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Laboratoire de Microbiologie et Génétique Moléculaires, UMR 5100 CNRS-Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse Cedex 9, France
Correspondence
Jean-Pierre Claverys
claverys{at}ibcg.biotoul.fr
| ABSTRACT |
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Present address: UMR1225 Interactions Hôtes-Agents Pathogènes, INRA-Ecole Nationale Vétérinaire de Toulouse, 23 chemin des Capelles BP 87614, 31076 Toulouse Cedex 3, France.
| INTRODUCTION |
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To avoid copy-number effects, alternative strategies based on single-copy gene expression have therefore been developed over the years. One of these makes use of the ectopic integration of a recombinant plasmid (non-replicative in S. pneumoniae) in the chromosome through transformation (Vasseghi et al., 1981
; Mannarelli & Lacks, 1984
). A chromosome-targeting fragment is inserted into the recombinant plasmid to obtain ectopic integration. A 354 bp fragment from the ami operon of S. pneumoniae has thus been used to direct integration of a recombinant plasmid harbouring the firefly luciferase gene, luc, and luciferase activity is observed in pneumococcal cells (Stieger et al., 1999
). Similarly, a qsrA fragment has been inserted into a new non-replicative plasmid, pEVP3qsrI, to obtain ectopic expression of the S. pneumoniae cbpD gene at the qsrA locus (Kausmally et al., 2005
). In this example, the recombinant plasmid carries two regions of homology with the recipient chromosome, qsrA (886 bp) and cbpD (1377 bp), and can therefore integrate preferentially at cbpD. Integration at qsrA is obtained through the use of a recipient deleted for cbpD. It can thus be necessary for efficient ectopic integration to delete from the recipient chromosome the counterpart of the complementing gene. In any case, duplication of the chromosome-targeting fragment occurs during integration of the recombinant plasmid and creates the potential drawbacks that the plasmid is either amplified (hence is no longer in single copy) or is excised and lost (Vasseghi & Claverys, 1983
).
A better system should thus allow stable single-copy integration at a neutral chromosomal site. Integration of an ectopic gene copy at the bgaA locus might fulfil this criterion (Robertson et al., 2002
, 2003
; Chan et al., 2003
). However, although it has been reported that insertion mutations of various kinds into bgaA do not affect growth, the function(s) of BgaA is not fully understood. Taking into account the overall length of the gene (
6·7 kb) and the surface location of the protein, it is not unlikely that BgaA has other function(s) in addition to the previously documented
-galactosidase activity (Zähner & Hakenbeck, 2000
). It is therefore difficult to consider bgaA as a neutral chromosomal site. Ectopic expression at the malM locus, which encodes amylomaltase (Stassi et al., 1982
), has been used to demonstrate that the 5' to 3' exonuclease activity of DNA polymerase I is essential for S. pneumoniae (Díaz et al., 1992
), but this system is not designed to allow easy further use. Ectopic expression of a gene inserted between aga, the gene encoding
-galactosidase, and rafE, under the control of a raffinose-inducible promoter, has also been used (Luo et al., 2003
). This insertion site is probably neutral with respect to the physiology of recipient cells, but this system also is not designed for easy repeated use. In view of these limitations, the construction of a new convenient single-copy gene-expression system, which is still lacking for S. pneumoniae, would be useful. In this paper, we describe the construction and evaluation of a versatile chromosomal expression platform (CEP), pre-assembled on a plasmid (pCEP) capable of replication in Escherichia coli, but not in S. pneumoniae. pCEP allows placement of the gene of interest under the control of a maltosaccharide-inducible promoter and provides flanking homology for its integration into a region of the pneumococcal chromosome originally devoid of expressed sequences.
