Suppression of an Escherichia coli dnaA mutation by the integrated R factor R100.1: generation of small plasmids after integration

Highly repressible expression system for cloning genes that specify potentially toxic proteins

A highly repressible expression vector system that allows the cloning of potentially deleterious genes has been constructed. Undesired expression of a cloned gene was prevented (i) at the level of initiation of transcription, by the presence of the strong but highly repressible leftward promoter of bacteriophage lambda, lambda pL, and (ii) at the level of transcript elongation or translation, through synthesis of antisense RNA complementary to the mRNA of the cloned gene. The system was tested by measuring the inhibition of expression of traT, the gene for the TraT major outer membrane lipoprotein. Direct detection and functional assays indicated that an essentially complete inhibition of traT expression was obtained. As a further test of the system, the gene encoding the EcoRI restriction endonuclease was cloned in the absence of the gene of the corresponding protective EcoRI modification methylase. Transformants harboring this construct were only viable when both repression controls were operational.

Phasmid P4: manipulation of plasmid copy number and induction from the integrated state

"Phasmid" P4 is unusual in that it is capable of (i) temperate, (ii) lytic, helper-dependent, and (iii) plasmid modes of propagation. In this report we characterize most of the known P4 genetic functions as to their essential or nonessential roles in the stable maintenance of plasmid P4 vir1 (pP4 vir1 (pP4 vir1). We also identify growth conditions that can be used to stably maintain pP4 vir1 at any one of several different copy number levels (n = 1 to 3, n = 10 to 15, or n = 30 to 40). Analyses of a temperature-sensitive alpha derivative of pP4 vir1 show that shifting the temperature from 37 to 42 degrees C allows this mutant to maintain an integrated copy of the plasmid, whereas replication of free copies is repressed because of the nonpermissive condition for their DNA synthesis. Conversely, a shift from 42 to 37 degrees C can be used to reinstate plasmid propagation. The utility of the inducible states of pP4 vir1 is discussed with respect to its attributes as a vector with the potential for cloning inserts of DNA up to 33,000 base pairs in a wide range of bacterial hosts.

dnaB analog function associated with plasmid R100drd-1

Plasmid R100 and a number of its derivatives were able to suppress the temperature sensitivity of strains carrying different alleles of the dnaB gene of Escherichia coli K-12. R100drd-l and pAR132 were able to rescue a strain carrying the dnaB266(Am) mutation in the absence of any known amber suppressors. This was taken as evidence for the existence of an R100drd-l dnaB analog function. The R100drd-l dnaB analog was different from those of bacteriophages P1 and P7 in that it was able to support the growth of bacteriophage lambda in a dnaB266(Am) background. The dnaB analog was also shown to be thermosensitive. The structural gene for this protein lies within the EcoRI fragment D of R100drd-l.

Isolation of the kanamycin resistance region (Tn2350) of plasmid R1drd-19 as an autonomous replicon

We have isolated a circular form of Tn2350, an IS1-flanked kanamycin resistance transposon forming part of the plasmid R1drd-19. This circle (pTn2350::9.6 kilobases) contains a single IS1 element and probably arises by recombination between the two directly repeated Is1 sequences of Tn2350. It can be used to transform Escherichia coli to kanamycin resistance. It is capable of autonomous replication but is not maintained stably in dividing cells and segregates under nonselective conditions. Cloning of a segment of pTn2350 on a conditional plasmid vector allowed us to assign the replication functions of this plasmid to a 1.6-kilobase restriction fragment. The plasmid R1drd-19 can thus be considered as a cointegrate between two replicons separated by IS1 sequences.

The structure of R1drd19: a revised physical map of the plasmid

We have analyzed derivatives of the plasmid R1drd19 carrying the transposon Tn10 by electron microscopy following denaturation and renaturation of the molecules, and by digestion with various restriction enzymes, gel electrophoresis and Southern blotting. We show: 1) that the published restriction map of R1drd19 is inconsistent with our results. We present a modified map which is consistent with our data. 2) that R1drd19 carries a single resident copy of the element IS10 which is normally associated with Tn10 as an inverted repeat, and 3) that R1drd19 carries three copies of the insertion element IS1 in the resistance determinant region.

