Single-strand breakage on binding of DNA to cells in the genetic transformation of Diplococcus pneumoniae

The acquisition of clinically relevant amoxicillin resistance in Streptococcus pneumoniae requires ordered horizontal gene transfer of four loci

Understanding how antimicrobial resistance spreads is critical for optimal application of new treatments. In the naturally competent human pathogen Streptococcus pneumoniae, resistance to β-lactam antibiotics is mediated by recombination events in genes encoding the target proteins, resulting in reduced drug binding affinity. However, for the front-line antibiotic amoxicillin, the exact mechanism of resistance still needs to be elucidated. Through successive rounds of transformation with genomic DNA from a clinically resistant isolate, we followed amoxicillin resistance development. Using whole genome sequencing, we showed that multiple recombination events occurred at different loci during one round of transformation. We found examples of non-contiguous recombination, and demonstrated that this could occur either through multiple D-loop formation from one donor DNA molecule, or by the integration of multiple DNA fragments. We also show that the final minimum inhibitory concentration (MIC) differs depending on recipient genome, explained by differences in the extent of recombination at key loci. Finally, through back transformations of mutant alleles and fluorescently labelled penicillin (bocillin-FL) binding assays, we confirm that pbp1a, pbp2b, pbp2x, and murM are the main resistance determinants for amoxicillin resistance, and that the order of allele uptake is important for successful resistance evolution. We conclude that recombination events are complex, and that this complexity contributes to the highly diverse genotypes of amoxicillin-resistant pneumococcal isolates.

An unstable competence-induced protein, CoiA, promotes processing of donor DNA after uptake during genetic transformation in Streptococcus pneumoniae

Natural genetic transformation in Streptococcus pneumoniae entails transcriptional activation of at least two sets of genes. One set of genes, activated by the competence-specific response regulator ComE, is involved in initiating competence, whereas a second set is activated by the competence-specific alternative sigma factor ComX and functions in DNA uptake and recombination. Here we report an initial characterization of CoiA, a ComX-dependent gene product that is induced during competence and is required for transformation. CoiA is widely conserved among gram-positive bacteria, and in streptococci, the entire coiA locus composed of four genes is conserved. By use of immunoblot assay, we show that, similar to its message, CoiA protein is transient, appearing at 10 min and largely disappearing by 30 min post-competence induction. Using complementation analysis, we establish that coiA is the only gene of this induced locus needed for transformability. We find no indication of CoiA having a role in regulating competence. Finally, using 32P- and 3H-labeled donor DNA, we demonstrate that a coiA mutant can internalize normal amounts of donor DNA compared to the wild-type strain but is unable to process it into viable transformants, suggesting a role for CoiA after DNA uptake, either in DNA processing or recombination.

Transformation of Streptococcus pneumoniae relies on DprA- and RecA-dependent protection of incoming DNA single strands

Seventy-five years after the discovery of transformation with Streptococcus pneumoniae, it is remarkable how little we know of the proteins that interact with incoming single strands in the early processing of transforming DNA. In this work, we used as donor DNA in transformation a radioactively labelled homologous fragment to examine the fate of the single-stranded (ssDNA) products of uptake in cells mutant for DprA or RecA, two proteins essential for transformation. Fifteen minutes after uptake, the labelling of specific chromosomal restriction fragments that demonstrated homologous integration in the wild type was not detected in dprA or recA cells, indicating that in the mutants incoming ssDNA could not be processed into recombinants. Investigation of the fate of donor label 1 min after uptake revealed that incoming ssDNA was immediately degraded in the absence of DprA or RecA. Our results demonstrate that incoming ssDNA requires active protection prior to the RecA-driven search for homology and that both DprA and RecA are needed for this protection.

Cloning and expression of pneumococcal genes in Streptococcus pneumoniae

An overview of gene cloning in Streptococcus pneumoniae is presented. The advantages of such cloning, especially for pneumococcal genes, are enumerated. The molecular fate of DNA in transformation of S. pneumoniae, in particular, the conversion of DNA to single-strand segments on entry, determines the mechanisms for plasmid establishment and interaction with the chromosome. One of these mechanisms, the chromosomal facilitation of plasmid establishment, is useful for obtaining recombinant plasmids and for introducing an allele from the chromosome into a plasmid. The difference between linear and circular synapsis of donor DNA strands with the chromosome is illustrated. Circular synapsis can give rise to circular integration, which is useful for insertional mutagenesis of chromosomal genes, for coupled cloning in Escherichia coli, and for sequential cloning of DNA along the pneumococcal chromosome. Cloning in S. pneumoniae is not notably affected by DNA mismatch repair or restriction systems in the host cell. Unusual features of gene expression in S. pneumoniae are discussed. Transcription begins most often at promoters with extended -10 sequences, and in a small but significant number of cases, translation does not require a ribosome-binding site with a Shine-Dalgarno sequence.

