Nonreplicating Plasmid Research Articles

The Site-Specific Recombination System of theLactobacillusSpecies Bacteriophage A2 Integrates in Gram-Positive and Gram-Negative Bacteria

The region of the bacteriophage A2 genome involved in site-specific recombination with the DNA ofLactobacillusspp. has been identified. Twoorfs, transcribed from the same strand, have been found immediately upstream of the phage attachment site (attP). Theorfadjacent toattPpredicts a 385-amino-acid protein that presents significant similarity with site-specific recombinases of the integrase family. The otherorfencodes a basic polypeptide of 76 amino acid residues. The junctions of the prophage with the genomes of its hosts have been determined, allowing the identification of the host attachment site (attB), which has a common 19-nucleotide core region withattP. TheattBsite is located at the 3′ end of the transfer RNALeugene (anticodon CAA). Nonreplicative plasmids containing the A2-specific recombination cassette integrate into different lactobacilli but also into unrelated Gram-positive bacteria such asLactococcus lactisand even intoEscherichia coli. InLc. lactis, integration occurs in a previously unknown intergenic region, whereas inE. coli, it maps within therrnDoperon, 5′ ofrrsDgene. Comparison of the integration sites in the different hosts indicates that some flexibility is permitted in theattBsequence, sinceLc. lactisandE. colionly share 13 and 11 nucleotides, respectively, with the 19-nucleotide core sequence of the lactobacilli.

Transposon Tn916insertional mutagenesis ofPasteurella multocidaand direct sequencing of disruption site

The transposon Tn916, when introduced intoPasteurella multocidaby electroporation on a nonreplicating plasmid, integrates into the bacterial chromosome. Efficiencies of approximately 8×104mutants/μg of plasmid DNA were obtained. Restriction digestion and Southern analysis indicate that the Tn916element integrates in a quasi-random fashion throughout the genome. Most transformants had a single copy of the transposon but approximately 5% had two copies. Furthermore, the nucleotide sequence at the disruption site of any desired mutant was obtained by capitalizing on the differential sensitivity of the transposon and the genome to the restriction enzymeHhaI; molecular cloning or amplification by polymerase chain reaction was not required. The Tn916element has a singleHhaI site. On the other hand, this restriction enzyme frequently cleaves theP. multocidachromosome with the vast majority of the resulting genomic fragments being less than 7 kb in length. Tn916integration adds a 12 kb segment to the genomicHhaI fragment at the site of disruption. The resulting chimeric DNA fragment was isolated on the basis of size from digests of mutant genomic DNA separated on agarose gels. DNA sequencing with primers corresponding to the terminus of the Tn916element was used to determine the sequence at the disruption site. In summary, Tn916can be used to disrupt and to clone genes ofP. multocidain a rapid and facile fashion.

Allelic retrieval: a scheme to facilitate the repeated isolation of a specific segment of the Bordetella pertussis chromosome

A plasmid vector was designed, constructed, and used for the repeated retrieval of the bvgA gene from a number of Bordetella pertussis strains that, due to mutations in this gene, exhibited interesting phenotypes regarding the regulation of virulence genes. The vector was used in a scheme called allelic retrieval that exploits two cross-overs between cloned plasmid and native chromosomal sequences flanking the bvgA gene. This scheme is very similar to allelic exchange through the use of plasmid suicide vectors, but in the case presented here, the non-replicating plasmid that has received the chromosomal gene is recovered, rather than being allowed to be lost due to segregation. Incorporation of the counterselectable sacB gene of Bacillus subtilis in place of the plasmid copy of bvgA allows selection, after recovery in Escherichia coli, for only those plasmids that have retrieved the chromosomal bvgA gene. The validity of this approach was demonstrated by the retrieval of bvgA alleles with distinctive physical markers, as well as by the reintroduction of retrieved bvgA alleles to demonstrate that they conferred the expected phenotypes. It is expected that this approach will be applicable to the analysis of other genes in other bacterial species.

