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Antimicrobial Agents and Chemotherapy, May 2009, p. 1907-1911, Vol. 53, No. 5
0066-4804/09/$08.00+0     doi:10.1128/AAC.00052-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Genetic Identification of the Bacteriocins Produced by Enterococcus faecium IT62 and Evidence that Bacteriocin 32 Is Identical to Enterocin IT{triangledown}

Esther Izquierdo,1 Yimin Cai,2 Eric Marchioni,1 and Saïd Ennahar1*

Laboratoire de Chimie Analytique et Sciences de l'Aliment, IPHC-DSA, Université de Strasbourg, CNRS, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France,1 National Institute of Livestock and Grassland Science, Functional Feed Research Team, Nasushiobara, Tochigi 329-2793, Japan2

Received 14 January 2009/ Returned for modification 22 February 2009/ Accepted 1 March 2009


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ABSTRACT
 
Enterococcus faecium IT62, a strain isolated from ryegrass in Japan, produces three bacteriocins (enterocins L50A, L50B, and IT) that have been previously purified and the primary structures of which have been determined by amino acid sequencing (E. Izquierdo, A. Bednarczyk, C. Schaeffer, Y. Cai, E. Marchioni, A. Van Dorsselaer, and S. Ennahar, Antimicrob. Agents Chemother., 52:1917-1923, 2008). Genetic analysis showed that the bacteriocins of E. faecium IT62 are plasmid encoded, but with the structural genes specifying enterocin L50A and enterocin L50B being carried by a plasmid (pTAB1) that is separate from the one (pTIT1) carrying the structural gene of enterocin IT. Sequencing analysis of a 1,475-bp region from pTAB1 identified two consecutive open reading frames corresponding, with the exception of 2 bp, to the genes entL50A and entL50B, encoding EntL50A and EntL50B, respectively. Both bacteriocins are synthesized without N-terminal leader sequences. Genetic analysis of a sequenced 1,380-bp pTIT1 fragment showed that the genes entIT and entIM, encoding enterocin IT and its immunity protein, respectively, were both found in E. faecium VRE200 for bacteriocin 32. Enterocin IT, a 6,390-Da peptide made up of 54 amino acids, has been previously shown to be identical to the C-terminal part of bacteriocin 32, a 7,998-Da bacteriocin produced by E. faecium VRE200 whose structure was deduced from its structural gene (T. Inoue, H. Tomita, and Y. Ike, Antimicrob. Agents Chemother., 50:1202-1212, 2006). By combining the biochemical and genetic data on enterocin IT, it was concluded that bacteriocin 32 is in fact identical to enterocin IT, both being encoded by the same plasmid-borne gene, and that the N-terminal leader peptide for this bacteriocin is 35 amino acids long and not 19 amino acids long as previously reported.


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INTRODUCTION
 
Enterococci are a prominent group of bacteriocin producers, mainly due to the diversity of the bacteriocins (enterocins) produced and the potential for their use as food biopreservatives. In fact, species of Enterococcus produce a wide array of structurally diverse antimicrobial peptides, often more than one by a single strain, some of which are atypical and distinct from known bacteriocins. Atypical enterocins, such as enterocin L50A (EntL50A), enterocin L50B (EntL50B) (6), and enterocin Q (5), could not fit in the traditional classification of bacteriocins, which has in part prompted the recent reclassification of class II bacteriocins into a new scheme (15).

The diversity of enterocins is linked 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 (15). Such attractive traits have increased the interest for 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 (4, 14-16, 21).

