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Journal of Bacteriology, November 2008, p. 7079-7086, Vol. 190, No. 21
0021-9193/08/$08.00+0 doi:10.1128/JB.00519-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Unité de Chimie des Interfaces, Université catholique de Louvain, Croix du Sud 2/18, B-1348 Louvain-la-Neuve, Belgium,1 Mucosis BV, Nijenborgh 4, NL-9747 AG Groningen, The Netherlands,2 Unité de Génétique, Institut des Sciences de la Vie, Université catholique de Louvain, Croix du Sud 5/6, B-1348 Louvain-la-Neuve, Belgium3
Received 16 April 2008/ Accepted 21 August 2008
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-D-glutamate-meso-diaminopimelate muropeptidases LytE and LytF of B. subtilis (20, 24, 25, 29), muramidase-2 produced by Enterococcus hirae, and the major autolysin AcmA of L. lactis (32, 33).
There is increasing evidence supporting the notion that LysM is a general peptidoglycan-binding module (5, 8, 19, 20, 22-25, 29, 31-33). Partially purified muramidase-2 of E. hirae, a protein similar to AcmA and containing six LysM repeats, binds to peptidoglycan fragments of the same strain (22). The p60 protein of L. monocytogenes contains two LysM repeats and was shown to be associated with the cell surface (31). The
-D-glutamate-meso-diaminopimelate muropeptidases LytE and LytF of B. subtilis have three and five repeats, respectively, in their N termini and are both cell wall bound (20, 24, 25, 29). Notably, Steen et al. (32) showed that the LysM domain of AcmA binds to many gram-positive bacteria with different peptidoglycan structures, including L. lactis, Enterococcus faecalis, Streptococcus thermophilus, B. subtilis, Lactobacillus sake, and Lactobacillus casei. The LysM domain showed similar affinity for both A-type and B-type peptidoglycan. As repetition of the disaccharide N-acetylglucosamine (GlcNAc) and N-acetylmuramic acid (MurNAc) is the only part common to both A-type and B-type peptidoglycan, LysM modules most likely bind to this component (8). Immunofluorescence microscopy revealed that the LysM domain interacts with specific loci on the cell surface (32). In addition, specific chemical treatments of cells and cell walls indicated that a cell wall component, extractable with trichloroacetic acid (TCA), is responsible for hindering LysM recognition, thereby causing this localized binding (32).
Despite the multiple important roles played by LysM domains (8), the forces and dynamics underlying their interaction with peptidoglycan as well as the spatial distribution of LysM binding sites on bacterial cell walls remain essentially unknown. Here, we used atomic force microscopy (AFM) (10) in the single-molecule force spectroscopy (SMFS) mode (18, 27) for exploring specific LysM-peptidoglycan interactions between AFM tips modified with the recombinant AcmA cell wall-binding domain (three LysM repeats) and model surfaces coated with peptidoglycan. Moreover, AcmA tips were used to detect and localize single LysM interactions on the surfaces of L. lactis cells. Major differences were found between native and TCA-treated cells, demonstrating that the binding of LysM to native L. lactis surfaces is hindered by cell surface constituents.
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Chemical treatment of the cells. For some experiments, cells were treated with TCA as previously described (6, 32). Briefly, cells were harvested from exponentially growing culture by centrifugation, washed two times with Tris-maleate, resuspended in a 10% solution of TCA (Sigma), and boiled for 10 min. Treated cells were then washed three times with Tris-maleate and directly used for AFM experiments.
Preparation of LysM-modified supports and tips. Recombinant AcmA cell wall-binding domains (PA3), purified as described before (6) and each bearing a cysteine residue near the extremity of its N-terminal end, were immobilized onto gold-coated supports and AFM tips. Silicon nitride AFM cantilevers (Microlevers; Veeco Metrology Group, Santa Barbara, CA) and silicon wafers (Siltronix, France) were coated, by thermal evaporation, with a 5-nm-thick Cr layer followed by a 30-nm-thick Au layer. Before use, gold-coated cantilevers and supports were cleaned for 5 min by UV-ozone treatment (Jelight Co., Irvine, CA), rinsed with ethanol, and dried with a gentle nitrogen flow. They were immersed overnight in phosphate-buffered saline (PBS) solutions (10 mM PBS, 150 mM NaCl, pH 7.4) containing 10 µg·ml–1 of recombinant peptide for 12 h, rinsed three times with PBS, and briefly sonicated to remove aggregates that may be adsorbed.
