Journal of Bacteriology, March 2005, p. 2218-2223, Vol. 187, No. 6
0021-9193/05/$08.00+0 doi:10.1128/JB.187.6.2218-2223.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.
Institut de Biologie Moléculaire et d'Ingénierie Génétique, Equipe de Microbiologie Fondamentale et Appliquée, UMR CNRS 6008, Université de Poitiers, Poitiers, France
Received 27 September 2004/ Accepted 10 December 2004
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Most of the bacteriocins from LAB are synthesized as prepeptides that undergo cleavage of a leader peptide during export across the cell membrane (22). Besides some bacteriocins secreted via the Sec pathway (5, 17, 19, 32), two different types of bacteriocin leaders have been described. The FLNV-type leaders are restricted to some lantibiotics such as nisin (6, 20, 23). The most abundant double-glycine (GG)-type extensions, characterized by a glycine doublet at the C-terminal end, were found in class II, as well as in some class I LAB pre-bacteriocins (6, 7, 20, 23). Secretion of the GG-type leader bacteriocins is achieved by a specific ATP-binding cassette (ABC) transporter, often associated with an accessory factor (7, 20). The ABC transporter possesses an N-terminal cysteine protease domain, which is responsible for cleavage of the leader peptide after the double-glycine motif (13, 31). This cleavage occurs on the cytoplasmic side of the membrane during secretion of the antibacterial peptide (9). Recently (28), it was demonstrated that a class IIa bacteriocin precursor, carnobacteriocin B2 (25), displayed in a lipophilic solvent an
-helical structure containing 18 amino acids in the leader peptide. This structure was suggested to be involved in the loss of activity of the precursor compared to that of the mature bacteriocin and in the recognition of the leader peptide by the ABC transporter responsible for export and processing (28).
In the case of mesentericin Y105, a class IIa bacteriocin produced by Leuconostoc mesenteroides (15), the GG-type leader peptide possess 24 amino acids (11). As described for carnobacteriocin B2 (26), the mesentericin Y105 precursor was demonstrated to be less active than the mature bacteriocin (3). We demonstrated previously that the bacteriocin is secreted and processed by the ABC transporter MesD (3) and the membrane binding protein MesE (1). Recently, we showed that this dedicated transport system is involved in the export from L. mesenteroides Y105 of two mesentericins, Y105 and B105, having distinct leader peptide sequences (1).
In this work, we studied the role of the conserved amino acids in the leader peptide with respect to the production of mesentericin Y105 by using our heterologous production system (21) and site-specific mutagenesis. We have shown that the N-terminal extension of the ABC transporter MesD, named MesDp, cleaved the peptide leader of the mesentericin Y105 precursor in vitro. Finally, MesDp cleavage of the mutant pre-bacteriocins was performed and compared to the extent of maturation of the wild-type prepeptide.
Strains and plasmids. The strains and plasmids used in this study are listed in Table 1.
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TABLE 1. Strains and plasmids used in this study
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FIG. 1. Overview of the generated site-directed mutations in the mesentericin Y105 leader peptide conserved motif. Amino acid alterations, indicated by the arrows, are given in one-letter code. The symbols in parentheses indicate, for each amino acid alteration, the modification in the secreted activity related to the wild type (Table 2) as follows: ±, activity higher than 60%; , residual activity lower than 50%; 0, mutation responsible for complete loss of activity.
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FIG. 2. Helical-wheel representation of the putative leader helices of pre-mesentericin Y105. The curve shows the hydropathy for a three-residue window moving on the wheel surface and using Kyte and Doolittle's scale. The inner circle is for zero hydropathy. The grey zone corresponds to the predicted polar face of the helix.
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As presented in Table 2, decreases in antilisterial activity in the culture supernatant related to secretion of mesentericin Y105 and ranging from 0 to 100%, depending on the nature and position of the mutation, were observed. The glycine residues at positions 1 and 2 appeared to be of major importance for the secretion of mesentericin Y105. However, the nature of the residue at 2 was essential for secretion of the bacteriocin since with a conservative change (alanine instead of glycine) the secreted activity was only half of that of the wild type and other substitutions led to complete loss of mature bacteriocin in the culture supernatant. The high level (85.5%) of secretion of the G-1A mutant was expected because the cleavage site of the class I pre-bacteriocins with leader peptides of the GG type can contain a GG, GA, or GS motif (30). However, in previous studies of the leader peptide of lactacin F
(10), a class IIb bacteriocin, as well as the leader peptide of mutacin II (4), a class I bacteriocin, modifications of the GG doublet involved complete loss of bacteriocin production. Indeed, replacement of glycine with alanine at position 1, as well as position 2, resulted in complete loss of mutacin II production. Replacement of glycine with valine at position 1 or glycine with arginine or serine at position 2 eliminated lactacin F activity (10). On the contrary, our results showed a higher susceptibility of the glycine at position 2 than at position 1 since three of four modifications at position 2 led to a nonsecretable mutant (G-2D, G-2T, and G-2P) and only one of six at position 1 led to a nonsecretable mutant (G-1D). The major impact of charge is illustrated by the complete loss of activity with insertion of aspartic residues at positions 1 and 2. This could imply an acidic function at the active site of the maturase part of MesD.
