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Conservation of key elements of natural competence in Lactococcus lactis ssp.

Natural competence is active in very diverse species of the bacterial kingdom and probably participates in horizontal gene transfer. Recently, the genome sequence of various species, including Lactococcus lactis, revealed the presence of homologues of competence genes in bacteria, which were not previously identified as naturally transformable. We investigated the conservation among lactococcal strains of key components of the natural competence process in streptococci: (i) comX which encodes a sigma factor, allowing the expression of the late competence genes involved in DNA uptake, (ii) its recognition site, the cin-box and (iii) dprA which encodes a protein shown to determine the fate of incoming DNA. The comX and dprA genes and the cin-box appeared conserved among strains, although some L. lactis ssp. lactis strains presented an inactivated dprA gene. We established that ComX controls the expression of the late competence genes in L. lactis. In conclusion, our work strongly suggests that ComX has the same role in streptococci and L. lactis, i.e. the regulation of late competence genes. It also allowed the identification of a set of L. lactis strains and the construction of a comX overexpression system, which should facilitate the investigation of the natural competence activity in lactococci.

Amino Acid Sequence↗

Clonal distribution of natural competence in Actinobacillus actinomycetemcomitans.

The competence for natural transformation was investigated in 67 Actinobacillus actinomycetemcomitans strains. The transformation assays were performed with both cloned DNA fragments and chromosomal markers of A. actinomycetemcomitans. Competence was found in 12 of 18 serotype a strains, 0 of 21 serotype b strains, 0 of 14 serotype c strains, 3 of 6 serotype d strains, 3 of 4 serotype e strains, 0 of 3 serotype f strains, and 0 of 1 nonserotypeable strain. The transformation frequencies varied from 5 x 10(-3) to 4 x 10(-6) (median 1.5 x 10(-4)). The distribution pattern of natural competence is concordant with the major clonal lineages of A. actinomycetemcomitans. Serotype a strains are predominantly competent for transformation, while serotypes b and c strains are apparently non-competent.

Aggregatibacter actinomycetemcomitans↗

Identification of DNA binding sites for ComE, a key regulator of natural competence in Streptococcus pneumoniae.

Natural competence in Streptococcus pneumoniae is regulated by a quorum-sensing mechanism consisting of a competence-stimulating peptide (CSP), its dedicated secretion apparatus (ComAB), its histidine kinase receptor (ComD) and a response regulator (ComE). In this report, we show that ComE is a DNA-binding protein that acts autocatalytically by binding to a region in its own promoter. Two additional ComE binding sites were identified in the pneumococcal genome, one in the promoter region of comAB and the other upstream of an ABC transporter of unknown function. A comparison of the ComE-binding sequences with the sequence motif previously found to be involved in the co-ordinated expression of the late genes revealed that they are unrelated. These findings indicate that ComE activates transcription of the late genes indirectly, i.e. via one or more intermediate factors.

ATP-Binding Cassette Transporters↗

Association of metronidazole resistance and natural competence in Helicobacter pylori.

To study whether the capability of horizontal DNA transfer is associated with metronidazole resistance in Helicobacter pylori, a total of 81 clinical isolates were tested for MICs of metronidazole (MTZ). The MIC assays were performed by using the E-test and reconfirmed by the agar dilution method. Natural competence assays were performed by transferring a chloramphenicol acetyltransferase cassette and a 23S rRNA gene from a clarithromycin-resistant strain (with an A-to-G mutation at nucleotide 2143) by using natural transformation. Of the 81 isolates, 65 (80.2%) were naturally competent while 16 were not. Among the 65 naturally competent strains, 39 (60%) were highly resistant to MTZ (MICs, >32 microg/ml) while only 2 of 16 (12.5%) noncompetent strains were highly MTZ resistant (P, <0.001). Therefore, there is an association between natural competence and MTZ resistance.

Anti-Bacterial Agents↗

Aflagellated mutants of Helicobacter pylori generated by genetic transformation of naturally competent strains using transposon shuttle mutagenesis.