Bacteriophages of Streptococcus pneumoniae: a molecular approach

We have characterized four families of pneumococcal phages with remarkable morphologic and physiological differences. Dp-1 and Cp-1 are lytic phages, whereas HB-3 and EJ-1 are temperate phages. Interestingly, Cp-1 and HB-3 have a terminal protein covalently linked to the 5' ends of their lineal DNAs. In the case of Dp-1, we have found that the choline residues of the teichoic acid were essential components of the phage receptors. We have also developed a transfection system using mature DNAs from Dp-4 and Cp-1. In the later case, the transfecting activity of the DNA was destroyed by treatment with proteolytic enzymes, a feature also shared by the genomes of several small Bacillus phages. DNA replication was investigated in the case of Dp-4 and Cp-1 phages. The terminal protein linked to Cp-1 DNA plays a key role in the peculiar mechanism of DNA replication that has been coined as protein-priming. Recently, the linear 19,345-bp double-stranded DNA of Cp-1 has been completely sequenced, several of its gene products have been analyzed, and a complete transcriptional map has been ellaborated. Most of the pneumococcal lysins exhibit an absolute dependence of the presence of choline in the cell wall substrate for activity, and phage lysis requires, as reported for other systems, the action of a second phage-encoded protein, the holin, which presumably forms some kind of lesion in the membrane. The two lytic gene cassettes, from EJ-1 and Cp-1 phages, have been cloned and expressed in heterologous and homologous systems. The finding that some lysogenic strains of Streptococcus pneumoniae harbor phage remnants has provided important clues on the interchanges between phage and bacteria and supports the view of the chimeric origin of phages.

DNA uptake in bacteria

Natural competence is widespread among bacterial species. The mechanism of DNA uptake in both gram-positive and gram-negative bacteria is reviewed. The transformation pathways are discussed, with attention to the fate of donor DNA as it is processed by the competent cell. The proteins involved in mediating various steps in these pathways are described, and models for the transformation mechanisms are presented. Uptake of DNA across the inner membrane is probably similar in gram-positive and gram-negative bacteria, and at least some of the required proteins are orthologs. The initial transformation steps differ, as expected, from the presence of an outer membrane only in the gram-negative organisms. The similarity of certain essential competence proteins to those required for the assembly of type-4 pili and for type-2 protein secretion is discussed. Finally several hypotheses for the biological role of transformation are presented and evaluated.

Polarity of recombination in transformation of Streptococcus pneumoniae

In transformation of Streptococcus pneumoniae DNA enters the cell as single-strand fragments and integrates into the chromosome by homologous recombination. Deletions and insertions of a few hundred base pairs frequently stop the recombination process of a donor strand. In this work we took advantage of such interruptions of recombination to compare the transformation efficiencies of the segments 5'- and 3'-ward from a deletion. The deletion was created in the center of a fragment of the ami locus, and sites around the deletion were labeled by a frameshift generating a restriction site. Heteroduplexes were constructed containing two restriction sites on one strand and two different ones on the complementary strand. ami+ bacteria were transformed with such heteroduplexes. ami- transformants were isolated and individually underwent amplification of the transformed ami region. We have obtained two kinds of amplification products: short when the deletion was integrated, long when recombination stops at the deletion. Each long fragment was tested by the four restriction enzymes to detect which strand and which side of the deletion had recombined. We found that 80% of the cuts were located 5' to the deletion, showing that, in vivo, the 5' side is strongly favored by recombination. Further results suggest that exchanges occurring from 5' to 3' relative to the donor strand are more efficient than in the opposite direction, thus accounting for the 5' preference.

A competence regulon in Streptococcus pneumoniae revealed by genomic analysis

Transformation in bacteria is the uptake and incorporation of exogenous DNA into a cell's genome. Several species transform naturally during a regulated state defined as competence. Genetic elements in Streptococcus pneumoniae induced during transformation were identified by combining a genetic screen with genomic analysis. Six loci were discovered that composed a competence-induced regulon. These loci shared a consensus promoter sequence and encoded proteins, some of which were similar to proteins involved in DNA processing during transformation in other bacteria. Each locus was induced during competence and essential for genetic transformation.