The efficient gene transfer mechanisms and the fact that bacteriocin genes are often located on transmissible genetic entities are also used to explain the production of multiple bacteriocins by single strains and the multiple isolation of the same enterocins by different work groups (15). Hence, many enterocins such as AS-48, L50A, L50B, A, B, and P are produced by Enterococcus faecium strains of various origins (1, 8, 9, 12, 18, 19, 24). EntL50A and EntL50B in particular are widespread bacteriocins that are produced by several strains from very diverse sources such as Spanish dry fermented sausages (6), Spanish green olive fermentation (13), Malaysian mold-fermented tempeh (25), Moroccan soft cheese (2), and Mongolian airag (3). Moreover, we recently reported the production of these two bacteriocins by E. faecium IT62, a strain isolated from ryegrass in Japan (23). This strain was also shown to produce a third and new bacteriocin, called enterocin IT (EntIT), consisting of a 6,390-Da, 54-amino-acid peptide identical to the C-terminal part of bacteriocin 32 (Bac 32) (22) and 16 amino acids shorter than the latter (23). The three bacteriocins were purified to homogeneity, and their primary structures were determined by amino acid sequencing.

In the present work, we report the identification of the genetic loci involved in the production of EntL50A, EntL50B, and EntIT by E. faecium IT62. It is furthermore shown that the bacteriocin designated Bac 32 is in fact identical to EntIT.


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MATERIALS AND METHODS
 
Bacterial strains and cultures. The bacteriocin producer E. faecium IT62, previously isolated from Italian ryegrass (Lolium multiflorum Lam.), was maintained as a frozen stock held at –80°C in brain heart infusion broth with 30% glycerol (Bio-Rad, Marnes-La-Coquette, France). Prior to experimental use, the strain was cultivated twice for 18 h to 24 h in MRS broth at 37°C (Biokar Diagnostics, Beauvais, France).

DNA preparation from E. faecium IT62. Plasmid DNA was isolated from cells from 5-ml overnight cultures with a GeneJET plasmid miniprep kit (Fermentas, Hanover, PA) as described by the manufacturer.

PCR amplification and nucleotide sequencing. The oligonucleotide primers used in this study were obtained from Millegen (Labege, France). PCR was carried out using Taq (Invitrogen, Cergy Pentoise, France) and KOD (Novagen, Darmstadt, Germany) DNA polymerases under the following amplification conditions: an initial cycle of denaturation (97°C for 2 min), followed by 35 cycles of denaturation (94°C for 45 s), annealing (50 to 62°C for 30 s), and elongation (72°C for 15 s to 3 min), and a final extension step at 72°C for 7 min in a 2720 DNA thermal cycler (Applied Biosystems, Foster City, CA). The resulting PCR products were cleaned with a QIAquick PCR purification kit (Qiagen, Courtaboeuf, France) and analyzed by electrophoresis in 1% agarose gels with a Gel Doc 1000 documentation system (Bio-Rad). They were then purified from agarose gels using Ultraclean Gel Spin (Mobio, Solana Beach, CA) before they were used for nucleotide sequencing. The primers used for PCR amplification and the obtained PCR products are listed in Table 1.


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TABLE 1. Primers used in this studya

DNA sequence analysis. DNA sequencing was performed with a version 3.1 BigDye Terminator cycle sequencing ready reaction kit and an Applied Biosystems model ABI3130XL genetic analyzer (Applied Biosystems) at a DNA sequencing facility (Millegen). All products were used according to the instructions of the manufacturers. Analysis of the nucleotide sequence was done with the DNA Strider (version 1.2) program. A search for homology of the predicted amino acid sequences was done with the BLAST network service at the National Center for Biotechnology Information. Homology comparisons and calculations were done with the DNASTAR program.

Nucleotide sequence accession number. The nucleotide sequences reported here from pTAB1 and pTIT1 were submitted to GenBank under accession no. FJ618564 and FJ618565, respectively.


