Efficient introduction of cloned mutant alleles into the Escherichia coli chromosome.

An efficient method for moving mutations in cloned Escherichia coli DNA from plasmid vectors to the bacterial chromosome was developed. Cells carrying plasmids that had been mutated by the insertion of a resistance gene were infected with lambda phage containing homologous cloned DNA, and resulting lysates were used for transduction. Chromosomal transductants (recombinants) were distinguished from plasmid transductants by their ampicillin-sensitive phenotype, or plasmid transductants were avoided by using a recBC sbcB E. coli strain as recipient. Chromosomal transductants were usually haploid when obtained in a nonlysogen because of selection against the lambda vector and partially diploid when obtained in a lysogen. Pure stocks of phage that carry the resistance marker and transduce it at high frequency were obtained from transductant bacteria. The lambda-based method for moving mutant alleles into the bacterial chromosome described here should be useful for diverse analyses of gene function and genome structure.     

Identification and mapping of the replication genes of an R factor, R100-1, integrated into the chromosome of Escherichia coli K-12

A stable Hfr strain of Escherichia coli K-12 was obtained by integrative suppression by an R factor, R100-1. The R factor was integrated into the right of 81 min, and chromosome transfer occurred counterclockwise. Mating experiments revealed two linkage groups of genes on the R factor. Drug-resistant transductants of a dnaA-ts recipient from an R-factor Hfr and from an R(+) strain differ in their drug resistance patterns, temperature sensitivity, and transferability of drug resistance as well as chromosome markers. Transductants that transferred chromosome markers were further classified as to the origin and direction of chromosome transfer. For temperature-sensitive transductants, the reversion frequency to temperature resistance was determined, and these revertants were scored for transfer of drug resistance as well as chromosome markers. Two genes responsible for integrative suppression (designated as repA) and the other for autonomous replication (designated as repB) were identified and mapped. The arrangement of genes on the R factor is... (sul, str, cml)... repA... tra... (tet, repB).... The map of the autonomously replicating R factor is probably a circle connecting both sides of this linear map. Thus, a method has been established to map a plasmid that could not finely be analyzed under autonomous state by transduction. It also permits genetic analysis of genes responsible for replication of the plasmid without making use of a conditional mutant of itself but with that of the host, dnaA.     

Transduction of concatemeric plasmids containing the cos site of Lactococcus lactis bacteriophage sk1

Lactococcus lactis bacteriophage sk1 can transduce plasmids containing the phage cos site and surrounding DNA sequences at frequencies as high as 2x10(-3) transductants per PFU. Deletion analysis demonstrated that the presence of phage DNA spanning cos and putative R sites were the most important for efficient plasmid transduction. Inserts of 440 bp containing cos and the R sites were sufficient to induce transduction frequencies of 10(-4) transductants per PFU. The role of the R1 site was investigated by altering 14 of the 19 bases in the site. This resulted in a two-fold decrease in transduction frequency compared to a 26-fold decrease in transduction following deletion of the entire site. It was demonstrated that transducing plasmids were packaged as linear trimeric concatemers commencing at the cos site.     

Transduction of R plasmids by bacteriophages P1 and P22

Summary We demonstrated that bacteriophages P1 and P22 were able to form various types of hybrids with six out of seven different R plasmids tested. When the same R plasmid was used for isolation, P1-R hybrids usually carried more resistance markers than P22-R. Several genetical observations suggest that the hybrid prophages carried the resistance markers transposed to the phage genomes without loss of essential phage genes. Upon UV-irradiation the prophages produced phage lysates that transduced the relevant resistance markers at high frequencies by lysogenic conversion. The insertion of the resistance markers was even acquired by the P1 or P22 genomes during one-step growth in R⁺ cells. Some lytically prepared lysates grown on R⁺ cells contained the hybrids at a frequency of 10^-7 to 10^-6/plaqueforming unit. Analysis of P1-transductants for resistance markers of the R plasmids revealed in some cases more specialized transductants than generalized transductants. These results strongly indicate that a precise genetic map of an R plasmid can not be established only on the basis of co-transduction frequencies of the resistance markers of the R plasmid.     

Transduction of penicillinase production and other antibiotic-resistance markers in Staphylococcus epidermidis.

