Three highly homologous membrane-bound lipoproteins participate in oligopeptide transport by the Ami system of the gram-positive Streptococcus pneumoniae.

Oligopeptides are an important source of nutrients, but can serve also as signals for intercellular communication. Oligopeptide-binding proteins seem likely to play a role both in oligopeptide transport and in communication processes. One such protein, AmiA, has been identified in Streptococcus pneumoniae. amiA is the first gene of an operon, ami, which encodes a multicomponent oligopeptide transporter belonging to the family of ABC transporters (or traffic ATPases). This transporter was the first system of this type described in Gram-positive bacteria. To investigate the role and the subcellular location of the putative oligopeptide-binding protein in a bacterium devoid of periplasm, AmiA null mutants were first constructed. None was affected for oligopeptide uptake by the Ami system. Since this apparent dispensability of AmiA could result from a functional redundancy, we looked for chromosomal genes encoding homologues of AmiA. Two homologous genes were identified by DNA-DNA hybridization at low stringency with an amiA probe. Both genes (aliA and aliB) were cloned and shown to encode putative lipoproteins highly homologous to AmiA (close to 60% amino acid identity). Examination of all combinations of amiA, aliA and aliB mutations indicated that these proteins have overlapping specificities toward oligopeptides. The triple mutant is as deficient for oligopeptide transport as mutants in the amiCDE or F genes, which demonstrates that an oligopeptide-binding component is absolutely required for transport by the Ami system. Metabolic labelling with [3H]palmitic acid and cell fractionation were used to demonstrate that the three proteins are indeed membrane-bound lipoproteins in S. pneumoniae. This supports our previous hypothesis that substrate-binding lipoproteins are functionally equivalent to the periplasmic substrate-binding component of ABC transporters of Gram-negative bacteria. Finally, the observation that competence for genetic transformation was drastically reduced in a particular AliB mutant suggests that oligopeptide sensing is important for triggering competence.

Integration efficiency in DNA-induced transformation of Pneumococcus. I. A method of transformation in solid medium and its use for isolation of transformation-deficient and recombination-modified mutants.

A method of transformation on solid medium especially adapted for pneumococcus has been developed. Under specific conditions, all colonies that are allowed to grow in the presence of transforming DNA for six hours give rise to transformed bacteria. Combined with replica plating this technique has been used to isolate mutants modified with regard to recombination. Most of the mutants found are transformation-defective and show a large diversity in their response to ultraviolet light. Some of these mutants have lost their ability to take up transforming DNA. One shows a reduced yield of transformants for a given quantity of DNA taken up. Mutants that manifest altered behavior with regard to marker efficiencies have also been isolated. One of these exhibits a decrease in the transformation efficiency of only the high efficiency markers and two mutants show a decrease in the transformation efficiency of the low efficiency markers.

Repair of single- and multiple-substitution mismatches during recombination in Streptococcus pneumoniae.

The use as genetic markers, during transformation of Streptococcus pneumoniae, of 19 sequences differing from wild type, located throughout the amiA locus, enabled us to examine the fate of 24 single- and 11 multiple-mismatches during recombination. Tentative mismatch ranking as a function of decreasing repair efficiency by the Hex mismatch repair system is G/T = A/C = G/G (maximum repair: 90-95%) greater than C/T (mostly 75 to 90% repair) greater than A/A (from 50 to 90% repair) greater than T/T (50-65% repair) greater than A/G (from 0 to 20% repair) greater than C/C. No indication of correction of the latter has been obtained. Over the limited number of samples examined, we observed no influence of the base composition of the surrounding sequence on correction efficiency for both transition mismatches and for G/G and C/C. Variations in the surrounding sequence affect repair of A/G and C/T, and, even more strongly, of A/A and T/T. No simple correlation to the G:C content of the surrounding sequence is apparent from our results, in contrast to the conclusion drawn for the Mut mismatch repair system of Escherichia coli. Examination of the fate of multiple mismatches suggests that C/C may sometimes impede recognition of otherwise corrected mismatches.

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.

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.

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.

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.

