Department of Biochemistry, University of Oslo, Blindern, 0316 Oslo, Norway1
Department of Chemistry and Biotechnology, Agricultural University of Norway, s, Norway2
Author for correspondence: Gunnar Fimland. Tel:+47 22 85 73 51. Fax:+47 22 85 44 43. e-mail: gunnar.fimland{at}biokjemi.uio.no
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ABSTRACT |
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Keywords: bacteriocin resistance, lactic acid bacteria
Abbreviations: LAB, lactic acid bacteria
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INTRODUCTION |
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Putative immunity genes that have sequence similarities to the immunity genes of pediocin-like bacteriocins, but are not transcriptionally coupled to a bacteriocin gene, have been described; examples are dvnT2 (Métivier et al., 1998 ), orf-ß3 (Quadri et al., 1994
) and orfY (Brurberg et al., 1997
). In total, the primary structures of at least 17 immunity proteins from the pediocin family have been deduced from DNA sequences (Axelsson & Holck, 1995
; Aymerich et al., 1996
; Brurberg et al., 1997
; Cintas et al., 1997
; Fremaux et al., 1995
; Hastings et al., 1991
; Hühne et al., 1996
; Kalmokoff et al., 2001
; Le Marrec et al., 2000
; Marugg et al., 1992
; Métivier et al., 1998
; Quadri et al., 1994
; Tomita et al., 1996
; GenBank accession no. AF275938). Their size ranges from 81 to 115 amino acid residues, and they display 585% sequence similarity (Eijsink et al., 1998
). Functional analysis of two immunity proteins conferring immunity to mesentericin Y105 and carnobacteriocin B2 has shown that these immunity proteins are located intracellularly and that their intracellular pool is divided into a minor membrane-associated fraction and a major cytoplasmic fraction (Dayem et al., 1996
; Quadri et al., 1995
). The mode of action of these immunity proteins is not well known. Published results indicate that immunity proteins belonging to the pediocin family as well as the immunity protein of the non-pediocin-like class II bacteriocin lactococcin A do not interact directly with bacteriocins, at least not in aqueous solutions (Nissen-Meyer et al., 1993
; Quadri et al., 1995
; Venema et al., 1994
). It has also been pointed out that the intracellular immunity protein is unlikely to act by directly preventing binding of the (extracellular) bacteriocin to the membrane (Quadri et al., 1995
). On the basis of these observations, it has been suggested that immunity proteins act either by disturbing the process of bacteriocin aggregation and pore formation or by disturbing the interaction between the bacteriocin and a (putative) membrane-located bacteriocin receptor (Nissen-Meyer et al., 1993
; Quadri et al., 1995
; Venema et al., 1994
). Concerning the latter option, it is relevant to note that recent work indicates that the action of pediocin-like bacteriocins indeed depends on the presence of certain membrane proteins involved in sugar transport (Dalet et al., 2000
, 2001
; Héchard et al., 2001
; Ramnath et al., 2000
; Yan et al., 2000
).
Despite the fact that pediocin-like bacteriocins share a number of sequence characteristics, their immunity proteins display a large sequence variation. In fact, the sequence similarities between two immunity proteins may be small even though their corresponding bacteriocins may be very similar, and vice versa (Eijsink et al., 1998 ; Nes & Holo, 2000
). Thus, it is not possible to understand or predict the functionality of a particular immunity protein on the basis of its sequence. For example, one cannot predict to what extent an immunity protein belonging to one pediocin-like bacteriocin will give immunity to other pediocin-like bacteriocins (cross-immunity). To gain more insight into this matter, we have studied the functionality of seven different immunity proteins by heterologously expressing their genes in three different bacteriocin-sensitive strains. In addition to revealing protection patterns of these immunity proteins in three genetic backgrounds, the results also provide some clues as to which factors may determine large differences in bacteriocin sensitivity between closely related LAB.
