Cloning of Streptococcus pneumoniae DNA: its use in pneumococcal transformation and in studies of mismatch repair

Hyperrecombination in Streptococcus pneumoniae depends on an atypical mutY homologue

The unusual behavior of the mutation ami36, which generates hyperrecombination in two point crosses, was previously attributed to a localized conversion process changing A/G mispairs into CG pairs. Although the mechanism was found to be dependent on the DNA polymerase I, the specific function responsible for this correction was still unknown. Analysis of the pneumococcal genome sequence has revealed the presence of an open reading frame homologous to the gene mutY of Escherichia coli. The gene mutY encodes an adenine glycosylase active on A/G and A/7,8-dihydro-8-oxoguanine (8-OxoG) mismatches, inducing their repair to CG and C/8-OxoG, respectively. Here we report that disrupting the pneumococcal mutY homologue abolishes the hyperrecombination induced by ami36 and leads to a mutator phenotype specifically enhancing AT-to-CG transversions. The deduced amino acid sequence of the pneumococcal MutY protein reveals the absence of four cysteines, highly conserved in the endonuclease III/MutY glycosylase family, which ligate a [4Fe-4S](2+) cluster. The actual function of this cluster is still intriguing, inasmuch as we show that the pneumococcal gene complements a mutY strain of E. coli.

Insertion-duplication mutagenesis in Streptococcus pneumoniae: targeting fragment length is a critical parameter in use as a random insertion tool

To examine whether insertion-duplication mutagenesis with chimeric DNA as a transformation donor could be valuable as a gene knockout tool for genomic analysis in Streptococcus pneumoniae, we studied the transformation efficiency and targeting specificity of the process by using a nonreplicative vector with homologous targeting inserts of various sizes. Insertional recombination was very specific in targeting homologous sites. While the recombination rate did not depend on which site or region was targeted, it did depend strongly on the size of the targeting insert in the donor plasmid, in proportion to the fifth power of its length for inserts of 100 to 500 bp. The dependence of insertion-duplication events on the length of the targeting homology was quite different from that for linear allele replacement and places certain limits on the design of mutagenesis experiments. The number of independent pneumococcal targeting fragments of uniform size required to knock out any desired fraction of the genes in a model genome with a defined probability was calculated from these data by using a combinatorial theory with simplifying assumptions. The results show that efficient and thorough mutagenesis of a large part of the pneumococcal genome should be practical when using insertion-duplication mutagenesis.

Characterization of allelic replacement in Streptococcus parasanguis: transformation and homologous recombination in a 'nontransformable' streptococcus

We have obtained transformants of Streptococcus parasanguis FW213 containing allelic replacements in several chromosomal loci. Transformation occurred following electroporation with nonreplicating plasmids carrying two antibiotic-resistance-encoding genes, one of which is inserted into DNA homologous to the chromosomal target. In contrast with other streptococci, S. parasanguis FW213 is not transformed by linear DNA. Mutations in nonreplicating plasmid DNA preferentially replaced their homologues in the S. parasanguis FW213 chromosome by a double-crossover homologous recombination event, as shown by the fact that over 90% of transformants were sensitive to the vector-coded antibiotic marker. Southern blot analysis of these transformants showed that three of the five target loci had been mutated, and that the wild-type sequence had been replaced by the mutated sequence carried on the transforming plasmid. This bias toward homologous replacement rather than integration of the entire transforming plasmid DNA simplifies site-specific mutagenesis and genetic analysis of the streptococcal chromosome.

The difficulty of cloning Streptococcus pneumoniae mal and ami loci in Escherichia coli: toxicity of malX and amiA gene products

Stability problems are frequently encountered when cloning pneumococcal DNA in Escherichia coli multicopy plasmid vectors such as derivatives of ColE1. In this paper, we report our investigations of these problems using the pneumococcal mal and ami regions. We offer evidence that, in both cases, promoters are not the primary cause of cloning problems. Indeed, successful cloning of mal and ami promoters has been achieved with standard vectors (devoid of transcriptional terminators flanking the insertion site). Moreover, we show that the entire mal fragment can be introduced into an E. coli strain harboring a chromosomal mutation that reduces plasmid copy number. The cause of the cloning problems has been traced to the malX and amiA structural genes. Overexpression of these genes, which probably encode lipoproteins, could have deleterious effects on E. coli hosts, possibly as a result of impairing the protein export machinery.

