocols. Loading was normalized by estimating equal quantities of the OmpF and OmpC porins (34).
Localization of Protein in UT5600 Bacterial cells (UT5600) were washed with 10 mM Tris, pH 8.0, 0.1% Triton X-100, 5 mM MgCl2, by resuspending and incubating in 500 µl of buffer at room temperature for 15 min (35). The cells were then pelleted by centrifugation at 8500 x g for 10 min at 4 °C. The wash was removed and filtered through a 0.45-µm filter, and 15 µl was separated by SDS-PAGE in a 12.5% (w/v) polyacrylamide gel followed by anti-His6 immunoblotting analysis. The washed pellet was then resuspended in 500 µl of 10 mM Tris, pH 8.0, and 15 µl was added to an equal volume of 2x Laemmli buffer and subjected to anti-His6 immunoblot analysis as described above. Whole-cell limited tryptic digest (12, 36) was done by resuspending cell pellets from a secretion experiment in 500 µl of 10 mM Tris, pH 7.4, 0.5 mM MgCl2, 100 µg/ml trypsin, and incubating on ice for 15 min. The reactions were then stopped by adding soybean trypsin inhibitor to 200 µg/ml. The cells were centrifuged at 8500 x g for 10 min at 4 °C, and the reaction supernatant was removed from the pellet. 15 µl was separated by SDS-PAGE in a 12.5% (w/v) polyacrylamide gel, transferred overnight to polyvinylidene difluoride, and analyzed by immunoblotting with both anti-His6 and anti-EspP antibodies. The cell pellets were also resuspended in 500 µl of 10 mM Tris, pH 7.4. 15 µl of the cell suspension was used for immunoblot analysis as described for the reaction supernatant. Periplasmic extractions were performed by osmotic cold shock (37). Pellets from a secretion experiment were utilized and resulted in 1 ml of periplasmic contents. 500 µl was trichloroacetic acid-precipitated (38) and resuspended in 100 µl of Laemmli buffer. 20 µl of this was then subjected to immunoblot analysis with Sequence Comparison and PileupThe putative linker regions of nine SPATEs were aligned using ClustalW (39) from the European Bioinformatics Institute (EMBL-EBI; available on the World Wide Web at www.ebi.ac.uk/clustalw/). Hydrophobic residues were selected and shaded using GeneDoc (available on the World Wide Web at www.psc.edu/biomed/genedoc/).
EspP Contains a Functional Linker Domain as Part of Its Translocation UnitTo characterize the secretion of SPATE proteins, we first asked whether EspP contained a linker region required for outer membrane translocation, as has been shown for numerous other autotransporters (11, 1318). To this end, we utilized inverse PCR to construct a series of deletion mutants in the C terminus of the passenger domain, corresponding to the putative EspP linker as determined by homologies to other autotransporters (14, 16). Interestingly, Dutta and Nataro2 have shown that there is a proteinase K-sensitive site at the N terminus of this region in the closely related autotransporter Pet, proposing that this site separates two discrete domains. The EspP gene was manipulated in clone PB9-5 (21). Primers were designed to delete the passenger domain from residue 74 to 821 (Fig. 1A) and then sequentially toward the C terminus in the suspected linker domain; this leaves the signal sequence and 19 downstream residues intact. An MHT epitope was introduced into a NotI site created at the deletion point during PCR. Resulting constructs were transformed into HB101.