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METHODS |
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The indicator strains used for bacteriocin activity measurements were Lb. sake NCDO 2714 (type strain), Carnobacterium piscicola UI49 (Stoffels et al., 1992 ) and Enterococcus faecalis NCDO 581 with or without an immunity-gene-containing plasmid. All LAB strains except C. piscicola UI49 were grown in MRS broth (Oxoid) at 30 °C. C. piscicola UI49 was grown in M17 (Oxoid) supplemented with glucose and Tween 80 to final concentrations of 0·4% (w/v) and 0·1% (v/v), respectively. Agar plates for Lactobacillus transformants were made by adding 1·5% agar to MRS broth. Enterococcus and Carnobacterium transformants were grown on BSR agar plates made by adding 1·5% (w/v) agar to BSR medium (Holo & Nes, 1995
). Escherichia coli JM109 or Epicurian coli XL-1 Blue (Stratagene) were used for all plasmid cloning. They were grown in LuriaBertani (LB) medium (Difco) with vigorous agitation at 37 °C. LB agar plates were solidified by adding 1·5% (w/v) agar to the LB medium. Selective antibiotic concentrations used were 150 µg erythromycin ml-1 and 50 µg ampicillin ml-1 for E. coli. For Lb. sake and C. piscicola, the erythromycin concentrations that were used for initial selection and normal growth were 2 and 5 µg ml-1, respectively, whereas they were 5 and 10 µg ml-1 for Ent. faecalis. pGEM-7Zf(+) (Promega) was used to clone PCR products and DNA restriction fragments containing immunity genes. The LABE. coli shuttle vector pMG36e (van de Guchte et al., 1989
) containing the strong constitutive P32 promoter was used to express the immunity genes.
The natural sakacin P producer used for studying bacteriocin sensitivity was Lb. sake LTH673 (Tichaczek et al., 1994 ). As described previously, bacteriocin production by this strain depends on the presence of sufficient amounts of a peptide pheromone that induces expression of bacteriocin genes (Brurberg et al., 1997
; Eijsink et al., 1996
). Cultures with a stable Bac- phenotype were obtained by strong dilution of a Bac+ culture in MRS medium, as described previously (Eijsink et al., 1996
). For use as a bacteriocin indicator, a Bac- culture of Lb. sake LTH673 was grown overnight and diluted according to usual practice (see below).
Production, synthesis and purification of the bacteriocins.
Curvacin A, enterocin A, enterocin P, leucocin C, sakacin P and pediocin PA-1 were purified to homogeneity from 0·4 or 0·8 l cultures of their producer strains by ammonium sulphate precipitation, followed by cation-exchange chromatography, hydrophobic-interaction chromatography and reverse-phase chromatography, as described previously (Nieto Lozano et al., 1992 ). Leucocin A was obtained by peptide synthesis, as described previously (Fimland et al., 1996
).
The purity of the isolated bacteriocins was analysed by analytical chromatography on a µRPC SC 2.1/10 C2C18 column (Amersham Biosciences) using the SMART chromatography system (Amersham Biosciences) and water/2-propanol, containing 0·1% (v/v) trifluoroacetic acid, as the mobile phase. Primary structures were confirmed by mass spectrometry on a Voyager-DE RP matrix-assisted laser desorption time-of-flight mass spectrometer (Perseptive Biosystems); -cyano-4-hydroxycinnamic acid was used as the matrix.
Construction of plasmids containing immunity genes.
Plasmids containing cloned immunity genes and the sources of these immunity genes are listed in Table 1. PCR fragments containing the curvacin A, enterocin P or leucocin A immunity genes with flanking EcoRI and BamHI restriction sites were subcloned into pGEM-7Zf(+) (Promega), whereas a PCR fragment containing orfY (with no flanking restriction sites) was cloned into pCR2.1-TOPO (Invitrogen). The subcloned immunity genes were then excised with SacI and XbaI (curvacin A, leucocin A, orfY) or with SacI and PstI (enterocin P) and subcloned into the SacI and XbaI or SacI and PstI sites of pMG36e, respectively. Larger PCR fragments containing both the bacteriocin gene and cognate immunity gene and subcloned into the BamHI and EcoRI site of pGEM-7Zf(+) (Promega) (unpublished results) were used as a starting point for cloning the immunity genes of pediocin PA-1 and enterocin A. The pediocin PA-1 gene was removed by BamHINheI digestion followed by re-ligation of the remaining plasmid. The immunity gene (pedB) was then excised from the plasmid by XbaI and SacI and subcloned into the XbaI and SacI sites of pMG36e. The enterocin A immunity gene was excised from the pGEM-7Zf(+) subclone by RsaI and EcoRI digestion and subcloned into the SmaI and EcoRI sites of pGEM-7Zf(+) (Promega). From this, an XbaISacI restriction fragment containing the enterocin A immunity gene was subcloned into the SacI and XbaI sites of pMG36e. The sakacin P immunity gene was excised from plasmid pPT1000 (Tichaczek et al., 1994
) using PvuII and subcloned into the SmaI site of pGEM-7Zf(+) (Promega). A HindIIIXbaI fragment from this construct was then isolated and subcloned into the HindIII and XbaI sites of pMG36e.