Cloning of the amiA locus of Streptococcus pneumoniae and identification of its functional limits

Mutations in the amiA locus of the Gram-positive bacterium Streptococcus pneumoniae confer a complex phenotype including resistance to various antineoplastic drugs. As a first step towards the understanding of the molecular organization and the function(s) of this locus, we have cloned DNA fragments carrying its 5'- and 3'-extremities. We have isolated and characterized a down-promoter mutation and have located the functional limits of the locus. The amiA locus is between 5.8 and 7.5 kb long strongly suggesting that it encodes several proteins.

DNA sequences required to induce localized conversion in Streptococcus pneumoniae transformation

In pneumococcal transformation a particular point mutation belonging to the amiA locus is able markedly to enhance recombination frequency when crossed with any other markers of this gene. This results from a polarized conversion of the mutation towards the wild-type sequence. In this report, by site-directed oligonucleotide mutagenesis, we have generated a series of mutants showing various degrees of conversion. We have found that the substitution 5'-ATTCAT----5'-ATTAAT is a sufficient signal for localized conversion. Changing individual bases within this sequence results in decreased conversion frequencies to levels that depend on the mutation, suggesting that there is a family to related sequences which may act as a substrate for a conversion system. Moreover, the length over which this conversion occurs has been estimated to be 12 base pairs on the average.

Polarity of DNA entry in transformation of Streptococcus pneumoniae

DNA transport in Streptococcus pneumoniae was studied using donor molecules labelled either at the 3' or at the 5' end, on one strand only. In contrast to 5' end label, 3' end label was not taken up by the cells indicating that entry is a polarized process. Our results together with those of previous studies are consistent with a model for entry in which double-stranded donor DNA is nicked on binding at the cell surface. Entry of a single strand then proceeds linearly from a newly formed 3' end to the extremity of the donor fragment.

Searching for autolysin functions. Characterization of a pneumococcal mutant deleted in the lytA gene

The first mutant of Streptococcus pneumoniae showing a complete deletion in the lytA gene coding for the N-acetylmuramyl-L-alanine amidase has been isolated and characterized. This amidase was previously the only autolysin detected in this species. This mutant shows a normal growth rate and can be transformed using either chromosomal or plasmid DNA. The most remarkable biological consequences of the absence of the amidase are the formation of small chains (six to eight cells) and the absence of lysis in the stationary phase of growth. In addition, this mutant exhibits a tolerant response against the beta-lactam antibiotics.

Frame-shift mutants induced by quinacrine are recognized by the mismatch repair system in Streptococcus pneumoniae

We describe the isolation of amethopterin-resistant mutants induced by quinacrine treatment of exponentially growing cultures of Streptococcus pneumoniae. Only mutants located by recombination analysis in a few hundred base pairs were further studied. They were cloned and their DNA sequences show that most of them are +/-1-base frame-shift mutants. They are excised and repaired to a degree similar to transition mutants (low efficiency class), suggesting that the mismatches resulting from a transition or a +/-1-base mutation are similar substrates for the Hex mismatch repair system.

Cloning and expression of the pneumococcal autolysin gene in Escherichia coli

A 7.5 kb BclI-fragment of Streptococcus pneumoniae DNA has been cloned in Escherichia coli HB101 using pBR322 as a vector. The new plasmid (pGL30) of 12.0 kb expresses a protein that has been characterized by biochemical, immunological and genetic methods as the inactive form (E-form) of the pneumococcal N-acetyl-muramyl-L-alanyl amidase (EC 3.5.1.28). Our results demonstrate that the E-form is the primary product of the lyt gene of S. pneumoniae. The inactive E-form can be converted to the active C-form in vitro by incubation of the E-form enzyme with choline-containing pneumococcal cell walls at low temperature in a similar way to enzyme production in the homologous system. The production of this protein in E. coli HB101 was 500-fold higher than in the homologous host. E. coli CSR603 containing pGL30 and labeled with [35S]methionine synthesized a 35 kd protein. pGL30 can transform at high frequency an autolysin-defective mutant of S. pneumoniae to the lyt+ phenotype.