Vaccination against enteric pathogens: from science to vaccine trials

Recent advances in scientific research and clinical trials have shown promise for vaccine development against enteric pathogens. Identification of new virulence factors, such as the two distinct shigella enterotoxins, has allowed the development of new immunogen or new attenuated strains. Improved knowledge facilitated the development of safer attenuated live microorganism and construction of multivalent vaccines. Finally, an important advantance is the use of nonreplicating plasmid DNA vectors to express protective antigens in the host.

Analysis of promoters in Borrelia burgdorferi by use of a transiently expressed reporter gene.

A transient chloramphenicol acetyltransferase (CAT) expression system was developed for Borrelia burgdorferi. An Escherichia coli vector containing a promoterless Streptococcus agalactiae cat gene was constructed. Promoters for ospA, ospC, and flaB were placed upstream of this cat gene, and CAT assays were performed in E. coli from these stably maintained plasmids. The plasmids with putative promoters ospA and flaB were found to be approximately 20-fold more active than were the plasmids with ospC or no promoter. The level of activity correlated well with the resistance to chloramphenicol that each plasmid provided. Next, the nonreplicative plasmid constructs were transformed by electroporation into B. burgdorferi. CAT assays were performed by both thin-layer chromatography and the fluor diffusion method. Measurement of CAT activity demonstrated that the ospA promoter was again about 20-fold more active than the promoterless cat gene. The flaB and ospC promoters increased the activity seven- and threefold, respectively, over that with the promoterless construct. This simple transient-expression assay was shown to be an effective method to study promoter function in B. burgdorferi in the absence of a well-developed genetic system.

The Site-Specific Integration System of the TemperateStreptococcus thermophilusBacteriophage φSfi21

The temperate bacteriophage φSfi21 integrates its DNA into the chromosome ofStreptococcus thermophilusstrains via site-specific recombination. Nucleotide sequencing of the attachment sites identified a 40-bp identity region which surprisingly overlaps both the 18-terminal bp of the phage integrase gene and the 11-terminal bp of a host tRNAArggene. A 2.4-kb phage DNA segment, coveringattP,the phage integrase, and a likely immunity gene contained all the genetic information for faithful integration of a nonreplicative plasmid into theattBsite. A deletion within theintgene led to the loss of integration proficiency. A number of spontaneous deletions were observed in plasmids containing the 2.4-kb phage DNA segment. The deletion sites were localized to the tRNA side of the identity region and to phage or vector DNA with 3- to 6-bp-long repeats from the border region. A similar type of deletion was previously observed in a spontaneous phage mutant.

Inactivation of Streptococcus pyogenes extracellular cysteine protease significantly decreases mouse lethality of serotype M3 and M49 strains.

Cysteine proteases have been implicated as important virulence factors in a wide range of prokaryotic and eukaryotic pathogens, but little direct evidence has been presented to support this notion. Virtually all strains of the human bacterial pathogen Streptococcus pyogenes express a highly conserved extracellular cysteine protease known as streptococcal pyrogenic exotoxin B (SpeB). Two sets of isogenic strains deficient in SpeB cysteine protease activity were constructed by integrational mutagenesis using nonreplicating recombinant plasmids containing a truncated segment of the speB gene. Immunoblot analyses and enzyme assays confirmed that the mutant derivatives were deficient in expression of enzymatically active SpeB cysteine protease. To test the hypothesis that the cysteine protease participates in host mortality, we assessed the ability of serotype M3 and M49 wild-type strains and isogenic protease-negative mutants to cause death in outbred mice after intraperitoneal inoculation. Compared to wild-type parental organisms, the serotype M3 speB mutant lost virtually all ability to cause mouse death (P < 0.00001), and similarly, the virulence of the M49 mutant was detrimentally altered (P < 0.005). The data unambiguously demonstrate that the streptococcal enzyme is a virulence factor, and thereby provide additional evidence that microbial cysteine proteases are critical in host-pathogen interactions.