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Polymerase chain reaction and DNA sequencing.
Eurogentec, Belgium, produced all oligo primers used in this study. The immunity genes were amplified by PCR using a standard amplification protocol on a GeneAmp PCR System 2400 (Perkin Elmer) using a PfuTurbo DNA polymerase (Stratagene). PCR mixtures contained 50 ng plasmid DNA or 15 µl DNA preparations with unknown concentrations made from the bacteriocin producers (Table 1), 125 ng each primer, dNTP (Amersham Biosciences) to a final concentration of 0·05 mM of each nucleotide, 10x reaction buffer (Stratagene) and 2·5 U PfuTurbo DNA polymerase (Stratagene). Amplification proceeded through 25 cycles after a 3 min hot start at 95 °C with a programme including denaturation (1 min at 95 °C), primer annealing (1 min at 50 °C) and polymerization (1 min at 68 °C).
The DNA sequences of the cloned immunity genes were verified by automated DNA sequence determination, using an ABI PRISM 377 DNA sequencer and the ABI Prism Ready Reaction dye terminator cycle sequencing kit (Perkin Elmer).
Bacteriocin assay.
Bacteriocin activity was measured by using a microtitre plate assay system, essentially as described previously (Nissen-Meyer et al., 1992 ). Each well of a microtitre plate contained 200 µl of culture medium with bacteriocin fractions at twofold dilutions and an indicator strain at an OD610 of about 0·01 (inoculated from a 1620 h overnight culture at 30 °C). The microtitre plate cultures were incubated overnight (1416 h), at 30 °C, after which growth of the indicator strain was measured spectrophotometrically at 610 nm with a microtitre plate reader. The MIC was defined as the concentration of bacteriocin that inhibited growth of the indicator strain by 50%. The MIC values that are presented are the result of at least three independent measurements and had standard deviations of less than 50% of the value. Transformed indicator strains were grown in the presence of 5 µg erythromycin ml-1 to ensure that the plasmid containing the immunity gene was maintained in the cells. The protection pattern of each immunity protein was judged by comparing MIC values for a strain expressing an immunity gene with MIC values for the same strain containing the unmodified pMG36e plasmid. Control experiments showed that neither the presence of erythromycin nor the presence of plasmid pMG36e influenced the bacteriocin sensitivity of the indicator cells.
Biocomputational analysis.
The PILEUP program of the Genetics Computer Group sequence analysis program package (Wisconsin Package Version 8·1, Genetics Computer Group) was used to create phylogenetic trees to reveal evolutionary relationships between immunity proteins and their corresponding bacteriocins. The same program was used to set up multiple sequence alignments of immunity proteins and bacteriocins. The gap-creation and gap-extension penalties were set to 3·00 and 0·10, respectively. Protein sequences were taken from the Swissprot database or obtained by in computo translation of the corresponding DNA sequences as present in GenBank.
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RESULTS AND DISCUSSION |
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Despite high sequence similarities among pediocin-like bacteriocins (Fig. 1), most of their immunity proteins show little similarity. Nevertheless, it is possible to identify some common sequence motifs, and by combining multiple sequence alignments and phylogenetic analyses (results not shown), three subgroups became apparent (Fig. 2
). Group A contains the immunity proteins for bacteriocins that belong to group 2 and the four group 1 bacteriocins (enterocin A, divercin V41, pediocin PA-1 and coagulin) that contain a C-terminal disulphide bridge. Group A also contains the putative immunity protein orf-Y that lacks a cognate bacteriocin. Group B contains the immunity proteins for the group 1 bacteriocins that lack the C-terminal disulphide bridge and two putative immunity proteins (orf-ß3 and divT2) that lack cognate bacteriocins. Group C contains the immunity proteins for group 3 bacteriocins.
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All transformed indicator strains displayed immunity to the bacteriocin belonging to the cloned immunity gene (Table 2), showing that the immunity genes indeed were expressed. They also displayed immunity to several other bacteriocins (cross-immunity). With a few exceptions, these other bacteriocins belonged to the same group as the cognate bacteriocin. For example, the group C immunity proteins curA-im and entP-im both protected against group 3 bacteriocins curvacin A and enterocin P, but none of them yielded immunity to bacteriocins belonging to group 1 or 2 (Table 2
). Similarly, both ped-im and sakP-im protected cells against group 1 bacteriocins, pediocin PA-1, sakacin P and leucocin C, but not against any of the group 2 and 3 bacteriocins that were tested (Table 2
).