The hexB mismatch repair gene of Streptococcus pneumoniae: characterisation, cloning and identification of the product

A second gene involved in mismatch repair in Streptococcus pneumoniae, the hexB gene, has been characterised. The gene was cloned into a multicopy plasmid vector. The cloned hexB gene is expressed as judged by its ability to complement a chromosomal hexB- allele. Its direction of transcription and its functional limits were defined. Comparison of the proteins encoded by recombinant plasmids and by restriction fragments allowed us to identify an Mr 83,000 protein as the probable product of the hexB gene. We offer evidence that this gene together with the hexA gene is essential for repair of transition as well as frameshift mismatches.

Insertion of eukaryotic DNA into the Bacillus subtilis genome by means of a temperature-sensitive plasmid vector

A hybrid temperature-sensitive plasmid capable of integration into the Bacillus subtilis genome was constructed. By using this vector, we inserted a 3.2-kb fragment of eukaryotic DNA (wheat 'Chinese Spring') into the bacterial genome. The fragment of wheat DNA was stably retained and replicated as a part of the bacterial genome. The position of the integrated plasmid in the B. subtilis genome was mapped, as was the site in wheat DNA insert on plasmid at which the integration occurred.

Cloning of the hexA mismatch-repair gene of Streptococcus pneumoniae and identification of the product

The hexA mismatch repair gene of Streptococcus pneumoniae has been cloned into multicopy plasmid vectors. The cloned hexA gene is expressed as judged from its ability to complement various chromosomal hexA- alleles. Its direction of transcription was defined and the functional limits were localized by original methods relying on homology-dependent integration of nonautonomous chimeric plasmids carrying chromosomal inserts into the chromosome. Comparison of the proteins encoded by recombinant plasmids and by restriction fragments allowed us to identify an Mr 94 000 protein as the probable product of the hexA gene.

A plasmid vector allowing positive selection of recombinant plasmids in Streptococcus pneumoniae

A new plasmid, pSP2, was constructed as a cloning vector for use in Streptococcus pneumoniae. It allows direct selection of recombinant plasmids, even for DNA fragments not homologous to the S. pneumoniae chromosome, as based on the failure to maintain long inverted repeats (LIRs) hyphen-free in bacterial plasmids. Plasmid pSP2 contains a 1.4-kb BamHI fragment ("hyphen") flanked by 1.9-kb LIRs. The removal of the 1.4-kb BamHI fragment followed by ligation creates a plasmid containing a 1.9-kb insert-free LIR; plasmids with such non-hyphenated LIRs were not established when transferred into S. pneumoniae. Replacement of the original 1.4-kb insert by other restriction fragments restored plasmid viability. Investigation of plasmid transfer by transformation suggests that intrastrand synapsis between the LIRs could occur, thus facilitating plasmid establishment (a process we call self-facilitation). Such an intrastrand synapsis could also account for rare occurrences of insert-inversion noticed upon transfer as well as for the formation of palindrome-deleted derivatives at low frequency. Plasmid pSP2 carries two selectable genes, tet and ermC, and can be used for cloning of fragments produced by a variety of restriction enzymes (BamHI, Bg/II, Bc/I or Sau3A, and Sa/I or XhoI).

Effect of mismatched base pairs on the fate of donor DNA in transformation of Streptococcus pneumoniae

Investigation of the mechanism that discriminates against mismatched base pairs in transformation of Streptococcus pneumoniae of genotype hex+ was based on the use of a radioactively labeled cloned fragment of pneumococcal DNA as donor in transformation. The fate of the donor label was followed by lysis of the transformed cells and separation by agarose gel electrophoresis of DNA fragments generated by restriction endonucleases. As a result of Hex action, most of the donor DNA fragment, which was a few kilobases in length, was lost when a mismatched base pair occurred between donor and recipient DNA. This was not observed in hex- recipient cells. Kinetic studies of mismatch-induced donor DNA loss showed that the process is faster in strain 800, an R6 derivative, than in DP1601, a strain of different origin. In the latter strain, the amount of donor label that becomes double stranded rises substantially, indicating extensive formation of donor-recipient heteroduplex structures, before falling to the expected level. At 30 degrees C the process is essentially completed 15 min after entry.