Production of extrachromosomal r-determinant circles from integrated R100.1: involvement of the E. coli recombination system

The drug resistance plasmid R100.1 can integrate into the E. coli chromosome at several sites on the plasmid. Many of the resulting Hfr strains continuously produce extrachromosomal circular forms of the r-determinant. These r-det 'plasmids' seem incapable of stable autonomous replication. We show that their presence in the cell requires the continuous activity of functional recA and recC genes but does not require the lexA function. The production of r-det circular forms is correlated with an increased copy number of r-det sequences, relative to RTF sequences, This copy number increase is, however, also found in a recA- background where no circular forms of r-det are found. These results show that a specific replication of r-det sequences, not present in the wild-type R100.1 plasmid, occurs in these R-Hfr strains. They suggest that a rec promoted recombination, posterior to the specific replication event, is needed for the production of circular r-det forms.

Control of plasmid R1 replication: functions involved in replication, copy number control, incompatibility, and switch-off of replication

A small derivative of plasmid R1 was used to integratively suppress a chromosomal dnaA(Ts) mutation. The strain obtained grew normally at 42 degrees C. The integratively suppressed strain was used as recipient for various plasmid R1 derivatives. Plasmid R1 and miniplasmid derivatives of R1 could be established in the strain that carried an integrated R1 replicon, but they were rapidly lost during growth. However, plasmids also carrying ColE1 replication functions were almost completely stably inherited. The integratively suppressed strain therefore allows the establishment of bacteria diploid with respect to plasmid R1 and forms a useful and sensitive system for studies of interaction between plasmid R1 replication functions. Several of the chimeric plasmids caused inhibition of growth at high temperatures. All plasmids that inhibited growth carried one particular PstI fragment from plasmid R1 (the PstI F fragment), and in all cases the growth inhibition could be ascribed to repression of initiation of chromosome replication at 42 degrees C, i.e., they carry a trans-acting switch-off function. Furthermore, the analogous PstI fragments from different copy mutants of plasmid R1 were analyzed similarly, and one mutant was found to lack the switch-off function. The different chimeric plasmids were also tested for their incompatibility properties. All plasmids that carried the switch-off function (and no other plasmids) also carried R1 incompatibility gene(s). Since the PstI F fragment, which is present on all these plasmids, is very small (0.35 x 10(6)), it is suggested that the switch-off regulation of replication (by an inhibitor), incompatibility, and copy number control are governed by the same gene.

Direction of deoxyribonucleic acid transfer and replication in a derivative of plasmid R100-1

The site of integration and the molecular orientation of a prophage Mu integrated within the resistance transfer factor component of plasmid R100-1 have been determined on the physical map of the plasmid. This allowed us (i) to determine the direction of deoxyribonucleic acid transfer from oriT during conjugation and (ii) to demonstrate the unidirectionality of replication in conditions of exponential growth (by determining the strand preference of Mu-specific Okazaki fragments).

Some properties of the chloramphenicol resistance transposon Tn9

We have isolated variants of the plasmid RTF which have received the transposon Tn9 from bacteriophage P1Cm. We have shown by the formation of heteroduplex molecules between one RTF:Tn9 derivative and R100.1 that Tn9 is homologous to the r-determinant region of R100.1 which carries the determinants for chloramphenicol resistance. This suggests that Tn9 was derived from an r-det like structure by deletion, possibly mediated by one of the flanking IS1 elements. In spite of the similarity in structure between Tn9 and r-det however, we have demonstrated two distinct differences in the behavior of these two elements: 1) Tn9 but not r-det, is able to amplify, by a recA dependent mechanism, when cells harboring RTF::Tn9 are grown in the presence of chloramphenicol, and 2) Tn9, unlike r-det, does not form extrachromosomal circular molecules when RTF::Tn9 is tegrated into the bacterial chromosome.