Transduction of resistance from a multiply antibiotic-resistant strain of Staphylococcus epidermidis sub-group II was studied using the typing phage 108. The effect of increasing doses of ultraviolet radiation on the transducing phage was used to indicate the chromosomal or plasmid nature of the genes. Tetracycline and chloramphenicol resistance behaved as plasmid genes and streptomycin resistance as a chromosomal marker. It was also possible to transduce penicillin resistance (Pc) due to penicillinase production (bla+) using a low level of benzylpenicillin (0.03 microgram ml-1) for recovery. Approximately 10(-5) transductant colonies per phage input were obtained and ultraviolet kinetics indicated that Pc was plasmid carried. Pc transductants fell into two categories. In one group PC was stable as in the donor strain and transductants had the same phage sensitivity as the recipient. In the other, Pc was unstable at 37 degrees C and the instability was enhanced by growth at approximately 43.5 degrees C; these transductants also gained genes for restriction and modification of certain phages. Transductants that subsequently lost bla+ also lost the restriction and modification characters.     

Identification of the partitioning site within the repABC-type replicon of the composite Paracoccus versutus plasmid pTAV1

The replicator region of composite plasmid pTAV1 of Paracoccus versutus (included in mini-replicon pTAV320) belongs to the family of repABC replicons commonly found in plasmids harbored by Agrobacterium and Rhizobium spp. The repABC replicons encode three genes clustered in an operon, which are involved in partitioning (repA and repB) and replication (repC). In order to localize the partitioning site of pTAV320, the two identified incompatibility determinants of this mini-replicon (inc1, located in the intergenic sequence between repB and repC; and inc2, situated downstream of the repC gene) were PCR amplified and used together with purified RepB fusion protein (homologous to the type B partitioning proteins binding to the partitioning sites) in an electrophoretic mobility shift assay. The protein bound only inc2, forming two complexes in a protein concentration-dependent manner. The inc2 region contains two long (14-bp) repeated sequences (R1 and R2). Disruption of these sequences completely eliminates RepB binding ability. R1 and R2 have sequence similarities with analogous repeats of another repABC replicon of plasmid pPAN1 of Paracoccus pantotrophus DSM 82.5 and with centromeric sequences of the Bacillus subtilis chromosome. Excess RepB protein resulted in destabilization of the inc2-containing plasmid in Escherichia coli. On the other hand, the inc2 region could stabilize another unstable replicon in P. versutus when RepA and RepB were delivered in trans, proving that this region has centromere-like activity. Thus, it was demonstrated that repA, repB, and inc2 constitute a functional system for active partitioning of pTAV320.     

Transduction of certain genes by an autonomously replicating Bacillus thuringiensis phage.

A derivative of Bacillus thuringiensis subsp. kurstaki HD1 (HD1-9) released transducing phage (TP21) from late exponential cultures. Three of seven markers tested were transduced into Bacillus cereus, but only two of these (cysC and trpB/F) were transduced at a frequency of more than 100 times the reversion rates. A limited transduction capacity was given further support in that few chromosomal markers were carried in the HD1-9 lysate, as demonstrated by Southern hybridization. Restriction fragments from the phage DNA and from total B. thuringiensis DNA hybridized to an insertion sequence (IS231-like) probe, which may provide a region of homology for transduction. All of the B. cereus transductants contained the phage as a 44-kb plasmid, and each could transduce both the cys and trp genes to other B. cereus auxotrophs, albeit at lower frequencies than those for the B. thuringiensis transducing phage. In some cases, especially for cys, the transduced gene was integrated into the chromosome of the recipient, whereas the trp gene in many cases appeared to be lost with curing of the 44-kb plasmid. In addition, some B. cereus transductants lost prototrophy but retained a 44-kb plasmid, consistent with the presence of TP21 helper phage. These phage may mediate the subsequent transduction from B. cereus phototrophs. TP21 replicates as a plasmid and, at least under the conditions studied, selectively transfers markers to B. cereus.     

Transduction of Pseudomonas aeruginosa with a mutant of bacteriophage E79.

A mutant of the virulent bacteriophage E79 was isolated which mediated generalized transduction in Pseudomonas aeruginosa. Variable recovery of transductants as a result of phage killing was avoided by the use of recipients carrying the IncP-2 plasmid R38, and transduction frequencies of 4 X 10(-6) to 1 X 10(-5) per plaque-forming unit were obtained. Linkage studies have indicated that the coinheritance frequencies are less than would be expected from the published molecular weight of E79 deoxyribonucleic acid (120 X 10(6). By using recipients carrying R38, low-frequency transduction by wild-type E79 and two other virulent phages, F8 and phi 16, was demonstrated.     