Isolation of transformation-deficient Streptococcus pneumoniae mutants defective in control of competence, using insertion-duplication mutagenesis with the erythromycin resistance determinant of pAM beta 1

Several transformation-deficient mutants of Streptococcus pneumoniae were isolated after insertion-duplication mutagenesis. Mutagenesis was accomplished by transformation of competent cells with chimeric DNA formed by the ligation of TaqI fragments of pneumococcal DNA to the erythromycin resistance determinant of the streptococcal plasmid pAM beta 1. The two mutants described were characterized as defective in the control of competence induction, possibly due to a block in the production of the intercellular competence-inducing protein.

Identification of Streptococcus pneumoniae mismatch repair genes by an additive transformation approach

During transformation of Streptococcus pneumoniae, mismatch repair occurs on donor-recipient heteroduplexes harboring some mismatched base pairs. A few mutants defective in mismatch repair have been isolated and termed hex-. However, neither the number of genes involved nor their products have yet been identified. In an attempt to characterize such genes we have used an additive transformation approach--that is the inactivation of genes by insertion of chimeric plasmids. Pneumococcal DNA fragments were joined in vitro to a plasmid derivative of pBR325 that carries an erythromycin resistance determinant and does not replicate autonomously in S. pneumoniae. Ery-r transformants obtained with such a ligation mixture arise via homology-dependent integration of the chimeric plasmids into the chromosome. Hex- mutants have been selected among the ery-r population. Comparison of these mutants by Southern blot hybridization with a vector probe reveals that at least two genes are involved in mismatch repair.

Hyperrecombination at a specific DNA sequence in pneumococcal transformation

In pneumococcal transformation, recombination frequency between point mutations is usually proportional to physical distances. We have identified an aberrant marker belonging to the amiA locus that appeared to markedly enhance recombination frequency when crossed with any other markers of this gene. This mutation results from the C-to-A transversion in the sequence A-T-T-C-A-T----A-T-T-A-A-T. This effect is especially apparent for short distances as small as 27 base pairs. The hyperrecombination does not require the wild-type function of the pneumococcal gene for an ATP-dependent DNase (which is homologous to the product of the Escherichia coli recBC genes) or of the hex genes, which correct certain mismatched bases in transformation. The hyperrecombination is affected by the presence of nearby mismatched bases that trigger an excision-repair system. It is proposed that the mutation that shows hyperrecombination is sometimes converted to the wild-type allele at the heteroduplex stage of transformation.

Use of a cloned DNA fragment to analyze the fate of donor DNA in transformation of Streptococcus pneumoniae

The integration of donor label into the recipient fragment is followed during transformation of Streptococcus pneumoniae. The method used involves gel analysis of restriction endonuclease-treated recipient DNA after recombination with a radioactively labeled homologous cloned fragment.

Isolation and characterization of three new classes of transformation-deficient mutants of Streptococcus pneumoniae that are defective in DNA transport and genetic recombination

Transformation-deficient mutants of Streptococcus pneumoniae were isolated after nitrosoguanidine mutagenesis. Seventeen mutants developed normal peaks of competence, as tested by their ability to degrade one strand of donor DNA, but they yielded transformants for chromosomal point markers at efficiencies from less than 0.001 to 0.04 that of the wild type. Some of the mutants were defective in DNA uptake and are described as entry defective (Ent-). Others took up DNA in normal quantities, but they failed to give stable transformants and are described as recombination defective (Rec-). In two of the Rec- mutants, normal levels of transformation by plasmid DNA occurred; in the others, it was reduced as much as chromosomal transformation. Conjugative transfers of a chromosomal omega (cat tet) element and of the plasmid pIP501 occurred at normal levels both to and from Rec- mutants. Transfer of chloramphenicol resistance by transformation with omega (cat tet) donor DNA, however, was blocked in Rec- mutants to about the same extent as was transformation for point markers.