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TABLE 2. Antilisterial activity in culture supernatants and after in vitro maturation
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Computer analysis.
Recently, the solution structure of the precursor for carnobacteriocin B2 was determined by nuclear magnetic resonance analysis (28). An
-helix was detected between residues 5 and 15 of the leader peptide of this class IIa bacteriocin in a membrane-mimicking solvent. It was proposed that a similar
-helix was likely present in the corresponding region of all class IIa pre-bacteriocins (28). By taking advantage of these results, the structures of the peptide leader of mesentericin Y105 were calculated and compared to those of other class IIa bacteriocin leader peptides. The predicted structures of the leader peptides of the 13 known class IIa pre-bacteriocins displayed an
-helix from residue 3 to residue 15 (data not shown). However, the calculated helices for mesentericin Y105 and leucocin A, carrying longer leader peptides, appeared to be extended to residue 18. We decided in the present work to consider the longer helix (amino acids 3 to 18), named the leader helix, even if the amino acids at the 3 and 4 positions were not predicted to be included in the leader peptide helix of carnobacteriocin B2 determined by nuclear magnetic resonance analysis (28). According to the helical-wheel representation (Fig. 2), the leader helix for wild-type mesentericin Y105 appeared to be globally amphipathic but showed one polar face and another of mixed polarity.
The impact of the mutations on the leader helix of pre-mesentericin Y105 derivatives was evaluated by comparison of the structures of their leader peptides to that of the wild-type leader peptide. Four structural parameters (hydrophobicity, hydrophobic change along the helix, and value and orientation of the hydrophobic moment) were measured and correlated with the antilisterial activity in the culture supernatants (data not shown). The predicted secondary structure of the modified leader peptides in the glycine doublet (positions 1 and 2) appeared to be unaffected compared to that of the wild-type leader peptide. Interestingly, a marked decrease in antilisterial activity of the mutant culture supernatants was correlated with a decrease in the hydrophobicity of the mixed face of the leader helix (L-7D, L-12D, and to a lesser extent V-4K). On the contrary, an increase in hydrophobicity at the 8, 9, and 11 positions induced a slight decrease in activity (N-8A, Q-9V, and D-11V). These results suggest that the hydrophobic residues, located on the mixed face of the leader helix, but not the polar amino acids of the conserved motif, are of major importance for the interaction of pre-mesentericin Y105 with the ABC transporter MesD.
The N-terminal cytoplasmic extension of MesD cleaves the mesentericin Y105 precursor. To demonstrate the involvement of the N-terminal part of the ABC transporter MesD in the processing of the pre-mesentericin Y105, an in vitro assay was developed. The system was a modified form of one previously described by Havarstein et al. (13). A PCR fragment encoding the N-terminal extension of mesD was cloned into the NdeI and XhoI sites of expression vector pET21a (Novagen), leading to the pETDP plasmid, which was introduced into E. coli BL21/DE3. The substrate of this putative protease was obtained by cloning the mesY gene into the BamHI and HindIII sites of the pQE30 (QIAGEN) expression vector, giving rise to pPMWT. When induced by isopropyl-ß-D-thiogalactopyranoside (IPTG), the recombinant strains expressed MesDp, which corresponds to the 163 N-terminal amino acids of MesD followed at the C-terminal end by six histidine residues, and PreMesH, corresponding to pre-mesentericin Y105 with six histidine residues as an N-terminal extension, respectively. Both peptides were produced as inclusion bodies and purified by metal chelate affinity chromatography (16) on a HiTrap Chelating HP column (Amersham Biosciences).