Role of putative virulence factors of Streptococcus pyogenes in mouse models of long-term throat colonization and pneumonia.

To investigate the role of putative virulence factors of Streptococcus pyogenes (group A streptococcus; GAS) in causing disease, we introduced specific mutations in GAS strain B514, a natural mouse pathogen, and tested the mutant strains in two models of infection. To study late stages of disease, we used our previously described mouse model (C3HeB/FeJ mice) in which pneumonia and systemic spread of the streptococcus follow intratracheal inoculation. To study the early stages of disease, we report here a model of long-term (at least 21 days) throat colonization following intranasal inoculation of C57BL/10SnJ mice. When the three emm family genes of GAS strain B514-Sm were deleted, the mutant showed no significant difference from the wild type in induction of long-term throat colonization or pneumonia. We inactivated the scpA gene, which encodes a complement C5a peptidase, by insertion of a nonreplicative plasmid and found no significant difference from the wild type in the incidence of throat colonization. However, there was a small but statistically significant decrease in the incidence of pneumonia caused by the scpA mutant. Finally, we demonstrated a very important effect of the hyaluronic acid capsule in both models. Following intranasal inoculation of mice with a mutant in which a nonreplicative plasmid was inserted into the hasA gene, which encodes hyaluronate synthase, we found that all bacteria recovered from the throats of the mice were encapsulated revertants. Following intratracheal inoculation with the hasA mutant, the incidence of pneumonia within 72 h was significantly reduced from that of the control strain (P = 0.006). These results indicate that the hyaluronic acid capsule of S. pyogenes B514 confers an important selective advantage for survival of the bacteria in the upper respiratory tract and is also an important determinant in induction of pneumonia in our model system.

Sequence and analysis of the replication region of the Staphylococcus xylosus plasmid pSX267

The region of the 29.5-kb plasmid pSX267 from Staphylococcus xylosus DSM 20267 that is required for autonomous replication in staphylococci was isolated on a 1.8-kb DNA fragment. The sequence analysis of the fragment yielded two open reading frames, repA and orf2, encoding proteins of 37.2 and 13.2 kDa, respectively. The deduced amino acid sequence of repA showed similarity to the replication initiator protein of plasmid pAD1 from Enterococcus faecalis, to two proteins of unknown function encoded by the E. faecalis plasmid pCF10 and the Lactobacillus helveticus plasmid pLJ1, and surprisingly to the mouse interferon-response element binding factor 1. The repA gene of pSX267 is indispensable for replication suggesting that it encodes the replication initiator protein of pSX267. Introduction of a frameshift mutation into repA or deletion of 26 codons at its 3'-end resulted in nonreplicative plasmids. Removal of sequences required for repA expression also abolished replication. Complementation experiments with repA in trans identified the ori of pSX267 within the repA coding region. The second orf, which is located downstream of repA, could be deleted without affecting plasmid replication. It seems to be a nonfunctional remainder of a rolling circle plasmid of the pC194/pUB110 family, since its deduced amino acid sequence resembles the pC194/pUB110-type replication proteins. The minimal replicon of pSX267 defined so far comprises 1255 bp. Besides repA, no other plasmid-encoded gene is required to mediate replication in staphylococci.

Illegitimate integration of single-stranded DNA in Saccharomyces cerevisiae.

We studied illegitimate recombination by transforming yeast with a single-stranded (ss) non-replicative plasmid. Plasmid pCW12, containing the ARG4 gene, was used for transformation of yeast strains deleted for the ARG4, either in native (circular) form or after linearization within the vector sequence by the restriction enzyme ScaI. Both circular and linearized ss plasmids were shown to be much more efficient in illegitimate integration than their double-stranded (ds) counterparts and more than two-thirds of the transformants analysed contained multiple tandem integrations of the plasmid. Pulsed-field gel electrophoresis of genomic DNA revealed significant changes in the karyotype of some transformants. Plasmid DNA was frequently detected on more than one chromosome and on mitotically unstable, autonomously replicating elements. Our results show that the introduction of nonhomologous ss DNA into yeast cells can lead to different types of alterations in the yeast genome.