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RESULTS AND DISCUSSION
 
According to the previously published biochemical data, E. faecium IT62 produces three different bacteriocins, EntL50A, EntL50B, and EntIT (23). Primers were constructed based on the amino acid sequences of these three bacteriocins, but also based on previously published nucleotide sequences (6, 22), and used for the amplification of their structural genes (Table 1). The three genes could be amplified using plasmid DNA isolated from E. faecium IT62, which showed they were plasmid encoded. The plasmid carrying the genes for EntL50A and EntL50B is, however, distinct from the one carrying the gene for EntIT. The amplified DNA was purified, and the nucleotide sequences were determined. A 1,475-bp fragment from plasmid pTAB1 was sequenced and corresponded to the region carrying the structural genes of EntL50A and EntL50B (Fig. 1). The sequences of these genes corresponded respectively to entL50A (with the exception of a single codon modification which did not result in a different amino acid) and entL50B, the two structural genes of these bacteriocins already identified in E. faecium L50 by Cintas et al. (5, 6). The resulting products corresponded to EntL50A (44 amino acids) and EntL50B (43 amino acids), with sequences confirming the previous biochemical determinations from E. faecium IT62 (23). These two peptides act synergistically and display a broad antimicrobial spectrum, which includes food-borne pathogens (6, 23).


Figure 1
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FIG. 1. Nucleotide sequence (accession no. FJ618564) of the pTAB1 plasmid region with the entL50A and entL50B genes encoding EntL50A and EntL50B, respectively. This sequence was obtained using primers EntL50S1, EntL50S2, EntL50R1, and EntL50R2. Potential Shine-Dalgarno ribosome binding sequences are double underlined. The deduced amino acid sequences of EntL50A and EntL50B which correspond to sequences obtained from automated Edman degradation and mass spectrometry (23) are underlined. Boldface characters indicate base pairs that are different from the sequence (accession no. AJ223633) previously published by Cintas et al. (6) for E. faecium L50. {dagger}, missing base pair in comparison with the sequence published by Cintas et al. (6).

With the exception of 9 bp, the sequenced fragment from pTAB1 (Fig. 1) was identical to the region 264 to 1739 of the 3,703-bp fragment (accession no. AJ223633) from the 50-kb pCIZ1 plasmid of E. faecium L50. As in E. faecium L50, EntL50A and EntL50B are not synthesized as inactive precursors since they lack N-terminal leader sequences or signal peptides (6). The two bacteriocins have also been reported to lack dedicated immunity proteins (6). The sequenced pTAB1 fragment is, however, not large enough to allow us to draw a conclusion in this regard for E. faecium IT62.

A 1,380-bp fragment from plasmid pTIT1 was sequenced and contained two open reading frames, including entIT the structural gene of EntIT (Fig. 2) with a sequence identical to that of bacA, the structural gene for Bac 32 already determined by Inoue et al. (22). The second open reading frame is entIM, which corresponded to bacB, the immunity gene identified for Bac 32 (22). This gene encodes a deduced 55-amino-acid potential immunity protein without a signal sequence. E. faecium IT62 exhibited a consistent pattern of bacteriocin producers with a dedicated immunity factor coordinately expressed with the bacteriocin. The immunity gene is located immediately downstream of the structural gene, which is a common feature of most nonlantibiotic loci from lactic acid bacteria (7, 11).


Figure 2
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FIG. 2. Nucleotide sequence (accession no. FJ618565) of the pTIT1 plasmid region with entIT and entIM genes encoding EntIT and its potential immunity protein, respectively. This sequence was obtained using primers EntITS1, EntITS2, EntITS3, EntITR1, and EntITR2. Potential Shine-Dalgarno ribosome binding sequences are double underlined. The deduced amino acid sequence of the EntIT preprotein, including the signal peptide and mature bacteriocin, is shown. The amino acid sequence of EntIT obtained by automated Edman degradation and mass spectrometry (23) is underlined, and the signal peptidase cleavage site is indicated by the inverted arrow. Boldface characters indicate base-pairs that are different from the sequence (accession no. AB158402) previously published by Inoue et al. (22) for E. faecium VRE200.