PreMesH was active against listeriae to a level similar to that of the unmodified pre-mesentericin Y105 (3; data not shown). Various amounts of purified MesDp, ranging from 0.8 to 10 µg, were incubated for 16 h at 37°C in 100 µl of a previously described buffer (13) containing an initial concentration of PreMesH chosen in order to give an inhibition zone diameter of less than 1 mm. Pre-bacteriocin cleavage was monitored by well diffusion bacteriocin assay (8). In all cases, inhibition zone diameters obtained for processing mixtures were higher than that of the control and consequently corresponded to the release of mature mesentericin Y105. The reaction mixtures were analyzed by reversed-phase high-performance liquid chromatography and mass spectrometry (data not shown). The peaks corresponding to both mesentericin Y105 and PreMesH were detected in all cases, indicating that proteolysis was incomplete. However, the diameter of the halo zones was proportional to the MesDp concentration in a reproducible manner in more than five independent assays (data not shown) and was considered to be related to the extent of PreMesH cleavage.
Mutations in the leader peptide modulate the cleavage yield of the precursor. To study the correlation between the extent of secretion and the proteolytic cleavage of the leader peptide, recombinant precursors with relevant sequence modifications were digested with MesDp. Mutants, named according to the amino acid substitution with a capital H for the histidine tag (Table 2), were constructed by the same PCR strategy described above with the same primers and pPMWT as the template DNA. We chose to produce six pre-bacteriocins with peptide leader mutations that confer reduced (G-1M and L-12K), highly reduced (L-7D and L-7K), or aborted (G-1D and G-2P) secretion of mesentericin Y105 (Table 2). Identical amounts of the purified pre-bacteriocins, including pre-MesH as the control, were submitted to MesDp processing. The amount of antilisterial activity released by proteolytic cleavage of the mutant proteins, measured by critical-dilution assay (11), was compared to that of the wild type (Table 2). The nonprocessing of peptides G-1DH and G-2PH by MesDp demonstrates that the absence of secreted mesentericin Y105 by corresponding mutants of L. mesenteroides DSM20484is clearly related to the absence of processing of the pre-bacteriocin (Table 2). The peptides L-7DH, L-7KH, and L-12KH appeared to be very poorly cleaved by MesDp compared to the native pre-mesentericin Y105. These results could indicate that the hydrophobic amino acids at positions 7 and 12, which are involved in the mixed face of the leader helix, are of major importance for positioning the peptide at the active site of the protease.
It was shown that the mutacin II mutants G-1A and G-2A accumulated pre-bacteriocin in the membrane of the cells (4). This may be attributed to the regular positioning of the G-1A and G-2A prepeptides in the proteolytic site of the transporter with no subsequent cleavage. Failure to detect pre-mutacin in the membrane of the other inactive mutants (I-4D and L-7K) could be related to our results for mutations at positions 4, 7, and 12. The absence of both the bacteriocin and precursor suggested an irregular interaction of the pre-bacteriocin that led to its incomplete cleavage before it was released in the cytosol and then proteolyzed.
Surprisingly, G-1MH was cleaved with greater efficiency (80%) and L-12KH was cleaved to a lesser extent (5%) in comparison with the secretion levels of mesentericin Y105 from the corresponding mutants, 34.8 and 30.4%, respectively (Table 2). This may be related to the folding of the recombinant peptides, MesDp and pre-mesentericins, in aqueous solution, which is probably different than in the membrane environment. Consequently, we can hypothesize that the L-12K mutant positioning in the proteolytic site was assisted by the transporter part of MesD, whereas L-12KH was unable to correctly interact with the active site of the soluble enzyme. Moreover, our computer-aided analysis showed that the G-1M mutant may be present, in a membrane environment, as an extended leader helix, until amino acid at position +1, which could decrease the affinity of the entire transporter, leading to incomplete processing (34.8%). Since the G-1MH peptide structure is probably a random coil in an aqueous solvent, its interaction with the recombinant protease MesDp led to an enhanced level of cleavage (80%).
According to the structure analysis of the pre-carnobacteriocin B2 (28) and mature mesentericin Y105 (21) and our computer analysis, the structure of pre-mesentericin Y105 is most likely composed of two
-helices, the amphipathic mature helix and the leader helix with one hydrophilic face and the other of mixed polarity in a membrane environment. As proposed by Sprules et al. (28), an interaction could be expected between the two helices that involves, in our opinion, their hydrophilic faces. Indeed, if this is the case, the prepeptide presents the hydrophobic conserved residues (4, 7, and 12) located on the mixed-polarity face of the leader helix, which can then be recognized by the proteolytic part of the ABC transporter MesD. At this stage, we can hypothesize that the hydrophobic face of the mature helix can interact with the substrate binding site of the transporter. The cleavage of the pre-bacteriocin at the GG site liberates the mature peptide, which is then transported across the cell membrane.
We acknowledge Lars Axelsson for generously providing L. ivanovii Li4(pVS2). Manilduth Ramnath is gratefully acknowledged for valuable review of the text.
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