Preparation of peptidoglycan-modified surfaces. Peptidoglycan solutions were prepared by dissolving peptidoglycan from B. subtilis (Fluka) in PBS solution at a concentration of 10 µg·ml–1 and sonicated for several minutes. Gold supports (see above) were immersed for 12 h in ethanol solution containing 1 mM of mercaptododecahexanoic acid (Sigma), rinsed three times with ethanol, and briefly sonicated. The supports were then immersed for 30 min into a solution containing 20 g/liter N-hydroxysuccinimide (NHS) and 50 g/liter 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide (EDC) (Sigma), rinsed with MilliQ water (Millipore), incubated with 10 µg·ml–1 of peptidoglycan solution for 1 h, rinsed further with PBS, and then immediately used.
Surface characterization. The chemical composition of the modified surfaces was assessed using X-ray photoelectron spectroscopy (XPS). Supports were rinsed with water and dried by flushing with a gentle nitrogen flow and then immediately introduced in the XPS vacuum chamber. The analyses were performed on a Kratos Axis Ultra spectrometer (Kratos Analytical, United Kingdom) equipped with a monochromatized aluminum X-ray source. The samples were fixed on a stainless steel multispecimen holder by using double-sided conductive tape. The angle between the normal to the sample surface and the electrostatic lens axis was 0°. The analyzed area was approximately 700 µm by 300 µm. The constant pass energy of the hemispherical analyzer was set at 40 eV. The following sequence of spectra was recorded: survey spectrum, C1s, N1s, O1s, Au4f, S2p, and C1s again to check the stability of charge compensation as a function of time and the absence of degradation of the sample during the analyses. The binding energies were calculated with respect to the C-(C,H) component of the C1s peak of adventitious carbon fixed at 284.8 eV. Following subtraction of a linear baseline, molar fractions were calculated (CasaXPS program; Casa Software Ltd., United Kingdom) using peak areas normalized on the basis of acquisition parameters, sensitivity factors, and the transmission function provided by the manufacturer.
AFM measurements.
AFM images and force-distance curves were obtained either in PBS (for supports) or in Tris-maleate (for cells) at room temperature using a Nanoscope IV multimode AFM (Veeco Metrology Group, Santa Barbara, CA). Native and treated cells were immobilized by mechanical trapping into porous polycarbonate membranes (Millipore) with a pore size similar to the bacterial cell size (10). After filtering a concentrated cell suspension, the filter was gently rinsed with PBS, carefully cut (sample size, 1 cm by 1 cm) and attached to a steel sample puck (Veeco Metrology Group) by use of a small piece of double-face adhesive tape, and the mounted sample was transferred into the AFM liquid cell while avoiding dewetting. All force curves were recorded with a maximum applied force of
450 pN. The spring constants of the cantilevers were measured using the thermal noise method (Picoforce, Veeco Metrology Group), yielding values (0.011 N/m) that were slightly larger than those announced by the manufacturer (0.01 N/m). Control experiments on the model surface were conducted by incubating tips in a solution of peptidoglycan (10 µg·ml–1) for 30 min and by injecting a peptidoglycan solution in the fluid cell. To account for the flexibility of the biomolecules, loading rates (pN·s–1) were estimated by multiplying the tip retraction velocity (nm·s–1) by the slope of the rupture peaks (pN·nm–1). Adhesion maps were obtained by recording 32-by-32 force-distance curves on areas of given size, calculating the adhesion force for each force curve and displaying the value as a gray pixel.
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To measure LysM-peptidoglycan interactions, AcmA LysM modules terminated with cysteine residues (Fig. 1A) were attached onto gold-coated AFM tips (Fig. 1B), while peptidoglycan from B. subtilis was covalently attached onto carboxyl-terminated surfaces via NHS/EDC chemistry (Fig. 1B). The chemical composition of the functionalized surfaces was assessed using XPS. Table 1 presents the XPS data obtained for gold supports prior to and after LysM and peptidoglycan immobilization. After incubation with LysM peptides, the gold samples showed a large increase of the nitrogen concentration, indicating the presence of a significant amount of peptide at the surface. Following treatment with COOH-terminated alkanethiols, the gold surfaces showed significant oxygen, sulfur, and nitrogen concentrations, consistent with the presence of an alkanethiol monolayer. Treatment with NHS/EDC and peptidoglycan led to an increase of the nitrogen, the oxygen, and the carbon concentration, essentially reflecting the presence of covalently bond peptidoglycan.