| METHODS |
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| RESULTS AND DISCUSSION |
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In choosing a regulatory system for inclusion at CEP, we were reluctant to use sublethal concentrations of antibiotic (tetracycline) or antibacterial peptide (nisin) as inducer. We also ruled out the use of CSP1, which induces the competence regulon (Dagkessamanskaia et al., 2004
; Peterson et al., 2004
), or BIP1, which induces the Blp regulon (de Saizieu et al., 2000
), because they could not be considered to be neutral with respect to pneumococcal physiology. We therefore retained a sugar-inducible system and selected the maltosaccharide-inducible system because of the extensive studies conducted by Lacks, Espinosa and coworkers. PM, the inducible promoter of the malMP operon (Stassi et al., 1982
), has previously been used for the construction of a tightly regulated plasmid vector for S. pneumoniae (Nieto et al., 2000
). PM is regulated by the MalR repressor, the binding of MalR to PM being relieved when pneumococcal cells are grown in maltose-containing media (Lacks, 1968
; Nieto et al., 1997
). A replicative plasmid containing the malR repressor gene (pAPM22; Puyet et al., 1993
; Table 1
) is available to increase the intracellular amount of MalR, thus ensuring high levels of repression.
Choice of CEP location
In our choice of a chromosomal location for CEP we looked for a transcriptionally silent site, at which integration of exogenous material would not perturb any known cellular function. We therefore chose to introduce CEP immediately downstream of the well-studied ami operon (Alloing et al., 1990
), and designed it so that its integration would occur by replacement-recombination. Upon integration, CEP substitutes for a truncated IS1167 element (Fig. 1
) between nucleotides 1 671 049 and 1 672 299 in the 2 038 615 bp R6 genome (Hoskins et al., 2001
). When an empty CEP is integrated, DNA segments of similar size are exchanged. Two transcription terminators, which flank CEP on each side, are retained after integration (Fig. 1
).
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The cassette is flanked on each side by more than 2 kb of pneumococcal DNA from the chromosomal region downstream of the ami operon (Fig. 1
), a situation predicted to strongly favour cassette insertion over integration of the entire pCEP plasmid during transformation in S. pneumoniae (Pozzi & Guild, 1985
). Transformants harbouring the appropriate construct can therefore be isolated directly following transformation of an S. pneumoniae strain with ligation products, with no need for an intermediate cloning step in E. coli. There are two main advantages to this strategy. First, the efficiency of pneumococcal transformation is much higher than that of E. coli. Second, it avoids potential cloning problems that arise in E. coli because of the previously documented frequent toxicity of cloned pneumococcal DNA fragments (Martin et al., 1989
).
Construction of pCEP and integration of CEP into the pneumococcal chromosome
Plasmid pCEP carries a chromosomal fragment, bordered by primers BM105 and BM112, in which most of the IS1167 remnant sequences (1249 bp) are substituted by a 1140 bp segment containing PM and the kan gene (Fig. 1
). Construction of the engineered BM105BM112 segment involved several PCR reactions with the AccuTaq LA DNA polymerase (Sigma), as follows (see primers with arrows in Fig. 1
). The PM and the KanR fragments were generated with primer pairs BM107M/BM108M and BM109/BM110.1 (Table 1
) using R800 chromosomal DNA and plasmid pR410 DNA as template, respectively (Fig. 1
). Fragments corresponding to the leftward and rightward flanking chromosomal regions were amplified from R800 chromosomal DNA with BM105/BM106 and BM111/BM112 primer pairs (Table 1
), respectively (Fig. 1
). After purification with a QIAquick nucleotide removal kit (Qiagen), fragments BM105BM106 and BM107MBM108M in one reaction, and BM109BM110.1 and BM111BM112 in another reaction, were mixed and used as template to generate, respectively, the BM105BM108M and BM109BM112 fragments (Fig. 1
). The BM105BM112 final PCR product was then amplified using the latter two PCR fragments as template. This fragment was digested with HindIII/XmaI and cloned into HindIII/XmaI-digested E. coli plasmid pJPB209 (Table 1
) to generate plasmid pCEP.
