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Antimicrobial Agents and Chemotherapy, June 2008, p. 1917-1923, Vol. 52, No. 6
0066-4804/08/$08.00+0 doi:10.1128/AAC.01409-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Laboratoire de Chimie Analytique et Sciences de l'Aliment, IPHC-DSA, ULP, CNRS, 74 route du Rhin, 67400 Illkirch-Graffenstaden, France,1 Laboratoire de Spectrométrie de Masse Bioorganique, IPHC-DSA, ULP, CNRS, 25 rue Becquerel, 67087 Strasbourg, France,2 National Institute of Livestock and Grassland Science, Functional Feed Research Team, Nasushiobara, Tochigi 329-2793, Japan3
Received 31 October 2007/ Returned for modification 27 February 2008/ Accepted 30 March 2008
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Enterococci are also promising for the biopreservation of food, especially by means of bacteriocin production (19). Bacteriocins are ribosomally synthesized antimicrobial peptides with activities that are usually directed against species closely related to the producing bacterium (26, 29). Much focus has been directed in the past few years toward enterococci which have emerged as a prominent group of bacteriocin-producing LAB, mainly because of the diversity of the bacteriocins (enterocins) produced and the potential for their use as food biopreservatives. In fact, species of Enterococcus are quite unique in that they produce a wide array of structurally diverse antimicrobial peptides, often more than one per strain, some of which are atypical and distinct from known bacteriocins. Some of these atypical enterocins, such as enterocins L50A and L50B (8) and enterocin Q (7), could not fit into the traditional classification of bacteriocins produced by LAB, which has largely prompted the recent reclassification of class II bacteriocins into a new scheme (19).
The diversity of enterocins is attributed to the robust nature of enterococci, which allows them to survive in a wide range of ecological niches, as well as their superior genetic exchange mechanisms (19). Such attractive traits could only increase the interest in the biotechnological use of enterocins or their producers in food preservation, especially since these bacteriocins are particularly active against many food-borne pathogens, such as bacilli, clostridia, staphylococci, and Listeria species (17, 19). As a result, enterocins are being extensively investigated for possible use as food preservatives in dairy and meat products (4, 20, 23). However, enthusiasm for enterococci has been somewhat diminished by the emergence of multiple-antibiotic-resistant enterococci among species of nosocomial pathogens and the presence of virulence factors among food isolates (11, 13, 18, 31). The potential health risk linked to enterococcal strains will therefore have to be carefully evaluated prior to any food application (17). Nevertheless, as pointed out by Franz et al. (19), enterococcal bacteriocins produced by heterologous hosts or added as cell-free preparations appear not to carry particular safety concerns when it comes to applications in food preservation.
A study by De Vuyst et al. (10) into the ecological distribution of enterocins involving a large number of strains from different sources did in fact not find a correlation between the origins of the strains and the types of inhibitory spectra of the bacteriocins produced. Results from a recent investigation by Inoue et al. (24) suggested, though, that the dominant type of bacteriocin in Enterococcus faecium clinical isolates may differ from the dominant type of bacteriocin found in food-grade E. faecium isolates. It was pointed out that the anti-Listeria activity of bacteriocins from food-grade strains may provide these bacteria with a selective advantage against Listeria species in their particular ecological niche. On the other hand, bacteriocins identified in clinical isolates of E. faecium, such as bacteriocin 32, which is not active against Listeria monocytogenes, would provide a competitive advantage in the clinical environment in association with multiple-drug resistance. This idea helped explain the high incidence of bacteriocin 32 among vancomycin-resistant isolates. The suggestion that the type of bacteriocin that becomes dominant within any environment is influenced by the surrounding ecology is interesting and may have important implications for the future of the biotechnological use of enterocins. However, reports on the ecological distribution of enterocins remain scarce, and further studies are needed. For instance, while research on enterocins has focused mainly on bacteriocinogenic enterococci of food or clinical origins (9, 17), less attention has been given to isolates from plant and environmental sources (30).