Mismatch repair in Streptococcus pneumoniae: relationship between base mismatches and transformation efficiencies

Genetic transformation in Streptococcus pneumoniae involves the insertion of single-stranded pieces of donor DNA into a recipient genome. Efficiencies of transformation strongly depend on the mutations (markers) carried by donor DNA. Markers are classified according to their transforming efficiencies into very high, high, intermediate, and low efficiency. The last is approximately 1/20th as efficient as the first. This marker effect is under the control of the Hex system, which is thought to correct mismatches at the donor-recipient heteroduplex stage in transformation. To investigate this effect, wild type, mutant, and revertant DNA sequences at five genetic sites within the amiA locus were determined. The results show that low-efficiency markers arise from transitional changes A . T to G . C. The transversion A . T to T . A corresponds to an intermediate-efficiency marker. Transversions G . C to T . A and G . C to C . G lead to high-efficiency markers. Among the eight possible mismatches that could exist transiently at the heteroduplex stage in transformation, only two--namely, A/G and C/C--are not corrected by the Hex system. It is noteworthy that the four possible base pairs (A . T, T . A, G . C, and C . G) have been encountered at the very same site (amiA6 site), which constitutes a good illustration of the marker effect. DNA sequence analysis also reveals that short deletions (33 or 34 bases long) are integrated with very high efficiencies. These results confirm that the Hex system corrects point mismatches harbored in donor-recipient heteroduplexes thousands of bases long. The correction pattern of the Hex system toward multiple-base mismatches has also been investigated. Its behavior toward double-base mismatches is complex, suggesting that neighboring sequences may affect the detection of mispaired bases.

Amplification of a chimeric plasmid carrying an erythromycin-resistance determinant introduced into the genome of Streptococcus pneumoniae

Hybrid plasmid molecules carrying an insert of pneumococcal DNA can integrate into the pneumococcal genome by homologous recombination. The resulting structure is a duplication of the pneumococcal DNA insert bracketing a vector genome. To select for plasmid integration, the vector plasmid was marked with an erythromycin (ery) resistance determinant (eryr) originating from pVA736, a streptococcal plasmid. Experiments with pR27 and pR28, two plasmids carrying the same insert of pneumococcal DNA but in opposite orientations, led to the following observation: (i) In one orientation of the ery region with respect to the amiA locus, cells exhibited a low-level resistance to ery; when these cells were grown in the presence of ery, amplification of the integrated plasmid occurred and cells became resistant to a high level of antibiotic. (ii) In the opposite orientation, a high level of resistance was observed, without need for amplification. These results indicate that, in the orientation conferring a high-level resistance without amplification, the ery region is transcribed both from its own promoter and from the promoter of the amiA locus. In the opposite orientation, a low level of transcription from the eryr promoter could account for a strong selective pressure for the amplified state, which then allows for rapid growth in the presence of ery.

Effect of strong promoters on the cloning in Escherichia coli of DNA fragments from Streptococcus pneumoniae

Attempts to clone wild-type DNA containing the malM gene of Streptococcus pneumoniae in plasmid pBR322 of Escherichia coli were unsuccessful. However, it was possible to clone a PstI fragment of DNA containing this gene in a plasmid of S. pneumoniae. Cells carrying the recombinant plasmid produced large amounts of the malM product, amylomaltase, and a fragment of the protein coded by the adjacent malX gene, apparently as a result of transcription in opposite directions from strong promoters located between the two genes in the plasmid insert. Under derepressed conditions these products represented 10% of the total protein. No transcription terminators appeared to be included within the cloned segment. The effect of various mutations in the segment on its ability to be cloned in pBR322 was examined. Of those tested, only a down promoter mutation that affected production of both the amylomaltase and the X-protein rendered the segment clonable in E. coli. Fragments of the S. pneumoniae vector, pMV158, which appear to lack strong promoters, were readily cloned in the pBR322-E. coli system. Although it is possible that large amounts of the X-fragment are toxic for E. coli, a more general explanation would be that excessive transcription of the pBR322 vector portion interferes with maintenance of the recombinant plasmid.

