Recombination between a thermosensitive kanamycin resistance factor and a nonthermosensitive multiple-drug resistant factor

A comprehensive list of genes required for the efficient conjugation of plasmid Rts1 was determined by systematic deletion analysis

While conjugation-related genes have been identified in many plasmids by genome sequencing, functional analyses have not yet been performed in most cases, and a full set of conjugation genes has been identified for only a few plasmids. Rts1, a prototype IncT plasmid, is a conjugative plasmid that was originally isolated from Proteus vulgaris. Here, we conducted a systematic deletion analysis of Rts1 to fully understand its conjugation system. Through this analysis along with complementation assays, we identified 32 genes that are required for the efficient conjugation of Rts1 from Escherichia coli to E. coli. In addition, the functions of the 28 genes were determined or predicted; 21 were involved in mating-pair formation, three were involved in DNA transfer and replication, including a relaxase gene belonging to the MOBH12 family, one was involved in coupling, and three were involved in transcriptional regulation. Among the functionally well-analysed conjugation systems, most of the 28 genes showed the highest similarity to those of the SXT element, which is an integrative conjugative element of Vibrio cholerae. The Rts1 conjugation gene set included all 23 genes required for the SXT system. Two groups of plasmids with conjugation systems nearly identical or very similar to that of Rts1 were also identified.

Electron microscopic structures, serum resistance, and plasmid restructuring of New Delhi metallo-β-lactamase-1 (NDM-1)-producing ST42 Klebsiella pneumoniae emerging in Japan

Enterobacteriaceae, carrying the New Delhi metallo-β-lactamase-1 (NDM-1) gene (bla (NDM-1)), have emerged and posed a threat since 2006. In Japan, bla (NDM-1)-carrying Escherichia coli was first described in 2010. In this study, we characterized NDM-1-positive Klebsiella pneumoniae strain 419 in Japan, which was isolated from the urine of a 90-year-old Japanese patient who had never been to the Indian subcontinent. K. pneumoniae 419 belonged to ST42. It possessed a surface capsule (with untypeable capsular PCR types) and was resistant to serum killing. K. pneumoniae 419 cells were occasionally flagellated or piliated and autoaggregated. K. pneumoniae 419 was resistant to β-lactams (including carbapenems), aminoglycosides, and fluoroquinolones, and was susceptible to imipenem (or biapenem), aztreonam, polymixin B, and colistin. It possessed at least eight plasmids; of those, a 74-kb plasmid (pKPJ1) of the replicon FIIA carried bla (NDM-1) and was conjugally transferred to E. coli strains, with a 71-kb transferable azithromycin-resistant (mphA (+)) plasmid of the replicon F (pKPJ2), as a large (145-kb) plasmid (pKPJF100) through a transposition event. In addition to bla (NDM-1), pKPJ1 carried arr-2, pKPJ2 carried mphA, and pKPJF100 carried both. They were negative for the 16S rRNA methylase gene, e.g., which is frequently associated with bla (NDM-1). The data demonstrate that K. pneumoniae 419 possessed virulence- and fitness-associated surface structures, was resistant to serum killing, and possessed a unique (or rare) genetic background in terms of ST type and bla (NDM-1)-carrying plasmid.

Complete nucleotide sequence of plasmid Rts1: implications for evolution of large plasmid genomes

Rts1, a large conjugative plasmid originally isolated from Proteus vulgaris, is a prototype for the IncT plasmids and exhibits pleiotropic thermosensitive phenotypes. Here we report the complete nucleotide sequence of Rts1. The genome is 217,182 bp in length and contains 300 potential open reading frames (ORFs). Among these, the products of 141 ORFs, including 9 previously identified genes, displayed significant sequence similarity to known proteins. The set of genes responsible for the conjugation function of Rts1 has been identified. A broad array of genes related to diverse processes of DNA metabolism were also identified. Of particular interest was the presence of tus-like genes that could be involved in replication termination. Inspection of the overall genome organization revealed that the Rts1 genome is composed of four large modules, providing an example of modular evolution of plasmid genomes.