Mutants of Streptococcus suis types 1 and 2 impaired in expression of muramidase-released protein and extracellular protein induce disease in newborn germfree pigs.

The contribution of muramidase-released protein (MRP) and extracellular factor (EF) to the virulence of Streptococcus suis type 1 and 2 infections was studied. For that aim, we constructed mutants of S. suis types 1 and 2 by inactivating the genes encoding MRP and EF. Moreover, we changed a type 2 strain producing the 110-kDa EF protein into a strain producing a modified protein (EF*) of increased molecular mass. The chromosomally located mrp and epf genes were inactivated by replacement recombination by using nonreplicative plasmids. Newborn germfree pigs were inoculated with pathogenic type 1 and 2 strains and with the isogenic mutant strains. Wild-type as well as mutant strains induced fever, specific signs of disease, and lesions. Moreover, all mutant strains could be reisolated from the central nervous system of infected pigs. These results showed that inactivation or alteration of the mrp and epj genes had no measurable effect on the pathogenicity of S. suis types 1 and 2.

Recombination-induced variants of Clostridium acetobutylicum ATCC 824 with increased solvent production.

Three sporulation-specific genes (orfA, sigE, sigG) from clostridium acetobutylicum ATCC 824 are arranged in a cluster, encoding the putative sigma E-processing enzyme, sigma E, and sigma sigma G respectively. When they were transformed into Clostridium acetobutylicum while on a plasmid functional in this organism, transformants did not survive. Three kinds of recombinations were then attempted with nonreplicative plasmids: duplication of orfA and sigE, replacement of all of the three genes, and inactivation of orfA. While the wild-type strain ceased to grow and produce solvents in batch cultures after approximately 24 h, mutant strains were isolated that showed sustained growth for a much longer time and produced a threefold increase in acetone and butanol in test tube cultures. In addition, one of the derived strains showed a significantly higher growth rate. Features of the restriction maps of the recombinants did not correlate with expected maps, indicating possible complications occurring during the recombination events.

Inactivation of an aldehyde/alcohol dehydrogenase gene from Clostridium acetobutylicum ATCC 824.

A nonreplicative plasmid containing an internal aad gene fragment has been integrated into the chromosome of Clostridium acetobutylicum ATCC 824. Transformation was accomplished by electroporation with relatively high concentrations of methylated plasmid DNA. Southern hybridization experiments revealed that integration occurred by single crossover homologous recombination inactivating the aad gene. Integrants were relatively stable after 25 generations. Inactivation of the aad gene drastically reduced solvent production. This result suggests that aldehyde/alcohol dehydrogenase(AAD) plays a important role in butanol production.

High-Efficiency Transfer of the T Cell Co-Stimulatory Molecule B7-2 to Lymphoid Cells Using High-Titer Recombinant Adeno-Associated Virus Vectors

Adeno-associated virus (AAV) is a single-stranded DNA virus that can either integrate or replicate in host cells. Production of recombinant viral particles (rAAV) requires expression of the viral structural genes and the viral inverted terminal repeats in cis. By using an SV40 replicon to amplify the structural genes, the yield of recombinant viral particles was increased 60-fold over a nonreplicating helper plasmid. The rAAV particles produced by this system have similar physical properties to wild-type particles, including buoyant density, size, and morphology. This novel rAAV packaging system was used to produce rAAV particles that contain the gene for the T cell co-stimulatory protein B7-2. Transduction of the human nonadherent lymphoid cell line LP-1 with these particles significantly increased the percentage of cells expressing B7-2 from 6.8% to 78.0%. Expression of B7-2 in the human lymphoid cell line RPMI-8226 was also substantially increased. Targeting of tumor cells grown in suspension was hampered by low-efficiency transduction using other viral or nonviral vector systems. Our new packaging system for recombinant AAV should allow generation of sufficient quantities of B7-2 containing particles to develop tumor vaccines for non-Hodgkin's lymphoma.