Three out of 10 Helicobacter pylori clinical isolates were found to be naturally competent for genetic transformation to streptomycin resistance by chromosomal DNA extracted from a spontaneous streptomycin-resistant H. pylori mutant. The frequency of transformation varied between 5 x 10(-4) and 4 x 10(-6), depending on the H. pylori isolate used. Transposon shuttle mutagenesis based on this natural competence was established using the flagellin gene flaA as the target. The cloned flaA gene was interrupted by insertion of TnMax1, a mini-Tn1721 transposon carrying a modified chloramphenicol-acetyltransferase gene, the catGC cassette. Natural transformation of competent H. pylori strains with plasmid constructs harbouring a catGC-inactivated flaA gene resulted in chloramphenicol-resistant transformants at an average frequency of 4 x 10(-5). Southern hybridization experiments confirmed the replacement of the chromosomal H. pylori flaA gene by the cat-inactivated cloned gene copy via homologous recombination resulting in allelic exchange. Phenotypic characterization of the mutants demonstrated the absence of flagella under the electron microscope and the loss of bacterial motility. Immunoblots of cell lysates of the H. pylori mutants with an antiserum raised against the C-terminal portion of recombinant H. pylori major flagellin (FlaA) confirmed the absence of the 54 kDa FlaA protein. This efficient transposon shuttle mutagenesis procedure for H. pylori based on natural competence opens up new possibilities for the genetic assessment of putative H. pylori virulence determinants.

Bacterial Proteins↗

Induction of natural competence in Streptococcus pneumoniae triggers lysis and DNA release from a subfraction of the cell population.

Naturally competent bacteria have the ability to take up free DNA from the surrounding medium and incorporate this DNA into their genomes by homologous recombination. In naturally competent Streptococcus pneumoniae, and related streptococcal species from the mitis phylogenetic group, the competent state is not a constitutive property but is induced by a peptide pheromone through a quorum-sensing mechanism. Recent studies have shown that natural genetic transformation is an important mechanism for gene exchange between streptococci in nature. A prerequisite for effective gene exchange is the presence of streptococcal donor DNA in the environment. Despite decades of study of the transformation process we still do not know how this donor DNA is released from streptococcal cells to the external milieu. Traditionally, it has been assumed that donor DNA originates from cells that die and fall apart from natural causes. In this study we show that induction of the competent state initiates release of DNA from a subfraction of the bacterial population, probably by cell lysis. The majority of the cells induced to competence take up DNA and act as recipients, whereas the rest release DNA and act as donors. These findings show that natural transformation in streptococci provides a natural mechanism for genetic recombination that resembles sex in higher organisms.

Amino Acid Sequence↗

The genome sequence of Mannheimia haemolytica A1: insights into virulence, natural competence, and Pasteurellaceae phylogeny.

The draft genome sequence of Mannheimia haemolytica A1, the causative agent of bovine respiratory disease complex (BRDC), is presented. Strain ATCC BAA-410, isolated from the lung of a calf with BRDC, was the DNA source. The annotated genome includes 2,839 coding sequences, 1,966 of which were assigned a function and 436 of which are unique to M. haemolytica. Through genome annotation many features of interest were identified, including bacteriophages and genes related to virulence, natural competence, and transcriptional regulation. In addition to previously described virulence factors, M. haemolytica encodes adhesins, including the filamentous hemagglutinin FhaB and two trimeric autotransporter adhesins. Two dual-function immunoglobulin-protease/adhesins are also present, as is a third immunoglobulin protease. Genes related to iron acquisition and drug resistance were identified and are likely important for survival in the host and virulence. Analysis of the genome indicates that M. haemolytica is naturally competent, as genes for natural competence and DNA uptake signal sequences (USS) are present. Comparison of competence loci and USS in other species in the family Pasteurellaceae indicates that M. haemolytica, Actinobacillus pleuropneumoniae, and Haemophilus ducreyi form a lineage distinct from other Pasteurellaceae. This observation was supported by a phylogenetic analysis using sequences of predicted housekeeping genes.