Bioenergetic aspects of the translocation of macromolecules across bacterial membranes

Bacteria are extremely versatile in the sense that they have gained the ability to transport all three major classes of biopolymers through their cell envelope: proteins, nucleic acids, and polysaccharides. These macromolecules are translocated across membranes in a large number of cellular processes by specific translocation systems. Members of the ABC (ATP binding cassette) superfamily of transport ATPases are involved in the translocation of all three classes of macromolecules, in addition to unique transport ATPases. An intriguing aspect of these transport processes is that the barrier function of the membrane is preserved despite the fact the dimensions of the translocated molecules by far surpasses the thickness of the membrane. This raises questions like: How are these polar compounds translocated across the hydrophobic interior of the membrane, through a proteinaceous pore or through the lipid phase; what drives these macromolecules across the membrane; which energy sources are used and how is unidirectionality achieved? It is generally believed that macromolecules are translocated in a more or less extended, most likely linear form. A recurring theme in the bioenergetics of these translocation reactions in bacteria is the joint involvement of free energy input in the form of ATP hydrolysis and via proton sym- or antiport, driven by a proton gradient. Important similarities in the bioenergetic mechanisms of the translocation of these biopolymers therefore may exist.

Genetic competence in Bacillus subtilis

Genetic competence may be defined as a physiological state enabling a bacterial culture to bind and take up high-molecular-weight exogenous DNA (transformation). In Bacillus subtilis, competence develops postexponentially and only in certain media. In addition, only a minority of the cells in a competent culture become competent, and these are physiologically distinct. Thus, competence is subject to three regulatory modalities: growth stage specific, nutritionally responsive, and cell type specific. This review summarizes the present state of knowledge concerning competence in B. subtilis. The study of genes required for transformability has permitted their classification into two broad categories. Late competence genes are expressed under competence control and specify products required for the binding, uptake, and processing of transforming DNA. Regulatory genes specify products that are needed for the expression of the late genes. Several of the late competence gene products have been shown to be membrane localized, and others are predicted to be membrane associated on the basis of amino acid sequence data. Several of these predicted protein sequences show a striking resemblance to gene products that are involved in the export and/or assembly of extracellular proteins and structures in gram-negative organisms. This observation is consistent with the idea that the late products are directly involved in transport of DNA and is equally consistent with the notion that they play a morphogenetic role in the assembly of a transport apparatus. The competence regulatory apparatus constitutes an elaborate signal transduction system that senses and interprets environmental information and passes this information to the competence-specific transcriptional machinery. Many of the regulatory gene products have been identified and partially characterized, and their interactions have been studied genetically and in some cases biochemically as well. These include several histidine kinase and response regulator members of the bacterial two-component signal transduction machinery, as well as a number of known transcriptionally active proteins. Results of genetic studies are consistent with the notion that the regulatory proteins interact in a hierarchical way to make up a regulatory pathway, and it is possible to propose a provisional scheme for the organization of this pathway. It is remarkable that almost all of the regulatory gene products appear to play roles in the control of various forms of postexponential expression in addition to competence, e.g., sporulation, degradative-enzyme production, motility, and antibiotic production. This has led to the notion of a signal transduction network which transduces environmental information to determine the levels and timing of expression of the ultimate products characteristic of each of these systems.

Role of uracil-DNA glycosylase in mutation avoidance by Streptococcus pneumoniae

Uracil-DNA glycosylase activity was found in Streptococcus pneumoniae, and the enzyme was partially purified. An ung mutant lacking the activity was obtained by positive selection of cells transformed with a plasmid containing uracil in its DNA. The effects of the ung mutation on mutagenic processes in S. pneumoniae were examined. The sequence of several malM mutations revertible by nitrous acid showed them to correspond to A.T----G.C transitions. This confirmed a prior deduction that nitrous acid action on transforming DNA gave only G.C----A.T mutations. Examination of malM mutant reversion frequencies in ung strains indicated that G.C----A.T mutation rates generally were 10-fold higher than in wild-type strains, presumably owing to lack of repair of deaminated cytosine residues in DNA. No effect of ung on mutation avoidance by the Hex mismatch repair system was observed, which means that uracil incorporation and removal from nascent DNA cannot be solely responsible for producing strand breaks that target nascent DNA for correction after replication. One malM mutation corresponding to an A.T----G.C transition showed a 10-fold-higher spontaneous reversion frequency than other such transitions in a wild-type background. This "hot spot" was located in a directly repeated DNA sequence; it is proposed that transient slippage to the wild-type repeat during replication accounts for the higher reversion frequency.