In the present work, we describe the isolation and identification of three bacteriocins produced by E. faecium IT62, a strain isolated from Italian ryegrass in Japan. The spectrum of activity and the chemical structure of each antibacterial peptide are reported.
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TABLE 1. Antimicrobial activities of purified enterocins L50A (peptide 2), L50B (peptide 1), and IT (peptide 3)
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To determine the antimicrobial spectrum of each bacteriocin, the effects of purified peptides on the growth of a wide range of microorganisms (Table 1) were assessed using a Bioscreen 200C automated turbidometer (Labsystems, Helsinki, Finland). Strains were grown for 18 h under the conditions indicated in Table 1. Cultures were diluted in fresh broth to reach a final concentration of ca. 105 CFU/ml, and 190-µl samples of each were loaded into microplate wells. Ten-microliter aliquots of purified bacteriocin solutions were added to wells containing indicator bacteria. Controls consisted of 190-µl samples of diluted cultures supplemented with 10 µl of sterile deionized water. All assays were done in duplicate. The growth of indicator strains at 30 or 37°C, depending on the species, was monitored at 600 nm for 24 h. Bacteriocin activity was expressed as the maximal difference in absorbance between control and assay samples, which was reached at the end of the exponential growth phase (between 7 and 14 h, depending on strains).
Bacteriocin purification. E. faecium IT62 was inoculated into 1 liter of MRS broth to yield an initial concentration of ca. 105 CFU/ml and incubated for 15 h at 37°C. Cells were removed by centrifugation at 4,000 x g for 15 min, and the supernatant was filter sterilized (using a 0.45-µm-pore-size Porafil cellulose acetate filter; Macherey-Nagel, Hoerdt, France). The obtained culture extract was adjusted to pH 6 with NaOH and purified by passage on a cation exchanger (SP-Sepharose HP; 100-mm length and 26-mm internal diameter [Amersham Biosciences, Orsay, France[). Equilibration and washing were done with 20 mM sodium acetate at pH 6 (buffer A), prior to elution over 60 min with an NaCl gradient from 0 to 1 M NaCl in buffer A at a flow rate of 5.0 ml/min. At this stage, two groups of active fractions (fraction group A and fraction group B) were observed, collected separately, and applied to a C8 reverse-phase column (Polaris C8-A; 250-mm length, 10-mm internal diameter, 180-Å pore size, and 5-µm particle size [Varian, Les Ulis, France]) for high-pressure liquid chromatography (HPLC). After a 20-min wash with 35% acetonitrile in water containing 0.1% trifluoroacetic acid (TFA) for fraction group A and with 20% acetonitrile in water containing 0.1% TFA for fraction group B, elution was done with a gradient of H2O-acetonitrile containing 0.1% TFA (see Fig. 1) at a flow rate of 2 ml/min. Bacteriocins were detected at 280 nm by using a Varian ProStar photodiode array detector. Samples containing the purified bacteriocins were stored at –20°C.
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FIG. 1. Profiles of HPLC elution from a C8 column at 280 nm. (A) Fraction group A obtained after cation-exchange chromatography; (B) peptides 1 and 2 purified to homogeneity; (C) fraction group B obtained after cation-exchange chromatography. Black arrows indicate the peaks corresponding to active fractions; dashed lines indicate acetonitrile percentage.
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Proteolytic digestion, liquid chromatography-nanospray MS/MS (nano-LC/MS/MS), and sequence analysis. Purified bacteriocins were vacuum dried using a Speed Vac SC100 system (Savant, MN) and resuspended in a solution of 40 µl of trifluoroethanol and 40 µl of 10 mM DL-dithiothreitol prepared in 50 mM ammonium bicarbonate. After heating of the mixtures at 65°C for 1 h, 40 µl of 25 mM ammonium bicarbonate containing 55 mM iodoacetamide was added. The solutions were left for 1 h at room temperature in the dark, and then 40 µl of 25 mM ammonium bicarbonate containing 20 mM DL-dithiothreitol was added and the mixtures were left for one more hour at room temperature in the dark. Samples were diluted to reach a final trifluoroethanol percentage of 5%, and digestion was performed overnight at room temperature in the presence of modified porcine trypsin (Promega, Madison, WI) at protein ratios of 1 to 20. Digestion was stopped by adding 0.1% formic acid.