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The general picture emerging from the results displayed in Table 2 is that the immunity proteins display a significant degree of specificity. Thus, despite the strong sequence similarities between pediocin-like bacteriocins (especially in the N-terminal part), none of the immunity proteins tested comes close to providing general immunity towards this class of antimicrobial peptides. From the data in Table 2
, one might conclude, though, that certain (sequence-based) subgroups of immunity proteins have a tendency to provide immunity to certain groups of bacteriocins that are characterized by similarities in their C-terminal parts. It is important to note that exceptions do exist that limit the applicability and predictive power of subgrouping bacteriocins and/or immunity proteins. For example, whereas sakP-im (B) and ped-im (A) both provide immunity to group 1 bacteriocins pediocin PA-1, sakacin P and leucocin C, they do not provide immunity to the group 1 bacteriocin enterocin A.
Immunity protein functionality is strain-dependent
The data in Table 2 show that the effectiveness of some of the overexpressed immunity proteins is strain-dependent. Obviously, parts of the observed strain-dependent differences may relate to different expression levels of the immunity proteins. However, the data do contain a few examples where such differences in expression levels are likely not to exist. For example, entA-im provides maximal immunity towards enterocin A and leucocin C in Lb. sake NCDO 2714 and in C. piscicola UI49, whereas it provides immunity towards enterocin A and sakacin P in Ent. faecalis NCDO 581. This shows that the gene is expressed in all three strains, but the strains obtain rather different degrees of immunity. Another example: in Ent. faecalis, leuA-im provides maximum immunity towards enterocin A, leucocin A and pediocin PA-1; in Lb. sake, the gene is also expressed, as shown by immunity to leucocin A, but immunity to enterocin A and pedicion PA-1 is not observed. Taken together, the results in Table 2
strongly indicate that immunity protein functionality in part depends on interplay with strain-dependent factors.
The putative immunity gene orfY encodes a protein that provides immunity to several pediocin-like bacteriocins
It is known from previous studies that putative immunity genes for which a cognate bacteriocin has not been identified may be expressed, e.g. orf-ß3 in bacteriocin-producing C. piscicola LV17B (Quadri et al., 1994 ). The orfY gene in the sakacin P producer Lb. sake LTH673 (Brurberg et al., 1997
) is expressed at low levels in bacteriocin-producing cells only, yielding a transcript whose length indicates that it contains only orfY (M. B. Brurberg & V. G. H. Eijsink, unpublished observations; Eijsink et al., 1998
).
The present results clearly show that orfY indeed is an immunity gene, as its overexpression made all three indicator strains immune to enterocin A and leucocin A. Overexpression of orfY also protected the Enterococcus strain against curvacin A (Table 2). Interestingly, orfY-im and sakP-im complement each other in the sense that they protect cells against different bacteriocins (Table 2
). Thus, sakacin P-producing Lb. sake LTH673 has at least two functional immunity genes, sakP-im and orfY-im, and should be immune to a broader spectrum of bacteriocins than if only the sakP-im gene had been present (see below).
Bacteriocin sensitivity of bacteriocin-producing strains
Bacteriocin-producing strains contain one or more known immunity genes and are thus expected to be immune to the bacteriocins identified by the heterologous expression studies described above. Table 3 shows that this is indeed the case for the curvacin A producer, Lb. curvatus LTH1174, and the enterocin P producer, Ent. faecium P13, which are known to contain curA-im and entP-im, respectively. Both strains were much more resistant to curvacin A and enterocin P than to the other bacteriocins tested, in accordance with the results obtained upon heterologous expression of the corresponding immunity genes curA-im and entP-im (Table 2
). It is interesting to note that there is a considerable general difference in bacteriocin sensitivity between the two producer strains.
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The pediocin PA-1 producer P. acidilactici LMG2351 was immune to all bacteriocins tested; that is, it was much more immune than could be expected on the basis of heterologous expression studies with its one known immunity gene, ped-im (Table 2). Thus, either this strain must possess and express other functional immunity genes, or its physiological state must be such that it has generally reduced sensitivity (resistance) for pediocin-like bacteriocins (see below for further discussion).