Genetic and structural characterization of endA. A membrane-bound nuclease required for transformation of Streptococcus pneumoniae

The endA gene encoding the membrane nuclease of Streptococcus pneumoniae, which is necessary for DNA uptake in genetic transformation, was cloned in a streptococcal vector. This was accomplished by insertional mutagenesis of the gene, cloning of the mutant allele, and substitution of the wild-type allele by chromosomal facilitation of plasmid establishment. Plasmids carrying the endA+ gene complemented cells with endA- in the chromosome to restore DNAase activity and transformability. Determination of its DNA sequence showed the gene to encode a 30 kDa protein, EndA, with a typical signal sequence for membrane transport at its amino end. In vitro synthesis of EndA showed the initial translation product to be enzymatically active without further processing. Comparison with EndA found in cell membranes indicated that the enzyme retained its signal sequence, which apparently anchored the otherwise hydrophilic protein to the membrane. From the nucleotide sequence in the vicinity of endA and the effect of various insertions and deletions, it appears that endA is the last gene in an operon containing at least two other genes. Neither of these upstream genes, nor the downstream gene, are essential for either cell viability or transformability.

The exoA gene of Streptococcus pneumoniae and its product, a DNA exonuclease with apurinic endonuclease activity

The gene encoding the major DNA exonuclease of Streptococcus pneumoniae, exoA, was cloned in a streptococcal host vector system. Its location was determined by subcloning and by insertion mutations. Transfer of a DNA segment containing the gene to an Escherichia coli expression vector showed that exoA was the structural gene for the enzyme and that it was adjacent to its promoter. DNA sequence determination indicated that the gene encoded a protein, ExoA, of molecular weight 31,263. Under hyperexpression conditions, the ExoA protein constituted 10% of total cellular protein. In addition to previously demonstrated 3' to 5' exonuclease and 3'-phosphatase activities, ExoA was shown to make single-strand breaks at apurinic sites in DNA. Its enzymatic activities are thus similar to those of exonuclease III of E. coli and other gram-negative bacteria. The nucleotide sequence of exoA revealed it to be homologous to xth of E. coli, with 26% identity of amino acid residues in the predicted proteins. So far, no null chromosomal mutants of exoA have been obtained, and the biological function of ExoA remains unknown.

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.

Genetic transformation in Streptococcus pneumoniae: molecular cloning and characterization of recP, a gene required for genetic recombination

A 225-base-pair fragment of a recombination gene was identified by insertion-duplication mutagenesis and used as a radioactive probe to clone the corresponding rec locus from Streptococcus pneumoniae in Escherichia coli plasmid vectors. Attempts to clone large pieces of this locus were unsuccessful, but small pieces of DNA from this region were cloned in the E. coli transcriptional terminator vectors pKK232-8 and pJDC9. The extent of the rec region, 2.1 to 2.2 kilobases, was defined by determining the competence phenotype of insertion mutations constructed in vitro. A deletion of the rec locus showed it to be necessary for chromosomal integration but not for plasmid establishment. A plasmid carrying the entire locus encoded a 72-kilodalton polypeptide in a cell-free E. coli transcription-translation system.

LiCl treatment releases a nickase implicated in genetic transformation of Streptococcus pneumoniae

When cells competent for genetic transformation of Streptococcus pneumoniae which could bind and enable entry of extracellular DNA molecules were treated with LiCl, they released a nickase that introduced nicks into a double-stranded DNA in the presence of EDTA. The nickase was specific for competent cells and coupled with DNA-binding activity. Furthermore, when noncompetent cells were treated with LiCl, they released the putative receptors for the competence activator.

Characterization of DNA uptake by the cyanobacterium Anacystis nidulans

The binding and uptake of nick-translated 32P-labeled pBR322 by Anacystis nidulans 6301 have been characterized. Both processes were considerably enhanced in permeaplasts compared to cells. The breakdown of labeled DNA was not correlated with binding or uptake by permeaplasts or cells. Uptake of DNA by permeaplasts was unaffected by: Mg2+ or Ca2+, light, or inhibitors of photophosphorylation such as valinomycin or gramicidin D in the presence or absence of NH4Cl. ATP at 2.5-10 mM inhibited both binding and uptake of labeled DNA by permeaplasts of A. nidulans whereas the ATP analog adenyl-5-yl imido-diphosphate was non-inhibitory in the same concentration range. In contrast to transformation of A. nidulans 6301 cells to ampicillin-resistance by pBR322, transformation to kanamycin-resistance by the plasmid pHUB4 was considerably enhanced in the dark. The transformation efficiency for permeaplasts by the plasmid pCH1 was 59% and 8% in the dark and light, respectively, whereas transformation of permeaplasts by pBR322 at an efficiency of 16% was absolutely light-dependent.