In vitro and in vivo transferrable beta-lactam resistance due to a new plasmid-mediated oxyiminocephalosporinase from a clinical isolate of Proteus mirabilis

A new plasmid-mediated beta-lactamase (FPM-1) with an isoelectric point of 7.2 and a molecular weight of 26,000 was found in a cefuroxime-resistant clinical isolate of Proteus mirabilis strain 6003. FPM-1 can be classified as a type I oxyimino-cephalosporinase on the basis of its substrate specificity and inhibition pattern by clavulanic acid etc., and its conferred resistance on both the strain and transconjugants against most oxyme-type cephalosporins as well as the older ones but not against cefamycins and a few exceptional oxyme-type cephalosporins such as ceftizoxime, ceftazidime and cefixime. In a murine systemic infection model, only these FPM-1-stable drugs exhibited protective activity against the FPM-1-producing P. mirabilis 6003 similar to that against a nonproducing derivative strain. The FPM-1-mediated cefuroxime resistance in P. mirabilis 6003 was transferred to co-infected Escherichia coli 7004 at frequencies between 3.8 x 10(-3) and 4.0 x 10(-2) in a murine ascending urinary tract infection model. In the same infection model due to the FPM-1-producing E. coli transconjugant, FPM-1-stable cefixime was significantly more effective than FPM-1-labile cefteram pivoxil, although both drugs had similar therapeutic effect against its FPM-1-nonproducing counterpart strain.

Identification of the Rts 1 DNA fragment responsible for temperature sensitive growth of host cells harboring a drug resistant factor Rts 1

We have placed a kanamycin resistance SalI fragment (3.65 Kb) from the drug resistance factor Rts1 into pUC19 and pBR322. These chimeric plasmids containing the kanamycin resistance fragment from Rts1 cause temperature sensitive growth in E coli. The orientation of the kanamycin resistance fragment in the vector plasmids does not influence this phenotype.

Cointegrate formation between homologous plasmids in Escherichia coli

Conjugation experiments were performed in which the donor was Escherichia coli K-12 strain KP245 containing either R plasmid NR1 plus an ampicillin-resistant derivative of ColE1 (*ColE1::Tn3, called RSF2124) or NR1 plus RSF2124 carrying a cloned EcoRI fragment of NR1. The recipient was the polA amber mutant JG112, in which RSF2124 cannot replicate. Ampicillin-resistant transconjugants can arise only when the genes for ampicillin resistance are linked to NR1 or are transposed to the host chromosome. When EcoRI fragment A of NR1 (20.5 kilobases) was cloned to RSF2124, the frequency of cotransfer of ampicillin resistance with tetracycline resistance was 25 to 60%. Plasmid DNA from these ampicillin-resistant transconjugant cells was analyzed by gel electrophoresis and was shown to be a cointegrate of NR1 and the RSF2124 derivative. Analysis of plasmid DNA isolated from donor cultures showed that the cointegrates were present before conjugation, which indicates that the mating does not stimulate cointegrate formation. When the cloned fragment was EcoRI fragment H of NR1 (4.8 kilobases), the frequency of cotransfer of ampicillin resistance with tetracycline resistance was about 4%, and the majority of the ampicillin-resistant transconjugants were found to contain cointegrate plasmids. When the donor contained NR1 and RSF2124, the frequency of cotransfer of ampicillin resistance was less than 0.1%, and analysis of plasmid DNA from the ampicillin-resistant transconjugants showed that Tn3 had been transposed onto NR1. These data suggest that plasmids which share homology may exist in cointegrate form to a high degree within a host cell.

The region controlling the thermosensitive effect of plasmid Rts1 on host growth is separate from the Rts1 replication region

Rts1 is a high-molecular-weight (126 x 10(6)) plasmid encoding resistance to kanamycin. It expresses unusual temperature-sensitive phenotypes, which affect plasmid maintenance and replication, as well as host cell growth. We have cloned the essential replication region of Rts1 from pAK8, a smaller derivative which is phenotypically similar to Rts1. Restriction endonuclease digests of isolated pAK8 deoxyribonucleic acid were allowed to "self-ligate" (ligation without an additional cloning vector) and subsequently were used to transform Escherichia coli strain 20SO to kanamycin resistance. Screening of these strains for the phenotypes of thermosensitive host growth and temperature-dependent plasmid elimination demonstrated that these two properties were expressed independently. Furthermore, it was shown that the Rts1 replication locus per se is not necessarily responsible for altered host growth at the nonpermissive temperature. The kanamycin resistance fragment of pAK8 was also cloned into pBR322. Electrophoretic analysis of BamHI restriction enzyme digests of this plasmid and similar digests of an Rts1 miniplasmid has allowed the identification of an 18.6-megadalton fragment carrying the replication locus and a 14.1-megadalton fragment carrying the kanamycin resistance gene.