To assay secretion, cultures at equal cell densities were pelleted, resuspended in fresh L-broth, and incubated for 3 h. EspP in supernatants was quantitated by ELISA; secretion of deletion mutants was expressed as percentage secretion of a 242291 deletion harboring the MHT epitope at the deletion site (essentially the full-length passenger). Both immunoblot analysis using anti-His6 antibodies and ELISA using anti-Myc antibodies (Fig. 1B) revealed that with successive passenger deletions extending past residue 868, secretion efficiency was decreased. Translocation was essentially undetectable when only 4 residues prior to the known EspP cleavage site remained. Outer membrane preparations of HB101 expressing the deletion constructs were prepared by differential Triton X-100 solubilization of the inner and outer membranes (32, 33). All constructs displayed comparable amounts of domain in the outer membrane, suggesting that the difference in secretion efficiency was not due to differences in transcription, translation, inner membrane secretion, domain outer membrane insertion, or processing from the domain (Fig. 1C). We did not detect maltose-binding protein (MBP) in the supernatants of these mutants (data not shown), suggesting that detection of the passenger was not due to outer membrane permeabilization. These data agree with the prediction of a putative linker domain for EspP, the minimal functional length of which is between 27 and 5 residues upstream of the processing site. As previously shown with AIDA-I (16), we clearly observed a decrease in secretion efficiency with deletions of increasing size, suggesting that the upstream regions of the linker domain may have a role in the secretion process.
The Putative C-terminal
The N-terminal Region of the Linker Is Important for Secretion of a Full-length Passenger DomainWe presumed that if mutations to the putative -helix of the linker were detrimental for secretion of 74928, then the same would be true for a construct containing the larger passenger domain. To test this, we removed the active protease site from EspP ( 242291, Fig. 2A) in order to prevent autodegradation. At the deletion site, we inserted the MHT epitope and mutagenized the passenger C terminus using the same primers employed in mutagenesis of 74928. Secretion efficiency was analyzed by anti-Myc ELISA (Fig. 2B). Surprisingly, we found that from the putative helical region (residues 10051031), only D1014K still conferred a significant decrease in secretion efficiency. However, a number of mutations upstream of D1014 now also demonstrated a significant effect on secretion (Fig. 2B). Again, the only construct showing a significant decrease in outer membrane domain insertion was D1014K (Fig. 2C), which did not yield an unprocessed passenger/ domain. We were unable to detect MBP in the supernatant for the nonpermissive mutants (data not shown). In light of these results, we hypothesized that small nested deletions in the linker region would yield a similar effect on secretion efficiency. Deletions were again constructed ( 928946, 946971, 971997, and 9971019) by inverse PCR, and an MHT epitope was inserted at the deletion site (Fig. 3A). Secretion was analyzed by ELISA and reported as a percentage of 242291 secretion (Fig. 3B). All of the nested deletions displayed a clear decrease in secretion efficiency. Outer membrane preparations showed equivalent outer membrane domain insertions and the MBP lysis controls were negative (data not shown). These data support our inference that the N-terminal region of the linker plays a role in translocation of a full-length passenger domain, although not necessarily a truncated construct.
Amino Acids of Hydrophobic Character Are Crucial to Linker N-terminal Domain FunctionUpon closer examination, we found that the large majority of mutations affecting secretion in the upstream linker region of EspP were to hydrophobic or aromatic amino acids. We hypothesized that the hydrophobic amino acids upstream of the putative helix were important in the secretion process of a full-length passenger domain and tested this hypothesis via site-directed mutagenesis. We chose various amino acids and created both conservative and nonconservative mutations in the 242291 construct. Secretion analysis was accomplished as above. When the hydrophilic amino acids were mutated to either hydrophobic or hydrophilic residues (Y995E, Y995T, Y995F, N948D, N948L, T958Y, and T958L), the mutations were tolerated with respect to secretion (Fig. 4). However, when the hydrophobic amino acids were mutated to aspartic acid residues (L951D, L992D, and F963D), there was a substantial diminution of secretion efficiency (1020% of wild type), which was not seen for conservative mutations of the same residues (L951I, F963W, F963Y, and L992I). All outer membrane preparations showed comparable amounts of domain insertion and all of the MBP lysis controls were negative (data not shown). We attempted to detect nonsecreted mutant constructs within whole-cell HB101 lysates by anti-His6 immunoblot analysis but were unable to do so, suggesting that the nonsecreted protein is being rapidly degraded.