Cloning of a gene encoding a DNA polymerase-exonuclease of Streptococcus pneumoniae

A procedure was developed for cloning and characterizing genes that encode proteins with nuclease activity in the Streptococcus pneumoniae [pLS1] host/vector system. Clones are screened for nuclease activity by a DNase colony assay and the nucleases that they produce are characterized by detection of enzyme activity after sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The method was used to clone the gene encoding a DNA polymerase (Pol)-exonuclease of S. pneumoniae. The activity of this enzyme, the predominant DNA Pol of S. pneumoniae, is tenfold greater in cells carrying the multicopy recombinant plasmid than in cells without the plasmid. The enzyme corresponds to a 100-kDa polypeptide, and its properties are similar to PolI of Escherichia coli. A restriction map of the pSM22 plasmid containing the pneumococcal polA gene was obtained. The gene was transferred into Bacillus subtilis and E. coli, and it was expressed in both species. Its direction of transcription was determined by placement of the gene in both orientations in an E. coli hyperexpression plasmid. In one of the orientations the pneumococcal PolI enzyme was produced at a level 50-fold greater than normally found in S. pneumoniae, and it comprised 5% of the total protein.

Transformation in Bacillus subtilis: further characterization of a 75,000-dalton protein complex involved in binding and entry of donor DNA

A 75,000-dalton protein complex purified from membranes of competent Bacillus subtilis cells was previously shown to be involved in both binding and entry of donor DNA during transformation. The complex, consisting of two polypeptides, a and b, in approximately equal amounts, showed strong DNA binding as well as nuclease activity (H. Smith, K. Wiersma, S. Bron, and G. Venema, J. Bacteriol. 156:101-108, 1983). In the present experiments, peptide mapping indicated that the two polypeptides are not related. Chromatography on benzoylated, naphthoylated DEAE-cellulose showed that polypeptide b generated single-stranded regions in double-stranded DNA. A considerable amount of the DNA was rendered acid soluble by polypeptide b. The nuclease activity of polypeptide b was reduced in the presence of polypeptide a. This resulted in an increased fraction of high-molecular-weight double-stranded DNA containing single-stranded regions. The acid-soluble DNA degradation products formed by polypeptide b consisted exclusively of oligonucleotides. In contrast to its nuclease activity, which was specifically directed toward double-stranded DNA, the DNA binding of the native 75,000-dalton complex to single-stranded DNA was at least as efficient as to double-stranded DNA.

Effects of Neurospora nuclease halo (nuh) mutants on secretion of two phosphate-repressible alkaline deoxyribonucleases

Various recently isolated nuh mutants of Neurospora crassa (i.e., mutants which show reduced nuclease haloes on DNA-sorbose plates flooded with HCl) were mapped in several new genes or gene clusters and checked for effects on DNA repair and nuclease secretion. Some of them were found to be sensitive to MMS (methylmethane sulfonate) and sterile in meiosis. Release of nuclease activities into filtrates of liquid cultures was analyzed by DEAE-Sepharose chromatography. In the wild type, three alkaline deoxyribonuclease activities (A, B, and C) can be separated after growth in sorbose minimal media [Fraser, M. J. (1979). Nucleic Acids Res. 6: 231]. When strains were grown in phosphate-free DNA sucrose media, high (200-fold derepressed) DNase levels were found, and crude dialyzed filtrates could be chromatographed. Only two peaks were found, namely, those of DNase A, a Ca2+-dependent strand-nonspecific endonuclease, and DNase B, a ss-DNA-specific Mg2+-dependent exonuclease. Of the nuh mutants analyzed by one or both of these methods, many resembled the wild type. A few showed poor derepression, since their sorbose filtrates were normal, while profiles from DNA media lacked all peaks. These grew variably in liquid media with organic phosphates and probably produced suppressors, as was regularly found for nuc-2. Other mutants, which lacked specific peaks, gave the same results with both methods. One of these, nuh-7, produced no peaks at all but secreted unusually high amounts of protein.

Transformation in Bacillus subtilis: a 75,000-dalton protein complex is involved in binding and entry of donor DNA

A 75,000-dalton protein complex involved in DNA binding during transformation was purified from membranes of competent Bacillus subtilis cells. Previous results (Smith et al., J. Bacteriol. 156:101-108, 1983) showed that the complex contained two polypeptides, polypeptide a (molecular weight, 18,000; isoelectric point, 5.0) and polypeptide b (molecular weight, 17,000; isoelectric point, 4.7) in approximately equal amounts. In the present experiments the two polypeptides were extracted from two-dimensional gels and studied separately and in combination with respect to DNA binding and nuclease activities. For DNA binding the interaction of both polypeptides was required. DNA binding occurred efficiently in the presence of EDTA. Nuclease activity was restricted to polypeptide b. The nucleolytic properties of b were identical to those of the native 75,000-dalton complex. Polypeptide a affected b by reducing its nuclease activity. Analysis of the nuclease subunit b on DNA-containing polyacrylamide gels revealed nuclease activities at four different molecular weight positions. These activities were identical to the major competence-specific nuclease activities which were previously implicated in the entry of donor DNA during transformation (Mulder and Venema, J. Bacteriol. 152:166-174, 1982). These results indicate that the 75,000-dalton protein complex is composed of two different competence-specific polypeptides involved in both binding and entry of donor DNA. The possible roles of the two polypeptides in the transformation of B. subtilis are discussed.