Characterization of R-plasmids coding for ampicillin resistance from Salmonella species

A sudden increase in the incidence of ampicillin resistance was observed among Salmonella species isolated within New Zealand in 1973--4. This increase was due mainly to the apperance and proliferation of Salmonella newington and Salmonella anatum serotypes resistant to ampicillin. The plasmid complements of 14 ampicillin-resistant S. newington and S. anatum isolates obtained from widely separated geographical areas within New Zealand between 1973 and 1974 were characterized by agarose gel electrophoresis. Each contained one or more plasmids ranging in molecular weight from 1.4 to 42 Mdal. Eleven isolates contained a self-transmissible plasmid of 33 Mdal which encoded resistance to ampicillin. After transfer to Escherichia coli, the 33 Mdal R-plasmids from each of these isolates were shown to be identical by restriction endonuclease analysis. The remaining three strains contained ampicillin R-plasmids having molecular weights of 35, 37.5 and 42 Mdal. These plasmids were shown by restriction endonuclease analysis to be related to the 33 Mdal R-plasmid. We conclude that the 33 Mdal plasmid and its derivatives were responsible for the increase in the incidence of ampicillin-resistant S. newington and S. anatum serotypes among the total Salmonella population.

The effects of an Escherichia coli dnaAts mutation on the replication of the plasmids colE1 pSC101, R100.1 and RTF-TC

The rate of replication of the plasmids colE1, pSC101, R100.1 and pAR132 (an RTF-TC derivative of the drug resistance factor R100.1) has been investigated directly by DNA:DNA hybridization. These rates have been compared, in a dnaAts strain, to that of various markers of the host chromosome at permissive and non-permissive temperatures. Chromosome initiation in the dnaAts strain stops rapidly after a shift to the non-permissive temperature, but plasmids R100.1 and pAR132 do not seem to be affected directly and continue replication for some time. The colE1 replication rate undergoes a large increase after the temperature shift, followed by a rapid decrease to a very low level 25 min after the shift. In contrast pSC101 replication stops immediately after the shift. ColE1 is able to replicate in an integratively suppressed dnaAts strain at 42 degrees C whereas pSC101 stops replication immediately under these conditions. We conclude that R100.1 and its derivative RTF-TC can replicate without a functional dnaA product; that colE1, while affected by a shift in temperature in a dnaAts strain, does not directly require dnaA; and that the plasmid pSC101 has an absolute requirement for dnaA. The absolute requirement of pSC101 for dnaA in the integratively suppressed Hfr strain provides a useful system for further investigation of the dnaA function.

Tn10 mediated integration of the plasmid R100.1 into the bacterial chromosome: inverse transposition

Upon integration into the bacterial chromosome the drug resistance plasmid R100.1 often loses its tetracycline resistance character. We have analyzed an Hfr strain formed by such an integration and an R-prime plasmid derived from it. We find that integration took place within the Tn10 transposon, that the two IS10 sequences were retained, but that at least 80% of the transposon segment located between them, and carrying the tetracycline resistance genes, had been lost. We suggest that integration of R100.1 was mediated by an inverse transposition using the IS10 sequences.

The contruction and replication properties of hybrid plasmids composed of the r-determinant of R100.1 and the plasmids pCRI and pSC201

We have cloned the entire r-determinant of the antibiotic resistance plasmid R100.1 on the plasmic vectors pCR1 and pSC201. We find that the hybrid plasmids segregate from cultures in which replication of the vector is blocked. This suggests that the r-det is not capable of autonomous replication.