Actinobacillus pleuropneumoniae↗

Genetic transformation in freshwater: Escherichia coli is able to develop natural competence.

Until now, Escherichia coli was thought to be unable to develop natural competence, i.e., genetic transformation could be achieved only artificially with the aid of nonphysiological concentrations of calcium ions or by other treatments. We have tested the competence development of E. coli through transformation under natural conditions in river water, springwater, and mineral water which contained between 0 and 11 mM Ca2+, using pUC18 DNA. The presence of calcium ions at concentrations as low as 1 to 2 mM was sufficient to obtain transformants. Variations in the temperature of incubation were not required for competence development but had an influence on the transformation frequency. Using water from mineral springs originating from calcareous regions, we have obtained transformation frequencies with laboratory strains of E. coli similar to those reported for other gram-negative bacteria known to develop natural competence. The competence development of E. coli is most probably internally regulated (as for the other gram-negative bacteria), and inadequate conditions chosen for the transformation tests in the laboratory might impair the detection of higher natural transformation frequencies. The results will enhance our knowledge about the fate of laboratory or production strains of E. coli cells reaching natural aquatic ecosystems.

Calcium↗

Natural competence in the genus Streptococcus: evidence that streptococci can change pherotype by interspecies recombinational exchanges.

To map the incidence of natural competence in the genus Streptococcus, we used PCR to screen a number of streptococcal strains for the presence of the recently identified competence regulation operon, containing the comC, -D, and -E genes. This approach established that the operon is present in strains belonging to the S. mitis and S. anginosus groups, but it was not detected in the other strains examined. Competence is induced in S. pneumoniae and S. gordonii by strain-specific peptide pheromones, competence-stimulating peptides (CSPs). With its unique primary structure, each CSP represents a separate pheromone type (pherotype), which is recognized by the signalling domain of the downstream histidine kinase, ComD. Thus, all bacteria induced to competence by a particular CSP belong to the same pherotype. In this study, we identified a number of new pherotypes by sequencing the genes encoding the CSP and its receptor from different streptococcal species. We found that in several cases, these genes have a mosaic structure which must have arisen as the result of recombination between two distinct allelic variants. The observed mosaic blocks encompass the region encoding the CSP and the CSP-binding domain of the histidine kinase. Consequently, the recombination events have led to switches in pherotype for the strains involved. This suggests a novel mechanism for the adaptation of naturally competent streptococci to new environmental conditions.

Amino Acid Sequence↗

Natural competence of mammalian mitochondria allows the molecular investigation of mitochondrial gene expression.

Respiration, a fundamental process in mammalian cells, requires two genomes, those of the nucleus and the mitochondrion (mtDNA). Mutations of mtDNA are being increasingly recognized in disease and may play an important role in the ageing process. Accepting the vital role of mtDNA gene products, our limited knowledge concerning the details of mitochondrial gene expression is surprising. This is, in part, due to our inability to transfect mitochondria and to manipulate their genome. There have been claims of successful DNA import into isolated organelles, but most reports lacked evidence of expression and no method has furthered our understanding of gene expression. Here, we report that mammalian mitochondria possess a natural competence for DNA import. Using five functional assays, we show imported DNA can act as templates for DNA synthesis or promoter-driven transcription, with the resultant polycistronic RNA being processed (5' and 3') and excised mt-tRNA matured. Exploiting this natural competence will allow us to explore mitochondrial gene expression in organello and provides the potential for mitochondrial transfection in vivo.

Animals↗

Naturally competent bacteria and their genetic parasites-a battle for control over horizontal gene transfer?