Length of foreign DNA in chimeric plasmids determines the efficiency of its integration into the chromosome of the cyanobacterium Synechococcus R2

The photosynthetic cyanobacterium Synechococcus R2 is efficiently transformed by DNA molecules that contain antibiotic genes from Escherichia coli linked to a segment of Synechococcus R2 chromosomal DNA. Antibiotic-resistant transformants result from integration of donor DNA into the cyanobacterial chromosome by homologous recombination. Foreign DNA interrupting the cyanobacterial sequence in the donor molecule integrates by replacement of homologous recipient DNA with donor DNA containing the foreign insert. Foreign DNA linked to the ends of the cyanobacterial fragment in a circular donor molecule integrates by a reciprocal cross-over between donor and recipient sequences. Using donor molecules that contain different lengths of foreign DNA in both of the above positions, we have determined that the probability of integration decreases by half for each increase of 2 to 3 kb in length of a foreign segment, regardless of its position in the donor molecule. The length of one of the two foreign segments has no effect on the integration of the other. Foreign DNA 20 kb in length is completely stable when it has integrated by the replacement mechanism. The ability to stably introduce large pieces of foreign DNA makes Synechococcus R2 an attractive organism in which to study and modify both native and heterologous genes involved in oxygenic photosynthesis.

Protease-sensitive transfection of Streptococcus pneumoniae with bacteriophage Cp-1 DNA

The transfecting activity of pneumococcal phage Cp-1 DNA was destroyed by treatment with proteolytic enzymes, although these enzymes did not affect transfection with bacteriophage Dp-4 DNA. This transfection was stimulated by calcium ions. Protease-treated Cp-1 DNA competes for binding and uptake with transforming pneumococcal DNA as well as with transfecting Dp-4 DNA to approximately the same extent as does untreated Cp-1 DNA. In addition, [3H]thymidine-labeled Cp-1 DNA, treated with proteases or untreated, was absorbed with the same efficiency. These data suggest that uptake of Cp-1 DNA is not affected by protease treatment. [3H]thymidine-labeled Cp-1 DNA showed remarkable resistance against surface nuclease activity of competent wild-type cells. The monomeric form of the Cp-1 DNA-protein complex showed a linear dose response in transfection.

Transformation in Bacillus subtilis: purification and partial characterization of a membrane-bound DNA-binding protein

In DNA binding-deficient mutants of Bacillus subtilis a competence-specific protein with a subunit molecular weight of 18,000 was absent. The native protein containing this subunit was purified from B. subtilis membranes by chromatography on hydroxyapatite, DEAE-cellulose, and Sephacryl S-200. This protein appeared to be complexed with a second protein of slightly lower molecular weight (17,000) and a different isoelectric point. The native protein complex (apparent molecular weight, 75,000) contained approximately equal amounts of the two polypeptides and showed a strong DNA-binding activity. Incubation of the complex with plasmid and bacteriophage DNA revealed nuclease activity, specifically directed toward double-stranded DNA. Predominantly single-stranded nicks and a limited number of double-stranded breaks were introduced in the presence of Mg2+ ions. In the presence of Mn2+ ions the complex produced low-molecular-weight breakdown products from the DNA.

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.

Pneumococcal bacteriophage Cp-1 contains a protein bound to the 5' termini of its DNA

The genome of the pneumococcal bacteriophage Cp-1 has been isolated as a DNA-protein complex. The transfecting activity of this complex is destroyed by treatment with proteolytic enzymes. The DNA-protein complexes do not enter into agarose or acrylamide gels and are retained on glass fiber filters. The protein is specifically associated with the two 5' termini of Cp-1 DNA on the basis of experiments carried out with restriction endonucleases, exonucleases, and radioactive labeling with [gamma-32P]ATP and polynucleotide kinase. The protein component, iodinated in vitro with 125I, has a molecular weight of 28,000 determined by SDS-polyacrylamide gel electrophoresis. The protein remains associated with the Cp-1 DNA after thermal or alkali denaturation, incubation with 6 M guanidinium chloride or 8 M urea, and boiling in 2% SDS, 2% mercaptoethanol, and 6 M urea. When the complex was incubated in 1 M sodium hydroxide or 2.5 M piperidine only a partial breakage of the DNA-protein bond was observed. These results indicate that the 28,000-Da protein is covalently bound to the 5' termini of the DNA.