Mating due to loss of surface exclusion as a cause for thermosensitive growth of bacteria containing the Rtsl plasmid

At 25 degrees C, Rtsl+ bacteria grow to about 5 X 10(9) bacterial/ml before leveling off, whereas at 42 degrees C they grow from 2.6 X 10(8) bacteria/ml for only 2-3 generations after temperature shift before the growth is inhibited with a zig-zag pattern at the plateau. When diluted, Rtsl+ bacteria grow rapidly at 42 degrees C, until the concentration reaches as high as the undiluted 42 degrees C culture when growth measured by colony counts stops and the zig-zag pattern again appears. This density-dependent growth inhibition is not due to the presence of stable growth inhibitor(s). Mating experiments show that at 42 degrees C, Rtsl+ bacteria retain good donor ability; at the same time, they become good recipients in mating with Hfr (Rtsl) bacteria. SDS-PAGE reveals that membranes are altered at 42 degrees C. Examination of DNA synthesis indicates that chromosomal DNA is synthesized at both 25 degrees C and 42 degrees C at high bacterial concentration, but that of the Rtsl plasmid is slowed down at 42 degrees C. The labeling experiments suggest that in 2 h there are 2 rounds of plasmid replication at 25 degrees C, 3.5 rounds at 42 degrees C when bacteria are diluted, and 0.6 rounds at 42 degrees C when bacteria are not diluted. These results suggest that the growth inhibition of Rtsl+ bacteria at 42 degrees C is probably the consequence of mating initiated due to loss of surface exclusion.

Bacteriophage T4-related macromolecular synthesis under restriction of plasmid Rts1

Rts1 is a plasmid which confers upon the host bacteria the capacity to restrict T4 bacteriophage growth at 32 degrees C but not at 42 degrees C. Pulse-labeling of phage-infected cells showed that Rts1 restricts the synthesis of T1 DNA. Despite efficient restriction of T4 phage growth and DNA synthesis, infected Escherichia coli 20SO harboring Rts1 synthesized both early and late T4 phage RNA. Synthesis of early T4 phage RNA under restrictive conditions (32 degrees C) was almost equal to that found under nonrestrictive conditions, and a lesser, but significant, amount of late T4 phage RNA was made in almost complete absence of T4 DNA synthesis. Moreover, very little, if any, T4 phage-coded lysozyme was detected in the infected E. coli 20SO/Rts1 at 32 degrees C, whereas normal amounts of lysozyme were present at 42 degrees C.

Further characterization of the R plasmid Rts1 and its mutant pTW2: replication and incompatibility of the plasmid

Incompatibility of the R plasmid Rts1 and its replication mutant pTW2 was studied in recA host cells of Escherichia coli. When the R plasmid R401, belonging to the same incompatibility group as Rts1, was used as a test plasmid, R401 was eliminated preferentially from (Rts-R401)+ cells irrespective of the direction of transfer. In contrast, pTW2 and R401 were mutually excluded. The decreased incompatibility of pTW2 was confirmed by a direct incompatibility test in which a derivative of Rts1 expelled pTW2 exclusively. Alkaline sucrose gradients of pTW2 and Rts1 DNA indicated that approximately one-fourth of the Rts1 genome was deleted in pTW2. In addition, both the various temperature-dependent properties of Rts1 and the inhibitory effect on phage T4 development were also lost in pTW2. A possible mechanism that regulates the stringent replication of Rts1 is discussed.

Host-dependent, thermosensitive replication of an R plasmid, pJY5, isolated from Enterobacter cloacae

The thermosensitive replication of an R plasmid, pJY5, isolated from Enterobacter cloacae, was studied. pJY5 consisted of 61 million daltons of covalently closed circular (CCC) deoxyribonucleic acid (DNA) with a buoyant density of 1.714 g/cm3 (55 mol % guanine plus cytosine). In Escherichia coli, this plasmid replicated stringently at 32 degrees C, but ceased its CCC DNA replication after a short incubation at 42 degrees C, resulting in production of R- segregants. The thermosensitive replication of pJY5 was not overcome by the coexistence of non-thermosensitive R plasmids. The plasmid manifested an inhibitory effect on host bacterial cell growth at 42 degrees C, although the effect was less prominent than that of R plasmids belonging to the T-incompatibility group, Rts1, R401, and R402. When the pJY5 plasmid was transferred into E. cloacae, however, no R- segregants were detected at any culture temperature, even 42 degrees C. Alkaline sucrose gradient analysis revealed that a significant amount of pJY5 CCC DNA was synthesized in E. cloacae at the high temperature but not in E. coli. Furthermore, the growth-inhibitory effect of pJY5 on hosts at 42 degrees C was not observed in E. cloacae. On the other hand, Rts1 and R401 were found to be thermosensitive in E. cloacae as well as in E. coli.