Transduction of certain genes by an autonomously replicating Bacillus thuringiensis phage

A derivative of Bacillus thuringiensis subsp. kurstaki HD1 (HD1-9) released transducing phage (TP21) from late exponential cultures. Three of seven markers tested were transduced into Bacillus cereus, but only two of these (cysC and trpB/F) were transduced at a frequency of more than 100 times the reversion rates. A limited transduction capacity was given further support in that few chromosomal markers were carried in the HD1-9 lysate, as demonstrated by Southern hybridization. Restriction fragments from the phage DNA and from total B. thuringiensis DNA hybridized to an insertion sequence (IS231-like) probe, which may provide a region of homology for transduction. All of the B. cereus transductants contained the phage as a 44-kb plasmid, and each could transduce both the cys and trp genes to other B. cereus auxotrophs, albeit at lower frequencies than those for the B. thuringiensis transducing phage. In some cases, especially for cys, the transduced gene was integrated into the chromosome of the recipient, whereas the trp gene in many cases appeared to be lost with curing of the 44-kb plasmid. In addition, some B. cereus transductants lost prototrophy but retained a 44-kb plasmid, consistent with the presence of TP21 helper phage. These phage may mediate the subsequent transduction from B. cereus phototrophs. TP21 replicates as a plasmid and, at least under the conditions studied, selectively transfers markers to B. cereus.     

Low-frequency, pbsi-mediated plasmid transduction in Bacillus pumilus.

Three bacteriophages were tested for ability to transduce the plasmid of pPL10 between W mutant derivatives of Bacillus pumilus NRS 576. Phage PBP1- and PMB1-generated plasmid transductants occurred at about 10% the frequency of transductants for a chromosome marker. Phage PBS1-generated plasmid transductants occurred at less than 0.1% the frequency of transductants for a chromosome marker. Possible reasons for the extremely reduced capacity of PBS1 to generate plasmid transductants are discussed.     

Sequence, identification and effect on conjugation of the rmoA gene of plasmid R100-1

The rmoA gene was recently identified from two partially overlapping sequences corresponding to a region close to the end of the tra operon of plasmid R100. Its putative amino acid sequence showed strong homology to the Hha protein of Escherichia coli and YmoA protein of Yersinia enterocolitica, which are modulators of gene expression in response to environmental stimuli. We have cloned the rmoA gene from plasmid R100-1 in pUC19 and obtained the complete nucleotide sequence, which was previously published only partially and may have contained some mistakes. The rmoA gene product has been identified in radiolabelled minicells as a protein of the predicted molecular mass. The wild-type rmoA gene of plasmid R100-1 has been mutated by gene replacement and its effect on the efficiency of conjugation has been analysed. When grown in LB medium, cells harbouring R100-1 plasmid with a disrupted copy of rmoA showed a five-fold increase in conjugation frequency compared to cells harbouring R100-1 plasmid with the wild-type rmoA gene, grown in the same conditions. When cells were grown in NaCl-free LB medium they showed a 50-fold increase in conjugation frequency.     

Impaired Transduction of R213 and Its Recovery by a Homologous Resident R Factor

Transduction by Plkc of drug-resistance markers of the factor R213 was shown to occur at an exceptionally low frequency (at less than 10(-8) of the input phage), and they could not be transduced by P22. When the recipient cells carried a homologous R factor derived from R213, markers were transduced by Plkc at a normal frequency (at about 10(-5) to 10(-6) of the input phage). Derivative R factors, transducible by Plkc at a normal frequency but being transferred by conjugation at a frequency lower than that of the original R213, were obtained. This type of transductant often segregated R(-) cells. In addition, several transductants contained R factors which were transferred normally by conjugation but were transduced by Plkc at as low a frequency as the original R213. This type of transductant was an effective recipient for transduction by Plkc of R213 when apparently "cured" by acridine treatment. No such effective "cured" recipients were obtained from the transductants with derivatives of R213 transducible at a normal frequency. Two possible interpretations are presented: (i) R213 produces a bacteriocin-like substance upon transduction, or (ii) the genome size of R213 is too large for all of its determinants to be transduced.     

Reduced recovery of plasmid transconjugants in crosses with Escherichia coli rho mutant recipients.

In crosses between Escherichia coli donors bearing conjugative plasmids and recipients carrying mutant rho alleles, the yield of transconjugants was almost always depressed in comparison with the isogenic rho⁺ strain. The effect was no longer shown by Rho⁺ revertants and segregated with the rho allele in transductional crosses. In cases where a rho⁺ transduction recipient carried R100 or derivatives of R1 (all of which show the effect in extreme degree), no rho^? transductants were obtained, suggesting that the combination of this plasmid with a chromosomal rho mutation adversely affects colony forming ability.     

Deletions in the r-determinant mer region of plasmid R100-1 selected for loss of mercury hypersensitivy.