Nonsecreted Linker Mutants Can Be Recovered from the Periplasm of UT5600 (OmpT) CellsOliver et al. (14) have described extracellular recovery of constructs harboring deletions in the analogous linker region of BrkA when they were expressed in strain UT5600, an OmpT() strain. OmpT is an outer membrane amphipathic barrel that has been shown to function as an extracellular protease (40). We chose three of our nonsecreted linker mutations (L951D, F963D, and L992D) and assayed their secretion from UT5600, as previously described. The results were normalized to secretion of nonmutated 242291 from strain UT5600. In contrast to Oliver et al. (14), we were unable to rescue secretion of our mutants from this strain (data not shown). In an attempt to localize the nonsecreted protein, we washed the cell pellet in 0.1% Triton X-100 for 15 min at room temperature, previously shown to release misfolded SPATEs (35). We observed a small amount of nonmutated 242291 in the cell wash solution, whereas the mutated nonsecreted constructs could not be detected (Fig. 5A). A limited tryptic digest of the solvent exposed surface proteins on UT5600 also demonstrated recovery of a small amount of nonmutated 242291 tryptic fragments, yet tryptic fragments of the nonsecreted mutants could not be found (Fig. 5B). However, these species were detected in the whole-cell lysates (Fig. 5C) and the periplasmic fraction (Fig. 5D) of UT5600 cells, whereas wild-type 242291 was barely detectable. These data would suggest that the nonsecreted mutants were not localized on the surface of the bacteria but are transiently present in the periplasm.
Hydrophobic Residues in the SPATE Linker Domain Are ConservedThe SPATE family has previously been studied for homology (2), clearly showing an increased amino acid conservation in the C-terminal region of the autotransporters, with the domain displaying the highest homologies. Based on our observations suggesting the existence of a hydrophobic core, we wished to examine the conservation of amino acid hydrophobicity and hypothesized that this region would have a significant conservation of amino acid character at the residues we mutated. Alignment of the SPATEs in the linker region was accomplished using ClustalW (39) (EMBL-EBI; available on the World Wide Web at www.ebi.ac.uk/clustalw/) and GeneDoc (available on the World Wide Web at www.psc.edu/biomed/genedoc/). As predicted, this analysis revealed substantial conservation of hydrophobic character, including residues we had targeted for mutagenesis (Fig. 6).
A growing body of literature implicates the C-terminal linker of the autotransporter passenger domain in secretion, yet the precise function of this region is not well characterized. We first sought to perform deletion experiments in the putative EspP linker domain to demonstrate the presence and role of this region in the translocation of EspP. We constructed a series of deletions, removing a majority of the passenger domain and successively decreasing the size of the linker domain. With successive deletions closer to the C terminus, we observed a decrease in translocation efficiency until secretion was essentially undetectable (Fig. 1). As has been shown for other autotransporters (11, 1318), EspP therefore possesses a linker as an integral component of the translocation unit, with a minimal length between 27 and 5 residues upstream of the processing site (1023/1024). We also found notable the consistent diminution of detectable epitope with successive deletions after residue 868. Although there is a minimal linker region crucial for outer membrane translocation, this observation was a first indication of the involvement of the SPATE upstream linker in translocation efficiency.