Replication of thermosensitive Rts1 plasmid deoxyribonucleic acid at the nonpermissive temperature

Replication of the thermosensitive drug resistance factor Rts1 was studied at the nonpermissive temperature (42 degrees C). It was concluded from the following observations that replication of this plasmid takes place at 42 degrees C without involving the covalently closed circular (CCC) form of deoxyribonucleic acid (DNA). (i) DNA-DNA- reassociation kinetics studies with purified Rts1 DNA showed that Rts1 DNA increased several-fold during cell growth at 42 degrees C while very little, if any, CCC DNA was synthesized. (ii) When Escherichia coli 20S0(Rts1) was labeled with [3H]thymidine at 42 degrees C, a significant amount of radioactive DNA hybridizable to Rts1 DNA was formed. This DNA was found in a fraction where DNA other than CCC DNA was expected in alkaline sucrose density gradient centrifugation analysis. When E. coli 20S0(Rts1) was labeled at 32 degrees C, the labeled CCC DNA did not disappear during a chase period at 42 degrees C. This indicates that preformed CCC DNA does not participate in replication at the nonpermissive temperature. These results are consistent with the hypothesis that there are two modes of replication of Rts1 DNA, one involving a CCC molecule and the other not involving this form, and that only the latter mode takes place at the nonpermissive temperature.

Incompatibility and bacteriophage inhibition properties of N-1, a plasmid belonging to the H2 incompatibility group

N-1, a plasmid isolated from a strain of Shigella flexneri in Japan more than 10 years ago, mediates the phage inhibition phenotype which has recently been found to be characteristic of plasmids of the H2 incompatibility group. Using the criteria of phage inhibition, surface exclusion and incompatibility, the N-1 plasmid is shown to be closely related to H2 plasmids isolated from non-typhoid salmonella and distantly related to H1 plasmids isolated from Salmonella typhi. Plasmids of other incompatibility groups did not show the H2 type of phage inhibition.

Temperature-sensitive R plasmid obtained from naturally isolated drug-resistant Vibrio cholerae (biotype El Tor)

A temperature-sensitive fi(-) R plasmid, pJY1, which confers resistance to chloramphenicol, streptomycin, and sulfonamide, was found in a drug-resistant strain of Vibrio cholerae (biotype El Tor) isolated in the Philippines in 1973. The R plasmid is temperature sensitive for transferability but not for stability in the hosts. pJY1 is stably maintained either in V. cholerae or in Escherichia coli at a range of culture temperatures from 27 to 42 degrees C. Compatibility tests with reference R plasmids revealed that pJY1 belongs to the J group. Growth of V. cholerae carrying pJY1 is poor on TCBS (thiosulfate-citrate-bile-sucrose) selective plates when the microbe is subcultured in nutrient broth at temperatures higher than 37 degrees C.

Chromosome-plasmid interaction in Escherichia coli K-12 carrying a thermosensitive plasmid, Rts1, in autonomous and in integrated states

An Hfr strain of Escherichia coli K-12 was obtained by integrative suppression with a thermosensitive plasmid, Rts1. The R plasmid was integrated into the chromosome between rif and thr, and transfer of the chromosome occurred counterclockwise. The thermosensitivity of host cell growth due to the dnaA mutation was markedly but not completely reduced in this integratively suppressed Hfr strain. When the dnaA mutation was removed by transducing the dnaA+ genome to this Hfr, the thermosensitivity of cell growth due to existence of Rts1 was suppressed in contrast to strains carrying it autonomously. Thermosensitivity of cell growth appeared again when the plasmid was detached from the chromosome to exist autonomously. Contrary to the effect on cell growth, the transfer of the chromosome and the plasmid itself and the ability to "restrict" T-even phages were still thermosensitive in all of these strains carrying Rts1, irrespective of its state of existence. The detached plasmid as well as the original Rts1 were segregated upon growth at 42 C. These data are discussed in relation to chromosome-plasmid interaction. One of the most important conculusions is that some plasmid genes, related to their replication, are phenotypically suppressed by the chromosome when it is integrated.

Change in the cell envelope of Escherichia coli carrying the thermosensitive drug resistance factor, Rts 1, at the nonpermissive temperature

Escherichia coli, harboring the temperature-sensitive drug-resistant factor Rts 1, formed filaments on solid medium at the nonpermissive temperature (42 C). In addition, the rate of adsorption of T4D phage progressively decreased during growth at 42 C. Susceptibility to a variety of antibiotics increased suggesting that the permeability barrier to these antibiotics may be disrupted at the nonpermissive temperature. These observations were interpreted to suggest that the target of the temperature-sensitive Rts 1 gene product responsible for altering host growth may be the cell envelope.