Concluding remarks
The subgrouping of pediocin-like bacteriocins on the basis of the amino acid sequences of their C-terminal halves (Fig. 1) may be open for debate and may need adjustments as more bacteriocin sequences become known. Nevertheless, the present results strongly suggest that the extent to which an immunity protein interacts (directly or indirectly) with a bacteriocin depends to a significant extent on the C-terminal part of the latter. The C-terminal part is also the region that interacts with the hydrophobic part of the membrane (Fimland et al., 1996
, 2000
, 2002a
; Miller et al., 1998
), which suggests that immunity proteins and bacteriocins directly or indirectly interact in this part of the membrane.
A major question is whether immunity proteins have direct interactions with bacteriocins or whether immunity is based on a more indirect effect, e.g. the blocking of receptors. Despite the fact that, so far, it has not been possible to demonstrate direct bacteriocin-immunity protein interactions (Quadri et al., 1995 ), the existence of such interactions cannot be excluded. For example, it is possible that the immunity protein and the bacteriocin interact only after the bacteriocin has become membrane-bound and structured (pediocin-like bacteriocins are largely unstructured in aqueous solutions but become structured in the presence of liposomes, for example; Fregeau Gallagher et al., 1997
; Wang et al., 1999
; Watson et al., 2001
). Interactions occurring in or near a membrane are difficult to reproduce in vitro and may therefore so far have remained undetected. The recent discovery that a membrane-bound protein that is part of a mannose phosphotransferase system permease (EIIMan) is involved in sensitivity of Listeria monocytogenes and Ent. faecalis towards pediocin-like bacteriocins (Dalet et al., 2001
; Héchard et al., 2001
; Ramnath et al., 2000
) opens up new perspectives. It is likely that this protein is the long sought-after receptor or docking molecule for at least some pediocin-like bacteriocins (Dalet et al., 2001
). Immunity proteins (located in the cytoplasm) may act by binding to the cytoplasmic side of this receptor, which somehow could block the receptors ability to interact with the bacteriocin in a fashion that is necessary for bacteriocin action.
Our results do not provide conclusive evidence for resolving this issue. Sequence variations in the immunity proteins and the C-terminal parts of the bacteriocins can in principle account for differences in immunity protein functionality in each of these models. The receptor model is attractive, not least in view of early work by Venema et al. (1994 ), which suggests that immunity towards the non-pediocin-like class II bacteriocin lactococcin A is mediated by a receptor. The fact that there is some strain-dependent variation in immunity protein functionality is consistent with the view that immunity is mediated via interactions with a specific proteinaceous receptor (e.g. EIIMan), since the receptor protein is likely to vary between the indicator strains (which belong to three different genera). However, one might expect a much larger strain-dependent variation if immunity really were mediated by such a receptor. Clearly, more work needs to be done, combining the strategies described here with the strategies used in the work on the permease receptors (Dalet et al., 2001
; Héchard et al., 2001
). The relatively high specificity of immunity proteins found in this study does already yield one important conclusion: it is quite unlikely that an immunity proteinreceptor complex still functions as a receptor for some bacteriocins but no longer for others. Thus, if the immunity proteins tested in this study act by blocking a receptor, there must be several receptors for pediocin-like bacteriocins, only some of which are blocked by a particular immunity protein.
It is well known that closely related LAB may differ strongly in terms of bacteriocin sensitivity. Variation in bacteriocin sensitivity depends in part on general inter-strain differences such as membrane composition and the presence of receptors (Crandal & Montville, 1998 ; Ennahar et al., 2000
). The present results indicate that the presence, expression and functionality of immunity proteins are also significant, if not major, factors in determining bacteriocin sensitivity of closely related LAB. First, immunity proteins that are directly related to a strains own bacteriocin production provide varying degrees of cross-immunity. Second, strains may contain genes that are expressed and code for functional immunity proteins but that lack cognate bacteriocins (e.g. orfY). As shown above, the functionality of some of these immunity proteins may be strain-dependent, providing an additional cause of variation in bacteriocin sensitivity.
The fact that the C-terminal part of bacteriocins plays a major role in determining target cell specificity (Fimland et al., 1996 , 2000
) and in the (direct or indirect) interaction with immunity proteins may be taken to support the notion that immunity proteins play a major role in determining bacteriocin sensitivity. If immunity proteins that lack cognate bacteriocins are widely spread in target bacteria, the (direct or indirect) interaction of these proteins with the C-terminal part of the bacteriocins may be one mechanism by which this C-terminal part is involved in determining the target-cell specificity.
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ACKNOWLEDGEMENTS |
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Received 25 April 2002;
revised 23 July 2002;
accepted 5 August 2002.