Host-mediated natural competence for transformation of DNA and mobile genetic element (MGE)-driven conjugation and transduction are key modes of horizontal gene transfer. While these mechanisms are traditionally believed to shape bacterial evolution by enabling the acquisition of new genetic traits, numerous studies have elucidated an antagonistic relationship between natural transformation and MGEs. A new role of natural transformation as a chromosome-curing mechanism has now been proposed. Experimental data, along with mathematical models, suggest that transformation can eliminate deleterious MGEs. Supporting this hypothesis, MGEs have been shown to use various mechanisms to decrease or block transformability, such as disrupting competence genes, regulating the development of competence, hindering DNA uptake machinery, producing DNases that target the exogenous (transforming) DNA, and causing lysis of competent cells. A few examples of synergistic relationships between natural transformation and MGEs have also been reported, with natural transformation facilitating MGE transfer and phages enhancing transformation by supplying extracellular DNA through lysis and promoting competence via kin discrimination. Given the complexity of the relationships between natural transformation and MGEs, the balance between antagonism and synergy likely depends on specific selection pressures in a given context. The evidence collected here indicates a continuous conflict over horizontal gene transfer in bacteria, with semiautonomous MGEs attempting to disrupt host-controlled DNA acquisition, while host competence mechanisms work to resist MGE interference.

Gene Transfer, Horizontal↗

Role of pili and the phase-variable PilC protein in natural competence for transformation of Neisseria gonorrhoeae.

The Gram-negative bacterial pathogen Neisseria gonorrhoeae is naturally competent for transformation with species-related DNA. We show here that two phase-variable pilus-associated proteins, the major pilus subunit (pilin, or PilE) and PilC, a factor known to function in the assembly and adherence of gonococcal pili, are essential for transformation competence. The PilE and PilC proteins are necessary for the conversion of linearized plasmid DNA carrying the Neisseria-specific DNA uptake signal into a DNase-resistant form. The biogenesis of typical pilus fibers is neither essential nor sufficient for this process. DNA uptake deficiency of defined piliated pilC1,2 double mutants can be complemented by expression of a cloned pilC2 gene in trans. The PilC defect can also be restored by the addition of purified PilC protein, or better, pili containing PilC protein, to the mutant gonococci. Our data suggest that the two phase-variable Pil proteins act on the bacterial cell surface and cooperate in DNA recognition and/or outer membrane translocation.

Bacterial Proteins↗

Sequential action of factors involved in natural competence for transformation of Neisseria gonorrhoeae.

We previously identified and genetically characterized several factors essential for the natural competence of transformation in Neisseria gonorrhoeae. Here we analyse the sequential action of these factors and dissect the overall transformation process into three distinct steps, (i) the sequence-specific uptake of transforming DNA into a DNase-resistant state, (ii) the transfer of DNA to the cytosol and (iii) the processing and recombination of the incoming with the resident DNA. While two pilus-associated factors, PilE and PilC, were previously implicated in the early DNA uptake event, we show here that three competence factors unrelated to pilus biogenesis, ComA, ComL and Tpc, are not essential for DNA uptake and rather act in a subsequent step. The respective mutants, however, lack the characteristic nucleolytic processing observed with the incoming DNA in both wild-type and non-transformable RecA-deficient N. gonorrhoeae, indicating that they are blocked in the processing and/or the delivery of DNA to the cytoplasm. A hypothetical model proposing a sequential action of the known gonococcal competence factors is presented.

Base Sequence↗

Transformation of naturally competent Streptococcus mutans with replicative and non-replicative Tn916-containing plasmids: implications for a mechanism of transposition.