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FIG. 1. Strategy for measuring the LysM-peptidoglycan interaction forces by use of AFM. (A) Schematic representation of the recombinant AcmA cell wall-binding domain. (B) Schematics of the surface chemistry used to functionalize AFM tips and supports with LysM and peptidoglycan. AcmA LysM modules terminated with cysteine residues were attached onto gold-coated AFM tips, while peptidoglycan was covalently attached onto carboxyl-terminated surfaces via NHS/EDC chemistry. The blue boxes represent the GlcNAc and MurNAc disaccharide repeating units of peptidoglycan and are cross-linked by pentapeptides. (C and D) AFM images, and cross-sections taken in the middle of the images (graphs below images), of the biologically modified supports in PBS, confirming the presence of smooth, homogeneous LysM (C) and peptidoglycan (D) layers. To determine the layer thicknesses, small square areas were first scanned under large forces (>10 nN), and this was followed by recording 5-µm by 5-µm images of the same areas under smaller forces.
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TABLE 1. Surface chemical composition of solid supports functionalized with either LysM peptides or peptidoglycan
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Forces and dynamics of the LysM-peptidoglycan interaction.
Having validated the functionalization strategies, the LysM-peptidoglycan binding forces were measured by recording force-distance curves between LysM-terminated tip and peptidoglycan-terminated support at a loading rate of 6,700 pN·s–1 (Fig. 2). As shown in Fig. 2A and B, 52% of a total of 750 curves displayed single or multiple binding forces, with the remaining curves exhibiting no adhesion. The corresponding histogram of binding forces showed two maxima centered at 75 ± 17 pN and 170 ± 28 pN. Several observations suggest that the 75-pN binding force reflects the rupture of a single LysM-peptidoglycan complex. First, the specificity of the interaction was confirmed by showing a dramatic reduction of adhesion probability when the same experiment was performed with a silicon nitride tip (data not shown) or in a solution containing 10 µg·ml–1 of peptidoglycan (Fig. 2C and D). Second, the observation of two maxima at 75 and 170 pN in the histogram suggests that the value of
75 pN corresponds to the adhesion strength quantum between individual molecules. Third, this value is in the range of those obtained at fairly comparable loading rates for other receptor-ligand complexes (18).
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FIG. 2. Force spectroscopy of the LysM-peptidoglycan interaction. (A and B) Representative retraction force curves (A) and adhesion force histograms (n = 750) (B) measured in PBS between a LysM tip and a peptidoglycan surface. Data were obtained using five independent samples and eight different tips. All curves were obtained using a retraction speed of 1,000 nm·s–1. (C and D) Force curves (C) and adhesion force histograms (n = 250) (B) obtained after the injection of free peptidoglycan (10 µg·ml–1).
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4.1 pN nm at room temperature) to the projected bond displacement, xβ, along the direction of the applied force. A slope of 8.2 pN was found, yielding a length scale of the energy barrier xβ of approximately 0.5 nm. Second, extrapolation to zero forces yielded the kinetic off-rate constant of dissociation at zero force, koff = rF = 0 xβ/kBT = 0.15 s–1. Note that given the error bars and distribution of the data points, the uncertainty on this extrapolation is fairly large, meaning the obtained koff value should be taken only as a rough estimate.
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FIG. 3. Dynamics of the LysM-peptidoglycan interaction. (A) Dependence of the adhesion force on the loading rate applied during retraction (mean ± standard error of the mean), measured between a LysM tip and a peptidoglycan surface at a constant approach speed (1,000 nm·s–1). (B) Dependence of the adhesion frequency on the interaction time, measured at a constant approach and a retracting speed of 1,000 nm·s–1.