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

EcoRI fragments of the amiA locus in Streptococcus pneumoniae were cloned either into a derivative of lambda or into pBR325 plasmid. Mutations in the amiA locus confer resistance to aminopterin. Pneumococcal DNA fractions were enriched for the desired EcoRI fragments by agarose gel electrophoresis. Recombinant clones were detected directly by transformation with DNA and lambda plaques or from single-colony lysates containing pBR325. The use of cloned DNA in pneumococcal transformation has revealed a number of features pertinent to transformation in general, and also the mismatch repair process. High transformation levels can be achieved, from 40 to 80% of a competent culture. These high levels of transformation with cloned DNA made in a foreign host are taken to confirm the absence of restriction effects on transformation in S. pneumoniae. At saturation, similar transformation levels are obtained with hybrid phage or hybrid plasmid DNAs, but the DNA amount required is 20 to 25 times lower for hybrid plasmid than for hybrid phage, probably because plasmid DNA is 10 times shorter than phage DNA. There is no "end effect" with intact hybrid DNA, i.e. similar transformation levels are achieved for markers whatever their map position on the cloned pneumococcal fragment. Cloned DNA has been used to study the action of the mismatch repair process (hex system). The presence of two mismatches in the same cell is not enough to saturate the hex system, and is not enough to kill the colony-forming center (cfc).

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.

Construction and evaluation of new drug-resistance cassettes for gene disruption mutagenesis in Streptococcus pneumoniae, using an ami test platform.

Although drug-resistance markers have been used frequently for gene-disruption mutagenesis in Streptococcus pneumoniae, none has yet been shown to be free of dependence on local transcription for its expression. Indeed, the erythromycin-resistance marker (erm), originating in pAM beta 1, has been used as an indicator of local transcription on several occasions. A procedure is demonstrated for evaluation of the autonomous expression of such a marker by placing it in a consistent background, at the pneumococcal ami (aminopterin resistance) locus, in combination with active or inactive alleles of the ami promotor (pA). Using this test platform, a chloramphenicol-resistance marker (cat) and a spectinomycin-resistance marker used in streptococcal gene disruption studies and derived from pJS3 and pDL269, respectively, were shown to depend on local transcriptional signals for expression when placed in the pneumococcal chromosome as single-copy genes. To overcome this limitation, new drug-resistance cassettes were designed and constructed, using pA as a model for synthetic promoters for the erm and cat genes. Both new cassettes were shown, by the same procedure, to be expressed after insertion in the pneumococcal chromosome, independent of local transcription. A new insertion-duplication vector, pEVP3, incorporating the new cat cassette and a lacZ reporter derived from pTV32, was also constructed. The ami test platform was used to demonstrate both the autonomous expression of cat and the reporter function of lacZ in chromosomal copies of pEVP3.

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).

Long- and short-patch gene conversions in Streptococcus pneumoniae transformation.

In pneumococcal transformation some point mutations are integrated by an excision-repair pathway which switches the heteroduplex DNA into homoduplex. This transfer of information is a gene conversion. We have reviewed some of the properties of this system especially those relating to heteroduplex specificity and given evidence that this extends over several kilobases of DNA. We then describe a new process of conversion in pneumococcal transformation which occurs over a very short distance (5 to 27 base-pairs) and is triggered by a single site mutation resulting from the transversion 5'-ATTCAT...to 5'...ATTAAT... Only one of the two heteroduplexes 5'...A...3'/3'...G...5', is converted.

A new family of high-affinity ABC manganese and zinc permeases.

Phylogenetic analysis of 47 extracellular putative metal binding receptors (MBRs) belonging to the newly defined cluster suggests the existence of two subclusters. The question of substrate specificity of the corresponding ATP binding cassette (ABC) permeases is discussed, based on data collected from 19 of them concerning their regulation, metal requirement of permease mutants, metal uptake and metal binding. The proposal that the two subclusters correspond to paralogous metal permeases dedicated primarily to manganese and to zinc transport is made. The question of a direct role of MBRs as adhesins of Gram-positive bacteria is then discussed and the importance of metal permeases for cellular processes and host-bacteria interactions is reviewed.

The adc locus, which affects competence for genetic transformation in Streptococcus pneumoniae, encodes an ABC transporter with a putative lipoprotein homologous to a family of streptococcal adhesins.

To identify new components involved in the phenomenon of transformation in Streptococcus pneumoniae, a library of potential mutants has been generated by random insertion of an erythromycin resistance gene. Transformation-deficient mutants were screened using an in situ colony transformation test. The adc locus, which was identified in this search, was cloned and sequenced. Sequence analysis revealed a putative operon of three ORFs (adcC, adcB and adcA) with homology to ATP-binding cassette (ABC) transport operons encoding streptococcal adhesins such as ScaA of S. gordonii and FimA of S. parasanguis. adcA can encode a lipoprotein of 313 amino acid residues containing a putative metal-binding site. The polypeptide shows about 30% sequence identity with ScaA and FimA. We discuss evidence which leads us to propose that AdcA, together with a set of 14 proteins including ScaA, FimA and homologous adhesins, defines a new family of external solute-binding proteins, cluster 9, specific for metals.

Is the Ami-AliA/B oligopeptide permease of Streptococcus pneumoniae involved in sensing environmental conditions?