Based on the observations reported here and what is known concerning transformation of naturally competent strains of S. mutans and other streptococcal species such as S. gordonii, we propose the model shown in Figure 2. The Tn916-intermediate transforms S. mutans as originally proposed for B. subtilis by Scott and coworkers [8]. It is not clear in either system (B. subtilis or S. mutans) whether the Tn916 intermediate enters the cell as ds-DNA or ss-DNA. Because it is likely that transformation of B. subtilis via formation of protoplasts involves a mechanism quite different from natural transformation in S. mutans, it would be unwise to extrapolate findings from their studies. If Tn916 enters S. mutans in a manner similar to plasmid or chromosomal DNA, we would assume that Tn916 binds to a cell receptor and as one strand enters, the other is degraded [9]. This leaves open the question of whether Tn916 recircularizes as ds-DNA before it inserts into the chromosome or whether it remains as ss-DNA, if, indeed, it enters as ss-DNA. The transformation efficiency for the Tn916 intermediate (approximately 10(-7) precluded kinetics studies such as those performed with pAM118. Poyart-Salmeron and coworkers [11] however, described a model in which Tn1545 inserts into the target site as a ds-DNA circular molecule, similar to that seen with lambda phage. Perhaps the most interesting finding presented here is that the predominant mechanism of insertion of Tn916 into the chromosome of the recipient occurs after Tn916 enters the cell. The replicative plasmid pAM118 evidently forms by two-hit kinetics followed by intracellular excision and transposition of Tn916. The helper-rescue experiment shows that in this system, the formation of Tcr transformants, and hence the integration of Tn916, was a function of the transformation efficacy of plasmid pAM118. Since intracellular excision of Tn916 probably follows the re-formation of the plasmid pAM118, the rate-limiting step in this system would be the formation of the transient, intracellular plasmid pAM118. (The transient white colony phenotype probably denotes the slower growth rate of transformants that acquire the large replicative plasmid pAM118). Our findings demonstrate that a practical way of promoting Tn916 insertions into chromosomal DNA for the purpose of obtaining mutations is to use a helper-rescue system. Our model supports the concept that the majority of Tn916 inserts arise from a mechanism similar to 'zygotic induction' as proposed for S. sanguis (gordonii) [1]. However, the frequencies for the co-establishment of the replicative plasmid (Emr) and Tn916 inserts (Tcr) in their paper (10(-6)) differ from our observations for S. mutans. We found nearly 100% of Tcr white colonies to be Emr whereas in S. gordonii, only a fraction (approximately 1%) exhibited the TcrEmr phenotype. If both phenotypes arose independently, the frequency of the TcrEmr phenotype would be 10(-8) rather than 10(-6) survivors/recipients as observed. It was surmised that both Tcr and Emr transformants arise dependently [1] where both the Tn916 intermediate and pAM118 contribute to the formation of Tn916 inserts. We conclude from their data, however, that most Tcr arose from the Tn916-intermediate formed in the donor, in agreement with the explanation of these data by Scott [12]. Support for the contention that the Tcr arose in S. gordonii from transformation by the Tn916-intermediate as in S. mutans (yellows), and not from intracellular excision from pAM118, comes from the observation that so few Tcr are Ems and because pAM150 (rep-) yields Tcr at the same frequency as the rep+ pAM118 in their experiments. In summary, the Tn916 intermediate is capable of transforming S. mutans. In contrast to the hypothesis of Scott [12], however, the Tn916 intermediate is not the only form involved in the transformat++t

Chromosomes, Bacterial↗

Natural competence for DNA transformation by Legionella pneumophila and its association with expression of type IV pili.

We have recently described the expression of two pili of different lengths on the surface of Legionella pneumophila (B. J. Stone and Y. Abu Kwaik, Infect. Immun. 66:1768-1775, 1998). Production of long pili requires a functional pilEL locus, encoding a type IV pilin protein. Since type IV pili in Neisseria gonorrhoeae are associated with competence for DNA transformation, we examined the competence of L. pneumophila for DNA transformation under conditions that allowed the expression of type IV pili. We show that L. pneumophila is naturally competent for DNA transformation by isogenic chromosomal DNA and by plasmid DNA containing L. pneumophila DNA. Many different L. pneumophila loci are able to transform L. pneumophila after addition of plasmid DNA, including gspA, ppa, asd, and pilEL. The transformation frequency is reduced when competing DNA containing either L. pneumophila DNA or vector sequences is added to the bacteria, suggesting that uptake-specific sequences may not be involved in DNA uptake. Competence for DNA transformation correlates with expression of the type IV pili, and a pilEL mutant defective in expression of type IV pili is not competent for DNA transformation. Complementation of the mutant for competence is restored by the reintroduction of a cosmid that restores production of type IV pili. Minimal competence is restored to the mutant by introduction of pilEL alone. We conclude that competence for DNA transformation in L. pneumophila is associated with expression of the type IV pilus and results in recombination of L. pneumophila DNA into the chromosome. Since expression of type IV pili also facilitates attachment of L. pneumophila to mammalian cells and protozoa, we designated the type IV pili CAP (for competence- and adherence-associated pili).