With the exception of 2 bp, the DNA fragment sequenced on pTIT1 (Fig. 2) was identical to the region 10091 to 11471 encompassing the Bac 32 genetic locus comprising bacA and bacB and carried by the 12.5-kb plasmid pTI1 (accession no. AB158402) in E. faecium VRE200 (22). The sequence of Bac 32 was deduced from the nucleotide sequence of bacA. Using computer analysis, Inoue et al. (22) suggested that the deduced bacA product, which is 89 amino acids in length, had a putative signal peptide of 19 amino acids at the N terminus and a potential signal peptidase processing site corresponding to the LLA sequence located at positions 17 to 19 (Fig. 2). This gave rise to a 7,998-Da and 70-amino-acid putative mature bacteriocin.

According to the previously reported biochemical data, EntIT is a 6,390-Da peptide made of 54 amino acids that is identical to but 16 amino acids smaller than Bac 32 (23). Yet, the same structural bacA gene obviously encodes an 89-amino-acid precursor that is processed to yield the active Bac 32 in the case of E. faecium VRE200 and EntIT in the case of E. faecium IT62. The combined biochemical and genetic data therefore conclusively show that in the case of EntIT, the precursor is processed by the signal peptidase at the VEA recognition region located at positions 33 to 35. This results in the 54-amino-acid EntIT, with a molecular mass of 6,390 Da and a deduced signal peptide of 35 amino acids at the N terminus (Fig. 2).

A review of bacteriocin signal peptides (20) showed that VEA is in fact a cleavage site for other sec-dependent bacteriocins such as bacteriocin 31 (27) and enterocin SE-K4 (10) and that VXA is found for enterolysin A, bacteriocin T8, enterocin P, dysgalacticin, and hiracin JM79 (15, 16, 17, 26). The LLA cleavage site reported for Bac 32, however, has not been reported for other bacteriocins. Given that the same genetic locus encodes both EntIT and Bac 32, it can be safely concluded that the cleavage region of the signal peptide sequenced by Inoue et al. (22) is not LLA, as suggested by computer analysis, but VEA, as shown by the structure of the active bacteriocin. Therefore, Bac 32 is most certainly 16 amino acids shorter than previously described, with exactly the same size and sequence as EntIT.

It has been reported that Bac 32 is encoded on the highly transferable plasmid pTI1, which resulted in a high incidence of dissemination of Bac 32 among strains of E. faecium of clinical origins (22). Our finding demonstrates that this dissemination would not be limited to clinical strains and that a particular enterocin structure may be widespread and not related to the producer's origin. This 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 Bac 32 or EntIT would occur in clinical settings, where they would be associated with drug resistance (20). In this regard, E. faecium IT62 is a good illustration, as it is an environmental strain that produces two bacteriocins (EntL50A and EntL50B) previously associated with food sources as well as a bacteriocin (EntIT) previously associated with clinical settings. Nonetheless, bacteria that produce the "right" bacteriocin in a particular ecological niche stand a better chance of surviving and becoming dominant.

Concluding remarks. This report presents the gene clusters of three bacteriocins produced by E. faecium IT62, isolated from ryegrass, that have already been identified in strains from other origins, although not the three of them in a single strain. This is further evidence of the superior ability of enterococci to exchange genetic material among strains and a confirmation of our assertion that the production of a particular bacteriocin may be spread among strains that do not necessarily originate from the same ecological niche, as previously suggested. This report also presents evidence that Bac 32 is identical to EntIT.


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FOOTNOTES
 
* Corresponding author. Mailing address: Laboratoire de Chimie Analytique et Sciences de l'Aliment, IPHC-DSA, Université de Strasbourg, CNRS, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France. Phone and fax: 33-390-244-325. E-mail: ennahar{at}pharma.u-strasbg.fr Back

{triangledown} Published ahead of print on 9 March 2009. Back


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Antimicrobial Agents and Chemotherapy, May 2009, p. 1907-1911, Vol. 53, No. 5
0066-4804/09/$08.00+0     doi:10.1128/AAC.00052-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.





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