Integration of CEP was readily obtained by transformation of the wild-type strain R800 with plasmid pCEP DNA and selection for KanR transformants. The frequency of KanR transformants was similar to that of SmR transformants obtained with the chromosomal marker str41 (data not shown). Since the KanR cassette is flanked on each side by more than 2 kb of pneumococcal DNA, integration of the engineered PMkan segment in place of the IS1167 remnant was expected to occur at a much higher frequency than insertion of the entire pCEP molecule through insertion-duplication mechanisms (Méjean et al., 1981
; Pozzi & Guild, 1985
). Analysis of a few KanR transformants confirmed the absence of pCEP vector sequences (data not shown). One of these transformants retained for further analysis, strain R1567, displayed growth and transformation properties indistinguishable from those of the parental strain (data not shown, but see Guiral et al., 2006
), suggesting that modifications introduced downstream of the ami operon have no significant effect on pneumococcal physiology.
Insertion of the luc gene at CEP
To evaluate ectopic gene expression at CEP, we used the luc gene as transcriptional reporter. Its placement at CEP under the control of PM was achieved as follows. A DNA fragment containing luc was amplified with the MP162/MP163 primer pair using plasmid pR414 DNA as template (Table 1
). After digestion with NcoI and BamHI, the fragment (1657 bp) was ligated with NcoI/BamHI-digested plasmid pCEP, and strain R800 was transformed with the ligation mixture. Ten out of 10 KanR transformants analysed harboured the CEPluc construct (Fig. 1
). One of them was retained as strain R1474. Note that the sequence of the luc gene was not checked, but further experiments revealed that it encoded a functional luciferase (see below).
Evaluation of ectopic, PM-driven luc expression
The effect of sugar concentrations on growth of pneumococcal cells was first evaluated (Fig. 2
). In C+Y containing only 0·1 % sucrose, the growth rate was essentially unaffected, but cells stopped growing at an OD492 value of 0·4, indicating that sucrose was limiting (Fig. 2A, C
). Addition of 0·05 and 0·1 % maltose increased final OD values, indicating that maltose was metabolized and suggesting that its concentration declined progressively with growth. Cultures with 0·2 and 0·4 % maltose attained final OD values (
0·8) similar to those of cultures in the presence of 0·3 % sucrose (Fig. 2
, compare panels A and C with panels B and D). In C+Y containing 0·3 % sucrose, addition of 0·050·4 % maltose had no significant effect on growth rate and final OD values, indicating that sucrose was not limiting (Fig. 2B, D
). Similar data were obtained when glucose (0·1 and 0·3 %) was substituted for sucrose (data not shown). A concentration of 0·3 % sucrose was employed in further expression studies.
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To investigate whether an increase in the intracellular level of the MalR repressor would lead to a better repression of the PM promoter, luc expression was monitored in a derivative of strain R1474 containing a recombinant plasmid carrying the malR gene (strain R1488; Table 1
). Luciferase activity in the control culture without maltose was reduced to 3·2±0·1 RLU (Fig. 2D
), suggesting that repression of PM was slightly reinforced by an increase in the intracellular level of MalR. In the presence of maltose (within the range 0·050·4 %), luciferase activity increased to 37·8±1·2 RLU (10·8±0·4-fold increase compared to the control culture; Fig. 2D
).
Expression of the luc gene was then measured in cultures grown in the presence of concentrations of maltose below 0·05 % (Fig. 3
). Luciferase activity was close to the maximum in the presence of 0·008 % maltose (48·9±0·6 compared to 53·9±0·2 RLU with 0·04 % maltose). While no significant induction of luc could be detected with 0·000064 % (0·64 µg ml1) maltose, intermediate expression values were obtained with 0·00032 % (3·2 µg ml1) and 0·0016 % maltose (17·5±0·4 and 38·5±1·3 RLU, respectively), indicating that maltose concentration can be adjusted to fine-tune gene expression at CEP.
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| ACKNOWLEDGEMENTS |
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Received 11 August 2005;
revised 20 September 2005;
accepted 21 September 2005.
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