A mutant of plasmid R100-1, which conferred cellular hypersensitivity to Hg2+ because of the insertion of Tn801 (TnA) into the gene determining synthesis of mercuric reductase enzyme, allowed further mutational events to be selected which resulted in either reversion to Hg2+ resistance (characteristic plasmid R100-1) or sensitivity at a level characteristic of plasmidless strains. Restriction endonuclease EcoRI and BamHI analysis showed that reversion to resistance resulted from loss of TnA from the R100-mer:Tn801 plasmid, whereas the change from hypersensitivity to sensitivity to Hg2+ usually resulted from deletion of part or all of Tn801 plus plasmid deoxyribonucleic acid sequences corresponding to the operator-proximal end of the mer operon.     

Complete nucleotide sequences of 84.5- and 3.2-kb plasmids in the multi-antibiotic resistant Salmonella enterica serovar Typhimurium U302 strain G8430

The multi-antibiotic resistant (MR) Salmonella enterica serovar Typhimurium phage type U302 strain G8430 exhibits the penta-resistant ACSSuT-phenotype (ampicillin, chloramphenicol, streptomycin, sulfonamides and tetracycline), and is also resistant to carbenicillin, erythromycin, kanamycin, and gentamicin. Two plasmids, 3.2- and 84.5-kb in size, carrying antibiotic resistance genes were isolated from this strain, and the nucleotide sequences were determined and analyzed. The 3.2-kb plasmid, pU302S, belongs to the ColE1 family and carries the aph(3')-I gene (Kan(R)). The 84.5-kb plasmid, pU302L, is an F-like plasmid and contains 14 complete IS elements and multiple resistance genes including aac3, aph(3')-I, sulII, tetA/R, strA/B, bla(TEM-1), mph, and the mer operon. Sequence analyses of pU302L revealed extensive homology to various plasmids or transposons, including F, R100, pHCM1, pO157, and pCTX-M3 plasmids and TnSF1 transposon, in regions involved in plasmid replication/maintenance functions and/or in antibiotic resistance gene clusters. Though similar to the conjugative plasmids F and R100 in the plasmid replication regions, pU302L does not contain oriT and the tra genes necessary for conjugal transfer. This mosaic pattern of sequence similarities suggests that pU302L acquired the resistance genes from a variety of enteric bacteria and underscores the importance of a further understanding of horizontal gene transfer among the enteric bacteria.     

Origin of transfer of IncF plasmids and nucleotide sequences of the type II oriT, traM, and traY alleles from ColB4-K98 and the type IV traY allele from R100-1.

The complete nucleotide sequences of the ColB4-K98 (ColB4) plasmid transfer genes oriT, traM, and traY as well as the traY gene of R100-1 are presented and compared with the corresponding regions from the conjugative plasmids F, R1, and R100. The sequence encoding the oriT nick sites and surrounding inverted repeats identified in F was conserved in ColB4. The adenine-thymine-rich sequence following these nick sites was conserved in R1 and ColB4 but differed in F and R100, indicating that this region may serve as the recognition site for the traY protein. A series of direct repeats unique to the ColB4 plasmid was found in the region of dyad symmetry following this AT-rich region. This area also encodes 21-base-pair direct repeats which are homologous to those in F and R100. The traM gene product may bind in this region. Overlapping and following these repeats is the promoter(s) for the traM protein. The traM protein from ColB4 is similar to the equivalent products from F, R1, and R100. The traY protein from ColB4 is highly homologous to the R1 traY gene product, while the predicted R100-1 traY product differs at several positions. These differences presumably define the different alleles of traM and traY previously identified for IncF plasmids by genetic criteria. The translational start codons of the ColB4 and R100-1 traY genes are GUG and UUG, respectively, two examples of rare initiator codon usage.     

TraM of plasmid R1 controls transfer gene expression as an integrated control element in a complex regulatory network

Site-directed mutagenesis was used to investigate the functions of the traM gene in plasmid R1-mediated bacterial conjugation. Three mutant alleles, a null mutation, a sense mutation and a stop mutation, were recombined back into the R1-16 plasmid, a transfer-derepressed ( finO  ⁻) variant of plasmid R1. The frequency of conjugative transfer of the traM null mutant derivative of R1-16 was 10⁷-fold lower than that of the isogenic parent plasmid, showing the absolute requirement for this gene in conjugative transfer of plasmid R1. Measurements of the abundance of plasmid specified traJ , traA and traM mRNAs, TraM protein levels, and complementation studies indicated that the traM gene of plasmid R1 has at least two functions in conjugation: (i) positive control of transfer gene expression; and (ii) a function in a process distinct from gene expression. Since expression of the negatively autoregulated traM gene is itself affected positively by the expression of the transfer operon genes, this gene constitutes a decisive element within a regulatory circuit that co-ordinates expression of the genes necessary for horizontal DNA transfer. Based on our studies, we present a novel model for the regulation of the transfer genes of plasmid R1 that might also be applicable to other IncF plasmids.