Streptococcus pneumoniae is a fastidious obligate parasite requiring several amino acids for growth. Oligopeptide uptake mediated by the Ami ABC permease is therefore important for nutrition but this could not account for the highly pleiotropic phenotype exhibited by Ami mutants. The hypothesis that peptide transport plays a pivotal role in sensing environmental conditions and indirectly modulates the expression of several genes is discussed.

Control of recombination rate during transformation of Streptococcus pneumoniae: an overview.

Despite the fact that natural transformation was described long ago in Streptococcus pneumoniae, only a limited number of recombination genes have been identified. Two of them have recently been characterized at the molecular level, recA which encodes a protein essential for homologous recombination and mmsA which encodes the homologue of the Escherichia coli RecG protein. After a survey of the available information regarding the function of RecA, RecG, and other proteins such as the mismatch repair proteins HexA and HexB that can affect the outcome of recombinants, the different levels at which horizontal genetic exchange can be controlled are discussed. It is shown that the specific induction of the recA gene which occurs in competent cells is required for full recombination proficiency. Results regarding the ability of the Hex generalized mismatch repair system to prevent recombination between partially divergent sequences during transformation are also summarized. A structural analysis of homeologous recombinants which suggests that formation of mosaic recombinants can occur independently of mismatch repair in a single-step transformation is also reported. Finally, arguments in favor of an evolutionary origin of transformation as a means of genome evolution are discussed and the different types of recombination events observed which could potentially contribute to S. pneumoniae genome evolution are listed.

Lack of SOS repair in Streptococcus pneumoniae.

Wild-type strains of Streptococcus pneumoniae were non-mutable by UV radiation and thymidine starvation. Moreover, UV-irradiated pneumococcal omega 2 phages were not reactivated in an irradiated host. This suggests that, in pneumoococcus, there is no efficient inducible repair process similar to the SOS repair described in detail for E. coli. We also report that mutations cannot be induced by a process thought to be linked to competence during transformation with isogenic wild-type DNA either on wild-type strains or in strains in which the hex function of excision and repair of mismatched bases is inactive.

DNA processing during entry in transformation of Streptococcus pneumoniae.

The current model for processing DNA during entry in the transformation of Streptococcus pneumoniae is that following double-strand cleavage of DNA bound at the cell surface, uptake of one strand proceeds linearly from a newly formed 3'-end with simultaneous degradation of the opposite strand. Two important predictions of this model have been tested in the work reported here: first that the polarity of DNA degradation is the opposite of that for entry, and second that the rate of DNA degradation is (at least) equal to the rate of entry. The processing of DNA during entry was investigated using donor molecules constructed in vitro and labeled in one strand only. With uniformly labeled donor molecules, an amount of label equivalent to that taken up by the cells was recovered in acid-soluble form in the transformation medium. Experiments with 3'- or 5'-end-labeled molecules revealed that whereas essentially all of the 3'-end label was susceptible to degradation, most 5'-end label was resistant. Kinetic analysis of both entry and degradation revealed very similar rates for these processes, about 100 nucleotides s-1 at 31 degrees C, suggesting that they occur concomitantly. Entry and degradation appear to proceed with opposite polarity, 3'-->5' for entry and 5'-->3' for degradation. A prediction of the entry model, that a single-strand interruption would inhibit the uptake of DNA sequences located 5' to the nick, was confirmed experimentally. Therefore, we suggest that an intact sugar phosphate backbone is required by the entry machinery for continuous uptake.

Strand targeting signal(s) for in vivo mutation avoidance by post-replication mismatch repair in Escherichia coli.

The involvement of GATC sites in directing mismatch correction for the elimination of replication errors in Escherichia coli was investigated in vivo by analyzing mutation rates for a gene carried on a series of related plasmids that contain 2, 1 and 0 such sites. This gene encoding chloramphenicol acetyl transferase (Cat protein) was inactivated by a point mutation. In vivo mutations restoring resistance to chloramphenicol were scored in mismatch repair proficient (mut+) and deficient (mutHLS-) strains. In mut+ cells, reduction of GATC sites from 2 to 0 increased mutation rates approximately 10-fold. Removal of the GATC site distal to the cat- mutation increased the rate of mutation less than 2-fold, indicating that mismatch repair can proceed normally with a single site. The mutation rate increased 3-fold after removal of the GATC site proximal to the mutation. In the absence of a GATC site, mutL- and mutS- strains exhibited a 2- to 3-fold increased mutation rate as compared to isogenic mutH- and mut+ strains. This indicates that 50%-70% of replication errors can be corrected in a mutLS-dependent way in the absence of any GATC site to target mismatch correction to newly synthesized DNA strands. Other strand targeting signals, possibly single strand discontinuities, might be used in mutLS-dependent repair.