Integration of R plasmid Rts1 to the gal region of the Escherichia coli chromosome

An R plasmid Rts1 was integrated into the gal region of the chromosome of Escherichia coli XA-7012 (galE) strain by the directed transposition technique. The integration of the Rts1 genome was confirmed mainly by conjugation studies and also by transduction experiments using phage P1. As a result, it was found that the integrated genome contained genes responsible for kanamycin resistance, conjugal transferability, and for autonomous replication. As reported previously, Rts1 is temperature sensitive in replication and inhibits the growth of the host at nonpermissive temperature. However, although a plasmid derived from the integrated Rts1 genome still demonstrates temperature sensitivity upon transfer and high level of kanamycin resistance, this plasmid no longer displays temperature sensitivity in replication and the inhibitory effect on the host. These results indicate that the temperature sensitivity of replication of Rts1 and its inhibitory effect on the host cell are due to the presence of a gene or gene cluster on the Rts1 genome and that the gene(s) is clearly discriminated from the one responsible for the temperature sensitivity of transfer.

Host cell growth in the presence of the thermosensitive drug resistance factor, Rts1

We have confirmed and extended the observation of Terawaki et al. that the R factor, Rts1, alters the growth of its host at 42 C. In all media tested there was a period during which total cell numbers increased linearly, while viable counts remained constant. During this period the rate of precursor incorporation per cell particle into deoxyribonucleic acid, ribonucleic acid, and protein declined steadily. These patterns were a consequence of the accumulation of increasing numbers of cells which had lost colony-forming ability. A temperature shiftdown experiment showed that the colony formers could, after a lag, go on to divide normally, whereas most of the noncolony formers could not undergo even a limited number of divisions after shiftdown. The number of normal divisions which occurred after shiftup of Rts1 cells to 42 C was medium dependent. In rich medium there were, on the average, two or three doublings; in glucose medium, one; and in glycerol medium, only a fraction of a doubling. Even in glucose medium, however, no increase in viable counts was observed during growth at 42 C if the cells were first starved for glucose for 1 h at 42 C. A temperature shiftdown from 42 C to 27 C during glucose starvation reversed the effect of starvation at 42 C alone. These results are consistent with the hypothesis that the thermosensitive Rts1 component(s) responsible for the host effects is present at permissive temperature, but can undergo a reversible temperature-induced alteration which then interferes with some essential host function. The detrimental effects of this R factor on its host were also reflected in a heightened sensitivity to kanamycin and actinomycin D at 42 C. Electron microscope observations revealed changes in the appearance of the cell membrane. Membranous invaginations were noted at discrete sites in the cell.

Genetic behavior of R factors in Vibrio cholerae

The fi(+) and fi(-) R factors are unstable in Vibrio cholerae even on selective media containing antibiotics, although a temperature-sensitive kanamycin resistance factor and its recombinants are stably maintained in V. cholerae at low temperatures.

Recombination and complementation between R factors in Escheichia coli K 12

Recombination between chloramphenicol-sensitive (Cms) mutants of Rl, and R100, has been demonstrated inEscherichia coliK12rec+; it occurs at reduced frequency inrecBandrecC, and is not detectable inreeA, indicating that R factor recombination depends on host functions. Some mutants of R1 also recombine with an R100 mutant in a similar way.recAcells carrying an R1 and an R100 Cmsmutant (hetero-R state) have a low level of chloramphenicol-resistance, and form a chloramphenicol acetyl transferase that has lower specific activity than enzyme from hosts carrying wild-type or recombinant factors. These results suggest the occurrence of interallelic complementation between mutant R factors.

Facilitation of the transfer of R factor by the resident R factor

Transfer of some R factors were shown to be facilitated by resident R factors. The sex factor itself may be responsible for this phenomenon.

Base composition of deoxyribonucleic acid of the temperature-sensitive kanamycin-resistant R factor, Rts1

The buoyant density of deoxyribonucleic acid (DNA) from the temperature-sensitive R factor, Rts1, was determined by CsCl density-gradient centrifugation. Rts1 was found to consist of a single species of DNA of density 1.705 g/cm(3), which corresponds to a base composition of 45% guanine plus cytosine. This value is distinct from the densities previously reported for other R factors, suggesting that Rts1 represents a new molecular class of R factors.