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From these data, we can estimate the interaction time needed for a half-maximal probability of binding (t0.5) of 5.5 x 10–3 s, and, in turn, the association rate constant, kon, of t0.5–1 NA Veff equal to 2.4 103 M–1 s–1, where Veff is the effective volume explored by the tip-tethered LysM, approximated here to a half-sphere of 2.2-nm radius (17), and NA is Avogadro's constant. Here again, we note that the accuracy of the estimated t0.5 and kon values is rather limited and should be considered with caution. Nevertheless, considering the above rate constant values, a rough estimate of the equilibrium dissociation constant can be obtained, namely, KD equals koff/kon equals 61 µM, which is on the order of that estimated for cadherin-cadherin interactions (2, 3). Taken together, the above data indicate that the LysM domain binds to peptidoglycan with high specificity and affinity.
Detection of single LysM-peptidoglycan interactions on L. lactis. Immunofluorescence microscopy studies have revealed that peptidoglycan of L. lactis and other gram-positive bacteria bind the AcmA LysM domain (8, 32). With this in mind, we used LysM tips to probe the surfaces of L. lactis cells (Fig. 4 and 5). Bacteria were immobilized in porous polymer filters, a method allowing AFM analysis of living cells while preserving their native macromolecular architecture. Topographic images of living L. lactis cells (Fig. 4C) revealed a smooth morphology, consistent with an earlier report (15). Interestingly, most force curves recorded either over the cell surface or over the filter with a LysM tip did not show any binding events (Fig. 5C and E). The very poor binding on the native L. lactis surface suggests that peptidoglycan is hindered by other cell wall constituents. These AFM data differ from earlier immunofluorescence results in that the latter showed some binding of the LysM domain on very specific locations of L. lactis (32). Presumably, this behavior reflects differences in the probing depths of the two techniques: while fluorescence microscopy probes peptidoglycan from the entire cell wall, AFM detects only those peptidoglycan molecules exposed on the outermost cell surface.
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FIG. 4. AFM imaging of single Lactococcus lactis cells, either in the native state or after treatment with TCA. (A) Schematic representation of the cell wall of L. lactis. Abbreviations: TA, teichoic acids; PR, proteins; PS, polysaccharides; PG, peptidoglycan; PM, plasma membrane. (B) Schematic of the cell wall after treatment with TCA, which is expected to remove peptidoglycan-associated polymers. (C) AFM deflection image in Tris-maleate buffer showing two dividing L. lactis cells trapped into a porous polymer filter for in situ imaging. (D) AFM deflection image in Tris-maleate buffer showing dividing L. lactis cells after treatment with TCA.
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FIG. 5. Detecting single LysM-peptidoglycan interactions on L. lactis cells. (A and B) Low-resolution AFM images with Tris-maleate buffer obtained for native (A) and TCA-treated (B) L. lactis cells. (C to F) Adhesion force maps (gray scale, 300 pN) (C and D) and adhesion force histograms (n = 1,024) (E and F) together with representative retraction force curves recorded with a LysM tip on the native (C and E) and TCA-treated (D and F) cell surfaces by use of a constant retraction speed (1,000 nm/s). The bright pixels, observed frequently on top of the treated cell but very rarely on the native cell or on the filter, document substantial binding of the LysM tip due to the exposure of peptidoglycan. Approach and retraction force curves were similar near the contact region.
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In summary, using SMFS (i) we measured the specific binding forces of single AcmA LysM-peptidoglycan interactions on model surfaces, thereby providing an estimate of association and dissociation rate constants; and (ii) we detected these interactions on L. lactis cell walls. Clearly, it would be most interesting in future research to further explore the force and dynamics of LysM interactions using other purified peptidoglycans and other bacterial strains. A crucial question is to clarify whether other moieties besides GlcNAc are also recognized (8), which could be achieved by SMFS using various possible peptidoglycan-based substrates. SMFS experiments could also help our understanding of how the number of LysM repeats in AcmA modulates its binding forces, since this factor is known to affect the binding efficiency and, consequently, the in vivo activity of the enzyme (33). In addition to providing novel insight into the structure-function relationships of bacterial surfaces, these single-molecule analyses may find promising applications for studying the heterologous display of proteins or peptides. Indeed, Bosma et al. (6) recently proposed a novel display system that allows a highly efficient immobilization of heterologous proteins on L. lactis surfaces. Nonliving gram-positive enhancer matrix particles were obtained from gram-positive bacterial cells by use of TCA treatment, e.g., and then used as substrates to bind externally added heterologous proteins by means of the high-affinity LysM binding domains. Hence, AFM may be powerful method in future research for assessing the quality of such novel surface display systems.
Published ahead of print on 29 August 2008. ![]()
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