Tryptic digests were analyzed by nano-LC/MS/MS using an 1100 series HPLC-chip/MS system (Agilent Technologies, Palo Alto, CA) coupled to an HCT ultra electrospray ion trap (Bruker Daltonics, Bremen, Germany) with a capillary cap voltage of –1,750 V. The three most abundant peptides, preferably doubly charged ions, corresponding to each MS spectrum were selected for further isolation and fragmentation. The MS/MS scanning was performed in the ultrascan resolution mode at a rate of change in the m/z of 26.000 per s. Results from a total of six scans were averaged to obtain an MS/MS spectrum. Mass data collected during nano-LC/MS/MS analysis were processed, converted into mgf files, and compared against the NCBInr database by using a local Mascot server (Matrix Science, London, United Kingdom).
N-terminal sequencing. In instances in which a bacteriocin could not be identified through nano-LC/MS/MS analysis, N-terminal sequencing was performed on a model 473A microsequencer (Applied Biosystems, Foster City, CA). Samples were loaded onto polybrene-treated, precycled glass fiber filters. Phenylthiohydantoin amino acids were identified by chromatography on a 2.1- by 200-mm phenylthiohydantoin C18 column.
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Structural analysis. Nano-LC/MS/MS analysis of tryptic digests of peptides 1, 2, and 2' allowed the identification of enterocins L50A and L50B (Table 2). Mascot searches including the possibility of methionine oxidation and N formylation were performed, given that such modifications are common features of bacteriocins (3, 34). In fact, two forms of L50A were identified: one was formylated at the N-terminal Met (peptide 2), and the second was oxidized at Met24 and formylated at the N-terminal Met (peptide 2'). Bacteriocin L50B formylated at the N-terminal Met (peptide 1) was identified. These results were in agreement with the molecular masses of intact peptides determined by ESI-MS analysis. Peptide 1' was not analyzed by MS/MS, but the analogy in the elution profiles of peptides 1 and 1' and the difference of 16 Da between these peptides suggested that peptide 1' corresponds to the N-formylated enterocin L50B with oxidation at Met24.
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View this table: [in a new window] |
TABLE 2. Tryptic peptide sequences observed by nano-LC/MS/MSa
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Activities of the purified bacteriocins. The activities of chromatographically isolated peptides (in sample volumes of 4 ml) were assessed by titration against the indicator strains E. faecium WHE 81 and L. lactis RO50. Enterocin L50A was more active against L. lactis RO50 (1,600 AU/ml) than against E. faecium WHE 81 (800 AU/ml). The same pattern was observed with enterocin L50B, which showed activities of 400 AU/ml when tested against L. lactis RO50 and 100 AU/ml when tested against E. faecium WHE 81. Enterocin IT, however, showed strong activity against E. faecium WHE 81 (102,400 AU/ml) but was not active at all against L. Lactis RO50.
The differences observed in the activity spectra of enterocins L50A, L50B, and enterocin IT were further investigated by testing the sensitivities of a wide range of bacteria to the three bacteriocins in liquid media by using an automated turbidometer. A strain was considered sensitive when its growth was partially or completely inhibited. In most instances, sensitive strains had their growth significantly slowed down, as was the case for L. lactis 72 and E. faecium WHE 81 (Fig. 2). The data for all indicator bacteria are summarized in Table 1, which presents the highest differences in population size obtained compared to controls during incubation.
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FIG. 2. Examples of the antimicrobial effects of purified bacteriocins on indicator bacteria. (A) L. lactis 72; (B) E. faecium WHE 81. , control; , enterocin L50A; -, enterocin L50B; , enterocin IT. Arrows show the maximal differences in absorbance at 600 nm between control and assay samples obtained during growth.