Cloning and characterization of EcoRI and HindIII restriction endonuclease-generated fragments of antibiotic resistance plasmids R6-5 and R6

DNA fragments generated by the EcoRI of HindIII endonucleases from the low copy number antibiotic resistance plasmids R6 and R6-5 were separately cloned using the high copy number ColE1 or pML21 plasmid vectors and the insertional inactivation procedure. The hybrid plasmids that were obtained were used to determine the location of the EcoRI and HindIII cleavage sites on the parent plasmid genomes by means of electron microscope heteroduplex analysis and agarose gel electrophoresis. Ultracentrifugation of the cloned fragments in caesium chloride gradients localized the high buoyant density regions of R6-5 to fragments that carry the genes for resistance to streptomycin-spectinomycin, sulfonamide, and mercury and a low buoyant density region to fragments that carry the tetracycline resistance determinant. Functional analysis of hybrid plasmids localized a number of plasmid properties such as resistances to antibiotics and mercury and several replication functions to specific regions of the R6-5 genome. Precise localisation of the genes for resistance to chloramphenicol, kanamycin, fusidic acid and tetracycline was possible due to the presence of identified restriction endonuclease cleavage sites within these determinants. Only one region competent for autonomous replication was identified on the R6-5 plasmid genome and this was localized to EcoRI fragment 2 and HindIII fragment 1. However, two additional regions of replication activity designated RepB and RepC, themselves incapable of autonomous replication but capable supporting replication of a linked ColE1 plasmid in polA- bacteria, were also identified.

Mapping of the drug resistance genes carried by the r-determinant of the R100.1 plasmid

We have cloned the EcoRI fragments of pLC1, a circular DNA element found in an Escherichia coli dnaAts strain integratively suppressed by R100.1 (Chandler et al., 1977a), using the plasmid vector pCR1. All the resistance genes known to be present on the r-determinant of R100.1 were found to be present on pLC1. The isolation of pCR1 derivatives carrying various EcoRI fragments of either pLC1 or R100.1 has allowed a more precise mapping of the position of the resistance genes on the R100.1 molecule.

Origin and direction of replication of the drug resistance plasmid R100.1 and of a resistance transfer factor derivative in synchronized cultures

The origin and direction of replication of the resistance plasmid R100.1 and its resistance transfer factor derivative, pAR132, were studied by electron microscopy autoradiography of partially denatured molecules and partial denaturation mapping of replicative intermediates. Results of these studies indicate the existence of an origin of replication at 8.8 kilobases on the R100 map. Replication from this origin in cultures synchronized for initiation of replication is predominantly unidirectional in a single direction.

Suppression of an Escherichia coli dnaA mutation by the integrated R factor R100.1: origin of chromosome replication during exponential growth

We have investigated the behavior, during exponential growth, of strains of Escherichia coli carrying a dnaA(Ts) mutation that has been suppressed by the integration of the F-like R plasmid R100.1. We present evidence showing that replication in these strains proceeds largely from the normal chromosome origin at 30 degrees C, a permissive temperature for the dnaA(Ts) gene product, whereas, at 42 degrees C, replication proceeds largely from the integrated plasmid. These conclusions are based on measurements made by deoxyribonucleic acid:deoxyribonucleic acid hybridization of the relative frequencies of the prophages Mu-1 and lambdaind- and R100.1 integrated at known locations on the E. coli chromosome in these Hfr strains.

Involvement of IS1 in the dissociation of the r-determinant and RTF components of the plasmid R100.1

The formation of the r-determinant pLC1 and of the RTF pAR132 from the composite plasmid R100.1 was investigated. The general location of IS1 sequences on the three plasmids was established by hybridization of lambdar14 CII::IS1 DNA to EcoRI generated fragments of the various plasmids separated by agarose gel electrophoresis and transferred directly to nitrocellulose filters. The position of IS1 sequences on these fragments and the homologies between fragments were analyzed by electron microscopy of heteroduplex molecules. The results show that the excision of both pLC1 and pAR132 occurred by an exchange between the two IS1 sequences present on R100.1.