Exciting Potential of DNA Vaccines Explored

A TOTALLY new step in vaccine development is nearing clinical trials and, if successful, is headed for clinical practice. The new work may open way to preventing diseases such as hepatitis C, tuberculosis, malaria, and those caused by herpes simplex and human papilloma viruses—and even by human immunodeficiency virus (HIV). However, influenza is likely to be first candidate for clinical trial, although it may share primacy with a test of a vaccine against HIV, or perhaps hepatitis B, according to some authorities. The technology has opened way to what Maurice R. Hilleman, PhD, director, Merck Institute for Therapeutic Research, West Point, Pa, calls the future of vaccinology. The new approach involves delivering gene sequences of desired antigen into host by inserting gene for antigen via a nonreplicating plasmid vector ( JAMA . 1994;271:929-931). This is in distinction to current approach, which

In vivo growth characteristics of leucine and methionine auxotrophic mutants of Mycobacterium bovis BCG generated by transposon mutagenesis.

Insertional mutagenesis in Mycobacterium bovis BCG, a member of the slow-growing M. tuberculosis complex, was accomplished with transposons engineered from the Mycobacterium smegmatis insertion element IS1096. Transposons were created by placing a kanamycin resistance gene in several different positions in IS1096, and the resulting transposons were electroporated into BCG on nonreplicating plasmids. These analyses demonstrated that only one of the two open reading frames was necessary for transposition. A library of insertions was generated. Southern analysis of 23 kanamycin-resistant clones revealed that the transposons had inserted directly, with no evidence of cointegrate formation, into different restriction fragments in each clone. Sequence analysis of nine of the clones revealed junctional direct 8-bp repeats with only a slight similarity in target sites. These results suggest that IS1096-derived transposons transposed into the BCG genome in a relatively random fashion. Three auxotrophs, two for leucine and one for methionine, were isolated from the library of transposon insertions in BCG. They were characterized by sequencing and found to be homologous to the leuD gene of Escherichia coli and a sulfate-binding protein of cyanobacteria, respectively. When inoculated intravenously into C57BL/6 mice, the leucine auxotrophs, in contrast to the parent BCG strain or the methionine auxotroph, showed an inability to grow in vivo and were cleared within 7 weeks from the lungs and spleen.

Efficient UV stimulation of yeast integrative transformation requires damage on both plasmid strands.

The nature of UV-induced pre-recombinational structures was studied using transformation of Saccharomyces cerevisiae cells with non-replicative plasmids. Transformation by double-stranded plasmids irradiated with UV was stimulated up to 50-fold, and both plasmid integration and conversion of the mutated chromosomal selective gene were found to be equally increased. The stimulation observed with such 'totally' irradiated plasmids was not found with plasmids bearing lesions in only one strand. This effect is attributed to the formation by excision repair of recombinogenic structures consisting of a pyrimidine dimer opposite a gap. When single-stranded integrative plasmids were irradiated, their transforming potential was decreased but the proportion of transformants that arose by gene conversion, rather than by plasmid integration, was increased from 8% to 49% as a function of the UV dose. Possible reasons why single-strand UV lesions favour gene conversion are discussed.