The C-terminal region of the linker has been shown to be helical for NalP and is inferred from the crystal structure to electrostatically interact with the inner face of the
We hypothesized that in a construct still containing a majority of the passenger domain, mutations to the putative C-terminal
Upon further inspection of secretion-deficient mutations, we found that the critical amino acids were consistently hydrophobic in character. We therefore designed both conservative and nonconservative mutations to select residues and observed their effects on secretion (Fig. 4). None of the mutations involving any of the hydrophilic residues (Y995E, Y995T, Y995F, N948D, N948L, T958Y, and T958L) had a significant effect on translocation of the MHT epitope in
We attempted to determine the location of three nonsecreted HSF mutants in HB101 and UT5600. Although we could recover neither the wild-type nor the mutants from HB101, each of the nonsecreted mutants could be recovered from the periplasmic space of UT5600 cells, but none from the surface of the bacteria or supernatant (Fig. 5). This suggests that alterations to the HSF region have a significant effect on some aspect of the EspP outer membrane translocation process. The Current models of autotransporter secretion still leave some important questions unanswered. Foremost, the conformation of the passenger domain during the secretion process and its relationship to barrel insertion are still unclear. Several investigators have proposed size and conformational limitations to the polypeptides capable of being efficiently secreted by the autotransporter barrel (41, 42), and the dimensions of the barrel aperture are suggested to be 2 nm or less by several methods, including crystallography (6, 9, 10). Yet experimental evidence has also suggested that some folding of both native passengers and foreign polypeptides is tolerated (4345). This folding may result in a secretion-competent, protease-resistant state (45), which would allow the passenger to efficiently traverse through the available pore. Indeed, the small size of the pore is in seeming contradiction to the ability of folded passengers to be secreted through the channel. One model that has not been adequately addressed in the autotransporter field would entail coupled folding and insertion of the barrel with passenger translocation, possibly assisted by an outer membrane protein such as Omp85 (6, 12). This model would predict the presence of an intermediate barrel conformation, which would exhibit a transiently larger pore size. Barrel folding and insertion coupled to the passenger translocation process could be driven by favorable folding energy, required to overcome entropy and transition to the extracellular space. This protein folding would be driven primarily by hydrophobic interactions (46). Our data suggesting that single disruptive mutations to hydrophobic amino acids in the HSF can significantly decrease passenger translocation efficiency suggest that the folding of this passenger domain is critical for translocation. Models that are most compatible with these observations are either (i) recognition of the barrel pore by the folded HSF domain or (ii) coupled HSF folding, barrel insertion, and passenger translocation. As noted above, the reported dimensions of the barrel are most compatible with the second model, and we strongly favor this secretion strategy. The presence of periplasmic proteases also suggests that autotransporter secretion may require an intermolecular or intramolecular chaperone. For example, it has been suggested that DegP may be functioning as a periplasmic chaperone of IcsA (47). Our nonpermissive mutations could also have abolished hydrophobic interactions necessary for periplasmic chaperone interactions, causing the passenger domain to be degraded at a rate greater than that of secretion, which would in turn yield a decreased secretion efficiency. Both Oliver et al. (14) and Ohnishi et al. (15) have suggested that the linker plays the role of an autochaperone in the extracellular space, thereby allowing for a protease-resistant state necessary after the translocation process. The linker region we have identified for EspP does overlap partially with the autochaperone region suggested as universal by Oliver et al. (14). However, for both BrkA and Ssp it was suggested that this region was functionally critical after translocation of the passenger, whereas in this study we found that mutations to the linker region significantly decrease the efficiency of translocation (to 1020% of wild type). We have not excluded the possibility of an EspP autochaperone in the extracellular space. However, in light of the observations of Oliver et al. (14) and Ohnishi et al. (15), it is possible that the EspP HSF may function as a periplasmic autochaperone as well, necessitating a hydrophobic interaction with the remaining passenger domain. The result of HSF disruption would then be similar to the disruption of interactions with a heterologous chaperone, namely a decrease in secretion efficiency. Future work on autotransporter secretion will be needed to address these various hypotheses, including the identification of critical intermediates.
* This work was supported by United States Public Health Service Grant AI-43615. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.
1 The abbreviations used are: SPATE, serine protease autotransporters of enterobacteriaceae; MHT, epitope containing the Myc epitope, His epitope, and TEV protease recognition sequence; MBP, maltose-binding protein.
2 P. R. Dutta and J. P. Nataro, unpublished observations.
We thank the members of the Pasetti laboratory for technical advice.
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