Staphylococcal plasmids that replicate and express erythromycin resistance in both Streptococcus pneumoniae and Escherichia coli

Plasmid pSA5700 from Staphylococcus aureus coding for erythromycin (EmR) and chloramphenicol (CmR) resistance was transformed into Streptococcus pneumoniae. High-copy-number and EmR constitutive mutants of this plasmid were isolated. Transformation frequencies in S. pneumoniae as high as 70% were obtained with a constitutive plasmid as donor DNA, into a recipient cell containing a resident, inducible, high-copy-number plasmid. With the aid of these high frequencies, the site of constitutive mutations could be mapped via a simple marker rescue technique that uses purified restriction endonuclease-generated fragments. One of the EmR constitutive mutants, pFB9, a plasmid originating from a Gram-positive host, was shown to replicate and express EmR and CmR in a Gram-negative organism, Escherichia coli. Four derivatives of pFB9 containing large (0.6-0.9 megadalton) insertion sequences that arose spontaneously in E. coli demonstrated unusual transforming activity, as well as enhanced EmR, in E. coli. The inserted elements mapped to the region in front of the EmR gene. Three of these inserted elements had the size and restriction patterns of insertion sequence IS1, IS2, and IS5. Plasmid pFB9 and derivatives are useful for isolation of new insertion sequences and for comparison of gene expression and illegitimate recombination between Gram-positive and Gram-negative species.

Rapid cloning of specific DNA fragments of Streptococcus pneumoniae by vector integration into the chromosome followed by endonucleolytic excision

A method for the rapid cloning of specific Streptococcus pneumoniae DNA fragments depends on the integration by homologous recombination into the bacterial chromosome of a plasmid which carries an insert of S. pneumoniae DNA, but which cannot be autonomously maintained in S. pneumoniae. Selection for plasmid integration employs aminopterin or erythromycin resistance. Host sequences adjacent to the site of insertion are easily cloned by enzymatic excision and recircularization of the plasmid, followed by propagation in Escherichia coli. This is particularly useful for repeated cloning of a given fragment that carries various mutations.

Relation between the transforming activity of a marker and its proximity to the end of the DNA particle

Transforming pneumococcal DNA is inactivated by treatment with restriction enzymes. For mutations belonging to the same locus (amiA locus), the extent of inactivation depends strongly upon the mutations and the enzymes. Two EcoRI and one BamHI restriction sites have been located within the amiA locus. After treatment of donor DNA with either one of these enzymes, the lowest transforming activity is observed for mutations that map near restriction sites. This effect of proximity to the nearest end of the DNA fragment extends over a distance of 1,400 nucleotides. The curve of transforming activity versus DNA size obtained with endonuclease-generated DNA fragments is very similar to that obtained previously with mechanically sheared DNA. Both curves show a striking slope change for donor DNA size around 2,700 base pairs, i.e. twice the length found for the extent of the 'end effect'. We suggest that for donor DNA fragments larger than 2,700 base pairs the transforming activity depends mainly upon the size of donor whereas for donor DNA fragments shorter than 2,700 base pairs both a size-dependent phenomenon and the 'end effect' contribute to reduce drastically the transforming activity.

Base specificity of mismatch repair in Streptococcus pneumoniae

DNA sequence analysis was undertaken to investigate the structural basis of mutations showing different integration efficiencies in Streptococcus pneumoniae. Wild type, mutant and revertant sequences at two sites in the amiA locus were determined. It appears that markers which transform efficiently or inefficiently can result from single base pair changes. A low efficiency (LE) marker corresponds to a C:G to T:A change and a high efficiency (HE) marker to a G:C to T:A change. In the latter case, two mismatches, G/A and T/C, can exist at the heteroduplex stage in transformation; only T/C appears to be recognized by the hex system which controls transforming efficiencies in pneumococcus. Each of the recognized mismatches, T/G and C/A, which result from transitional change, and T/C appears to involve at least one pyrimidine. It is proposed that the mismatch repair system of S. pneumoniae is directed against mismatched pyrimidines. DNA sequence analysis also reveals that short deletions (33 or 34 bases long) behave as very high efficiency markers, confirming that deletions are not recognized by the hex system.