Transformation in Bacillus subtilis: properties of DNA-binding-deficient mutants

Transformation-deficient mutants of Bacillus subtilis were selected after replica plating on agar plates containing transforming DNA. Out of 24 mutants tested, 3 showed highly reduced abilities to bind donor DNA; the residual levels of binding were similar to those of noncompetent cells. Transformation and transfection were reduced to nondetectable levels in the mutants. However, transduction with phage SPP1 occurred at normal frequencies. The nuclease activities involved in entry of donor DNA were present in the mutants. Comparison of protein patterns by two-dimensional gel electrophoresis revealed the absence of one major protein in the mutants as compared with the wild-type strain. This protein (molecular weight, approximately 18,000; isoelectric point, 5.0) appeared to be membrane associated. The protein was specific for competent cells, suggesting that it is involved in the binding of donor DNA.

Interactions of competent Streptococcus sanguis (Wicky) cells with native or denatured, homologous or heterologous deoxyribonucleic acids

Competent cell-deoxyribonucleic acid (DNA) interactions were examined using tritium-labeled homologous or heterologous native or denatured DNAs and competent Streptococcus sanguis Wicky cells (strain WE4). The DNAs used were extracted from WE4 cells, Escherichia coli B cells, and E. coli bacteriophages T2, T4, T6, and T7. The reactions examined were: (i) total DNA binding, (ii) deoxyribonuclease-resistant DNA binding, and (iii) the production of acid-soluble products from the DNA. Optimal temperatures for the reactions were as follows: reaction (i), between 30 and 40 degrees C; reaction (ii), 30 degrees C; and reaction (iii), greater than 40 degrees C. The rates for the reactions (expressed as molecules of DNA that reacted per minute per colony-forming unit) did not vary greatly from one DNA source to another. With a constant competent cell concentration and differing DNA concentrations below a saturation level (from a given source), a different but constant fraction of the added DNA was cell bound, deoxyribonuclease resistant, and degraded to acid-soluble products. In experiments where the number of competent cells was varied and the DNA concentration was held constant, again essentially the same result was obtained. The extent of reactions (i), (ii), and (iii) depended upon the numbers as well as the source of DNA molecules applied to competent cells. Calcium ion essential for native DNA-cell reactions was also found essential for denatured DNA-cell reactions. Data obtained from competition experiments lead to the conclusion that competent WE4 cells contain specific sites for native as well as denatured DNAs.

Purification and properties of deoxyribonucleic acid binding factor isolated from the surface of Streptococcus sanguis cells

Deoxyribonucleic acid (DNA) binding factor (BF) was found in surface fluids from competent and noncompetent cells of Streptococcus sanguis strains Challis, Wicky, and Blackburn. Fluids from noncompetent cells exhibited about 10% BF activity compared with extracts from competent cells. BF from competent Wicky cells was purified to homogeneity by electrophoresis and immunodiffusion. Purified BF preparations exhibited slight endonucleolytic activity, directed mainly against single-stranded DNA. Nucleolytic and DNA binding activities present in purified BF could be separated by polyacrylamide gel electrophoresis. Purified BF was sensitive to proteolytic enzymes and to phospholipase D, and its activity was stimulated in the presence of low Triton X-100 concentrations. The protein component of BF is a single, monomeric polypeptide with a molecular weight of 56,000 and an isoelectric point of pH 5.8. Binding of purified BF to DNA was a very rapid process at the optimum temperature, pH, and ionic strength and led to the formation of fast-sedimenting complexes. Purified BF was tested for several properties. It exhibited higher affinity to single- than to double-stranded DNA. It bound poorly to glucosylated phage T4 and single-stranded, synthetic polydeoxyribonucleotides and did not bind to RNA. It protected single-stranded DNA against nuclease S(1) action but did not protect native DNA against deoxyribonuclease I action. No evidence was found for unwinding activity, using double-stranded DNA as a substrate.

Mechanism of homospecific DNA uptake in Haemophilus influenzae transformation

DNA uptake by competent H. influenzae cells requires the presence of a specific base sequence (uptake site) on the entering DNA duplex. This sequence is probably recognized by a receptor on the cell surface. We have examined the kinetics and stoichiometry of DNA uptake by competent cells and have shown that the results are consistent with a simple model involving: 1) reversible binding of the DNA uptake site to a cell surface receptor, 2) an irreversible step resulting in a commitment toward DNA uptake, and 3) transport of the DNA duplex into the cell. We have also shown that a competent H. influenzae cell can absorb only 4 to 8 molecules of DNA, regardless of their length. To explain this counting mechanism, we suggest that each cell has only 4 to 8 receptors and that each receptor can be used to transport only one molecule of DNA.