Bacterial Proteins↗

Transformation of Leuconostoc carnosum 4010 and evidence for natural competence of the organism.

Plasmid transformation in Leuconostoc carnosum 4010 was analyzed. A successful transformation protocol for L. carnosum was established by modifying an existing protocol for Lactococcus lactis. Several parameters, including the number of generations that the cells had grown at the time of harvest, glycine concentration, the time of incubation for phenotypic expression, and the electrical field strength, were investigated and proved to have influence on the transformation frequency. Electrocompetence was found to be transient and to peak in the early exponential growth phase. Optimized conditions resulted in transformation frequencies of up to 6.7 x 10(5) transformants per microgram of plasmid DNA. A total of five plasmids in L. carnosum were successfully introduced and maintained. Interestingly, we discovered that DNA uptake was of a frequency of 3 x 10(-6) to 19 x 10(-6) transformants per CFU in the absence of an applied electrical field. We concluded that L. carnosum is naturally competent.

Culture Media↗

Plasmid transformation of naturally competent Acinetobacter calcoaceticus in non-sterile soil extract and groundwater.

The natural transformation of Acinetobacter calcoaceticus BD413 (trpE27) was characterized with respect to features that might be important for a possible gene transfer by extracellular DNA in natural environments. Transformation of competent cells with chromosomal DNA (marker trp+) occurred in aqueous solutions of single divalent cations. Uptake of DNA into the DNase I-resistant state but not the binding of DNA to cells was strongly stimulated by divalent cations. An increase of transformation of nearly 3 orders of magnitude was obtained as a response to the presence of 0.25 mM Ca2+. With CaCl2 solutions the transformation frequencies approached the highest values obtained under standard broth conditions, followed by MnCl2 and MgCl2. It is concluded that transformation requires divalent cations. DNA competition experiments showed that A. calcoaceticus does not discriminate between homologous and heterologous DNA. Furthermore, circular plasmid DNA competed with chromosomal DNA fragments and vice versa. The equally efficient transformation with plasmid pKT210 isolated from A. calcoaceticus or Escherichia coli indicated absence of DNA restriction in transformation. High efficiency plasmid transformation was obtained in samples of non-sterile natural groundwater and in non-sterile extracts of fresh and air-dried soil. Heat-treatment (10 min, 80 degrees C) of the non-sterile liquid samples increased transformation only in the dried soil extract, probably by inactivation of DNases. The results presented suggest that competent cells of A. calcoaceticus can take up free high molecular weight DNA including plasmids of any source in natural environments such as soil, sediment or groundwater.

Acinetobacter calcoaceticus↗

Identification of genes associated with natural competence in Helicobacter pylori by transposon shuttle random mutagenesis.

To identify genes involved in DNA transformation, we generated 1500 insertion mutants of a Helicobacter pylori strain by transposon shuttle mutagenesis. All mutant strains were screened for their frequency of natural transformation. A total of 20 mutant strains were found to exhibit a significantly decreased transformation frequency. DNA sequencing revealed seven genetic loci, including the reported comB locus, HP0017 (a putative virB4 homologue) and five loci without database match (HP0015, HP1089, HP1326, HP1424, and HP1473) from the 20 mutants. Reknockout of HP1326 revealed no impairment in natural transformation, while the other 5 mutants showed the same defective in natural transformation. Mutation of HP0017 severely impaired natural transformation both chromosome and plasmid DNA. Slot blot analysis revealed that some noncompetent strains had decreased virB4 RNA expression levels compared with competent strains. Nineteen ORFs had decreased expression levels in virB4 knockout mutant by microarray. Therefore, our data indicate that HP0017 is a virB4 homologue and is essential in the natural competence of H. pylori. HP0015, HP1089, HP1424, and HP1473 genes could be also involved in natural transformation.

Blotting, Southern↗