New in-vivo cloning methods by homologous recombination in yeast

We have devised a new strategy to clone DNA sequences from an yeast autonomously-propagating plasmid into a non-autonomous integrative vector by in-vivo recombination. The method consists of a first step in which the replicative plasmid carrying the DNA fragment of interest forms a co-integrate with the non-replicative plasmid by an induced in-vivo reciprocal exchange accompanied by gene conversion. The dimeric plasmid obtained is then purified and cut with an appropriate restriction enzyme and ligated independently to obtain the two intact monomeric plasmids, the original autonomous plasmid plus the new non-autonomous plasmid carrying the subcloned DNA fragment. The dimeric co-integrate can also serve as substrate for a second in-vivo reciprocal exchange that produces new autonomous plasmids carrying the desired DNA fragment. The technique considerably expands the applications of in-vivo cloning in yeast by complementing three important characteristics of previously published methods: (1) it can be used to clone into non-propagating vectors; (2) co-transformation experiments are not required; and (3) the intermediate co-integrate can be used to generate new types of autonomously-propagating plasmids directly. These characteristics are independent of whether the DNA insert is flanked by appropriate restriction sites or whether it does, or does not, express a detectable phenotype in yeast. The method is particularly useful for the cloning of large DNA fragments and can be used for plasmids from organisms other than yeasts.

Micrococcal nuclease digestion of nuclei reveals extended nucleosome ladders having anomalous DNA lengths for chromatin assembled on non-replicating plasmids in transfected cells.

The chromatin structures of a variety of plasmids and plasmid constructions, transiently transfected into mouse Ltk- cells using the DEAE-dextran procedure, were studied by micrococcal nuclease digestion of nuclei and Southern hybridization. Although regularly arranged nucleosome-like particles clearly were formed on the transfected DNA, the nucleosome ladders, in some cases with 13-14 bands, were anomalous. Most often, a ladder of DNA fragments with lengths of approximately 300, 500, 700, 900 bp, etc. was generated. In contrast, typical 180-190 bp multiples were generated from bulk cellular or endogenous beta-actin gene chromatin. Very similar results were obtained with all DNA's transfected, and in a variety of cell lines, provided that plasmid replication did not occur. Additionally, after digestion of nuclei, about 90% of the chromatin fragments that contained transfected DNA sequences could not be solubilized at low ionic strength, in contrast with bulk cellular chromatin, suggesting association with nuclear structures or nuclear matrix. The remaining 10% of transfected DNA sequences, arising from soluble chromatin fragments, generated a typical nucleosome ladder. These results are consistent with the idea that assembly of atypical chromatin structures might be induced by proximity to elements of the nuclear pore complex or by nuclear compartmentalization.

Single strand and double strand DNA damage-induced reciprocal recombination in yeast. Dependence on nucleotide excision repair and RAD1 recombination.

Single strand and double strand DNA damage-induced recombination were compared in the yeast Saccharomyces cerevisiae. The non-replicating plasmid pUC18-HIS3 was damaged in vitro and introduced into yeast cells; plasmid-chromosome recombinants were selected as stable His+ transformants. Single strand damage was produced by UV irradiation at 254 nm or by psoralen photoreaction at 390 nm. Double strand damage was produced by psoralen photoreaction at 350 nm or by restriction endonuclease digestion. Recombinants were classified as resulting from gene conversion without crossing over, single plasmid integration, or multiple plasmid integration. Single and double strand DNA damage produced different patterns of recombination. In repair proficient cells double strand damage induced primarily multiple plasmid integrations, while single strand damage induced higher proportions of gene conversions and single integrations. Reciprocal recombination depended on the RAD1 gene, which is involved in both excision repair and recombination; plasmid integration induced by all forms of damage was decreased in a rad1 disruption strain. Mutation of the RAD3 excision repair gene decreased plasmid integration induced by far UV irradiation and psoralen crosslinks, but not by double strand breaks, which are not substrates of nucleotide excision repair. Double strand break-induced plasmid integration was also decreased by disruption of RAD10, which forms a complex with RAD1; disruption of RAD4 had no effect. Thus, while nucleotide excision repair genes are involved in the processing of damaged DNA to generate recombination intermediates, RAD1 and RAD10 are additionally involved in reciprocal exchange.