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Enterocins L50A and L50B are widespread bacteriocins that are produced by several E. faecium strains isolated from very diverse food sources, such as Spanish dry fermented sausages (8), Spanish-stye green olive fermentations (16), Malaysian mold-fermented tempeh (28), Moroccan soft cheese (1), and Mongolian airag (3). Nevertheless, in some instances (1, 3), the experimental masses obtained after the purification of these bacteriocins have differed from the theoretical ones (5,190 Da for enterocin L50A and 5,178 Da for enterocin L50B). We suspect that these discrepancies are due to chemical modifications at Met residues which are likely to complicate the identification of enterocins.
The third bacteriocin isolated in the present work was a 6,390-Da peptide made of 54 amino acids that was named enterocin IT. The amino acid sequence of enterocin IT is identical to the sequence of the C-terminal part of the previously reported bacteriocin 32 (24) and 16 amino acids shorter than the sequence of the latter. The sequence of bacteriocin 32 was obtained based on the nucleotide sequence of its structural gene bacA (24), with an L L A sequence as the signal region for the cleavage of the prepeptide, i.e., at position 19 (Fig. 3). Comparison with other bacteriocin signal peptides (22) showed, however, that L L A is a less likely recognition region for the signal peptidase than V E A, which is located at positions 33 to 35 of the prepeptide. In fact, while L L A has not been reported as the cleavage site for other bacteriocins, V E A is the cleavage site for other sec-dependent bacteriocins, such as bacteriocin 31 (33) and enterocin SE-K4 (12). Also, the sequence V X A has been found for enterolysin A, bacteriocin T8, enterocin P, dysgalacticin, and hiracin JM79 (19, 21, 32). Provided that the cleavage region of the signal peptide sequenced by Inoue et al. (24) is not L L A but V E A, the bacteriocin obtained would have exactly the same size and sequence as the enterocin IT identified in the present work. However, bacteriocin 32 would have to be purified and sequenced to determine whether the cleavage site previously determined (24) is correct or not.
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FIG. 3. Amino acid sequence deduced by Inoue et al. (24) from the structural gene of bacteriocin 32. The putative signal region according to Inoue et al. is underlined with a single solid line, and the corresponding cleavage site is indicated by a white arrow. The bacteriocin 32 sequence is indicated by underlining with a dotted line. A more likely signal region is double underlined, and the corresponding cleavage site is indicated by a black arrow.
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E. faecium IT62, isolated from ryegrass, produced two kinds of bacteriocins with very different activities that were previously isolated from very different sources: on the one hand, enterocins L50A and L50B, two synergistic bacteriocins with a wide antimicrobial spectrum that were identified previously in several food isolates, and on the other hand, enterocin IT, a bacteriocin with a very narrow spectrum and a structure close to that of bacteriocin 32, which was identified previously in numerous clinical isolates of E. faecium. This finding goes against the idea of a particular ecological distribution of bacteriocins in which, for instance, the anti-Listeria bacteriocins would be found in food and bacteriocins such as bacteriocin 32 or enterocin IT would be found in clinical settings, where they would be associated with drug resistance (22). A bacterial strain can, in fact, as is the case for E. faecium IT62, produce bacteriocins with very different properties and activity spectra. Nonetheless, bacteria that produce the "right" bacteriocin in a particular ecological niche stand a better chance of surviving and becoming dominant.
In the search for bacteriocins, most purification processes are based on a single indicator strain, which offers a narrow vision of the antimicrobial activities of the bacteria investigated, especially when bacteriocins with narrow spectra are produced. These bacteriocins are likely to be neglected and discarded during the purification process in favor of bacteriocins with broader spectra. This pattern may explain why enterocin IT was not detected in the numerous cases in which enterocins L50A and L50B were found. The use of multiple indicator bacteria during the purification stages is therefore highly advisable in order to detect multibacteriocin production.
Published ahead of print on 7 April 2008. ![]()
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