Bacteriophages of Streptococcus pneumoniae. Physicochemical properties of bacteriophage Dp-4 and its transfecting DNA

The properties of Dp-4 phage and its DNA have been studied. The phage has a polyhedral head of 60 nm diameter, a tail 155 nm long and a buoyant density in CsCl of 1.48 g/cm3. Analysis by acrylamide gel electrophoresis indicates the presence of five polypeptides. Dp-4 DNA has a molecular weight of 37 x 10(6), a melting point of 83.5 degrees C (when dissolved in 0.15 M NaCl/0.015 M sodium citrate, pH 7.0) and a G + C content of about 33%. Denaturation of DNA yields two strands of different buoyant density in a neutral CsCl gradient. The interaction of poly(U, G) with the heavy strand strongly enhances its density and allows the preparative separation of both strands. Native Dp-4 DNA has unusual physical properties: abnormally low buoyant densities both in CsCl (1.666 g/cm3) and in Cs2SO4 (1.410 g/cm3) (which do not correspond to the value predictable from the G + C content of the DNA), and a high thermal stability at low ionic strength.

Transformation in pneumococcus: nuclease resistance of deoxyribonucleic acid in the eclipse complex

Donor deoxyribonucleic acid strands in the eclipse phase of genetic transformation of pnuemococcus (Streptococcus pneumoniae) are purified as a complex with a cf the deoxyribonucleic acid strand in this complex to digestion by nucleases was shown to be 50- to 1,000-fold less than that of uncomplexed single strands of deoxyribonucleic acid. Deoxyribonuclease I, micrococcal nuclease, Neurospora endonuclease, nuclease P1, and the major endogenous nuclease of cell-free extracts were studied. Sensitivity to nuclease attack was not uniform along the deoxyribonucleic acid strand; sequences of strongly protected bases were separated by more sensitive regions. The minimum size of protected fragments was about 70 bases. A complex of protein with the protected deoxyribonucleic acid segments was obtained after partial digestion. The sizes of these complexes, of the protected deoxyribonucleic acid segments, and of the protein subunit released by complete nuclease digestion, are all approximately identical, as determined by gel exclusion chromatography. Deoxyribonucleic acid strands of eclipse complex were also shown to be particularly well protected from attack by the major pneumococcal endonuclease in cell extracts.

Bacteriophage-associated gene transfer in pneumococcus: transduction or pseudotransduction?

Lysates of pneumococcal phage PG24 transferred genes from one host to another in a process with many of the properties of generalized transduction, in that the host genes were packaged in DNase-resistant particles that closely resembled infectious phage in physical properties, adsorbed to the recipient cells like phage, and were inhibited by antisera to the phage and by trypsin. However, phage processes did not complete the transfer of host DNA as they did phage DNA. Instead, gene transfer required development of competence and entry of the host DNA by the endonuclease-dependent pathway used for transforming and transfecting DNA. This process often occurred on the assay plate hours after adsorption of the particles to the cells, and the transfer was DNase sensitive if challenged at this time. Phenotypic expression was therefore also delayed. The product of entry was like that in transformation, a single strand of DNA that integrates by formation of a hex-sensitive donor-recipient heteroduplex. Whether this gene transfer process is unique to this system or is only the first one described is not clear. The term "pseudotransduction" may be useful in calling attention to its unexpected features. The DNA of PG24 phage has anomalous physical properties reflecting unusual bases.

Transformation in Bacillus subtilis: biological and physical evidence for a novel DNA-intermediate in synchronously transforming cells

Competent B. subtilis cells exposed to transforming DNA in the presence of EDTA bind, but do not take up DNA. Rapid and almost synchronous uptake of the bound DNA is achieved by the addition of Mg2+ ions in excess of the EDTA. At 30 degrees and at 17 degrees comparable numbers of transformants are produced from cells pre-loaded with DNA at 30 degrees (after termination of uptake by the addition of DNA ase the samples were incubated at 37 degrees). However, almost no transformants are produced when cells are exposed to DNA at 17 degrees, although binding does take place then. Because DNA is taken up at 17 degrees after having loaded the cells at 30 degrees, whereas no uptake occurs after binding at 17 degrees, it is suggested that binding of DNA to the cellular surface involves at least two steps. In DNA re-extracted from cells at 17 degrees, pre-loaded with DNA at 30 degrees, little recombinant type activity is present, indicating that integration is blocked at 17 degrees. However, physico-chemical analysis of the re-extracted DNA indicates that a complex between single-stranded donor DNA and the recipient chromosome is formed at 17 degrees. This complex has a higher buoyant density than donor-recipient complexes formed at 30 degrees.