Replication control functions of plasmid R1 act as inhibitors of expression of a gene required for replication

Plasmid R1--replication and its control

Plasmid R1 is a low-copy-number plasmid belonging to the IncFII group. The genetics, biochemistry, molecular biology, and physiology of R1 replication and its control are summarised and discussed in the present communication. Replication of R1 starts at a unique origin, oriR1, and proceeds unidirectionally according to the Theta mode. Plasmid R1 replicates during the entire cell cycle and the R1 copies in the cell are members of a pool from which a plasmid copy at random is selected for replication. However, there is an eclipse period during which a newly replicated copy does not belong to this pool. Replication of R1 is controlled by an antisense RNA, CopA, that is unstable and formed constitutively; hence, its concentration is a measure of the concentration of the plasmid. CopA-RNA interacts with its complementary target, CopT-RNA, that is located upstream of the RepA message on the repA-mRNA. CopA-RNA post-transcriptionally inhibits translation of the repA-mRNA. CopA- and CopT-RNA interact in a bimolecular reaction which results in an inverse proportionality between the relative rate of replication (replications per plasmid copy and cell cycle) and the copy number; the number of replications per cell and cell cycle, n, is independent of the actual copy number in the individual cells, the so-called +n mode of control. Single base-pair substitutions in the copA/copT region of the plasmid genome may result in mutants that are compatible with the wild type. Loss of CopA activity results in (uncontrolled) so-called runaway replication, which is lethal to the host but useful for the production of proteins from cloned genes. Plasmid R1 also has an ancillary control system, CopB, that derepresses the synthesis of repA-mRNA in cells that happen to contain lower than normal number of copies. Plasmid R1, as other plasmids, form clusters in the cell and plasmid replication is assumed to take place in the centre of the cells; this requires traffic from the cluster to the replication factories and back to the clusters. The clusters are plasmid-specific and presumably based on sequence homology.

Eclipse period during replication of plasmid R1: contributions from structural events and from the copy-number control system

The eclipse period (the time period during which a newly replicated plasmid copy is not available for a new replication) of plasmid R1 in Escherichia coli was determined with the classic Meselson-Stahl density-shift experiment. A mini-plasmid with the wild-type R1 replicon and a mutant with a thermo-inducible runaway-replication phenotype were used in this work. The eclipses of the chromosome and of the wild-type plasmid were 0.6 and 0.2 generation times, respectively, at temperatures ranging from 30 degrees C to 42 degrees C. The mutant plasmid had a similar eclipse at temperatures up to 38 degrees C. At 42 degrees C, the plasmid copy number increased rapidly because of the absence of replication control and replication reached a rate of 350-400 plasmid replications per cell and cell generation. During uncontrolled replication, the eclipse was about 3 min compared with 10 min at controlled replication (the wild-type plasmid at 42 degrees C). Hence, the copy-number control system contributed significantly to the eclipse. The eclipse in the absence of copy-number control (3 min) presumably is caused by structural requirements: the covalently closed circular plasmid DNA has to regain the right degree of superhelicity needed for initiation of replication and it takes time to assemble the initiation factors.

Molecular clocks reduce plasmid loss rates: the R1 case

Plasmids control their replication so that the replication frequency per plasmid copy responds to the number of plasmid copies per cell. High sensitivity amplification in replication response to copy number deviations generally reduces variation in copy numbers between different single cells, thereby reducing the plasmid loss rate in a cell population. However, experiments show that plasmid R1 has a gradual, insensitive replication control predicting considerable copy number variation between single cells. The critical step in R1 copy number control is regulation of synthesis of a rate-limiting cis-acting replication protein, RepA. De novo synthesis of a large number of RepA molecules is required for replication, suggesting that copy number control is exercised at multiple steps. In this theoretical kinetic study we analyse R1 multistep copy number control and show that it results in the insensitive replication response found experimentally but that it at the same time effectively prohibits the existence of only one plasmid copy in a dividing cell. In combination with the partition system of R1, this can lead to very high segregational stability. The R1 control mechanism is compared to the different multistep copy number control of plasmid ColE1 that is based on conventional sensitivity amplification. This implies that while copy number control for ColE1 efficiently corrects for fluctuations that have already occurred, R1 copy number control prevents their emergence in cells that by chance start their cycle with only one plasmid copy. We also discuss how regular, clock-like, behaviour of single plasmid copies becomes hidden in experiments probing collective properties of a population of plasmid copies because the individual copies are out of phase. The model is formulated using master equations, taking a stochastic approach to regulation, but the mathematical formalism is kept to a minimum and the model is simplified to its bare essence. This simplicity makes it possible to extend the analysis to other replicons with similar design principles.

Inhibition and restart of initiation of chromosome replication: effects on exponentially growing Escherichia coli cells

Escherichia coli strains in which initiation of chromosome replication could be specifically blocked while other cellular processes continued uninhibited were constructed. Inhibition of replication resulted in a reduced growth rate and in inhibition of cell division after a time period roughly corresponding to the sum of the lengths of the C and D periods. The division inhibition was not mediated by the SOS regulon. The cells became elongated, and a majority contained a centrally located nucleoid with a fully replicated chromosome. The replication block was reversible, and restart of chromosome replication allowed cell division and rapid growth to resume after a time delay. After the resumption, the septum positions were nonrandomly distributed along the length axis of the cells, and a majority of the divisions resulted in at least one newborn cell of normal size and DNA content. With a transient temperature shift, a single synchronous round of chromosome replication and cell division could be induced in the population, making the constructed system useful for studies of cell cycle-specific events. The coordination between chromosome replication, nucleoid segregation, and cell division in E. coli is discussed.

Control of replication of plasmid R1: the intergenic region between copA and repA modulates the level of expression of repA

The RepA protein of plasmid R1 is rate-limiting for initiation of R1 replication. Its synthesis is mainly regulated by interactions of the antisense RNA, CopA, with the leader region of the RepA mRNA, CopT. This work describes the characterization of several mutants with sequence alterations in the intergenic region between the copA gene and the repA reading frame. The analysis showed that most of the mutations led both to a decrease in stability of maintenance of mini-R1 derivatives and to lowered repA expression assayed in translational repA-lacZ fusion constructs. Destruction of the copA gene and replacement of the upstream region by the tac promoter in the latter constructs indicated that these mutations per se alter the expression of repA. In addition, we show that particular mutations in this region can directly affect CopA-mediated control, either by changing the kinetics of interaction of CopA RNA with the RepA mRNA and/or by modifying the activity of the copA promoter. These data indicate the importance of the region analysed in the process that controls R1 replication.

Isolation and characterization of a conditional replication mutant of the antibiotic resistance factor R1 affected in the gene of the replication protein repA

In vitro mutagenesis with hydroxylamine of a ParD- miniderivative of R1, pAB174, yielded mutants that were less stable in the cell than pAB174. Some of these mutants had a thermosensitive phenotype. The replication of pAB2623, one of the thermosensitive mutants, was inhibited in the cell at the restrictive temperature of 42 degrees C. The efficiency of the RepA protein of pAB2623 to promote replication of R1 in an in vitro assay was greatly reduced. Sequence analysis indicated that the repA gene of pAB2623 contains, close to its 3' end, two GC-AT transitions, separated by a single base, that change two consecutive codons of the gene. These results indicate that the phenotype of the mutant is the consequence of a mutated RepA protein and is consistent with the requirement of RepA for the in vivo replication of this plasmid.

Heat stress in the presence of low RNA polymerase activity increases chromosome copy number of Escherichia coli

A temperature shift-up accompanied by a reduction in RNA polymerase activity in Escherichia coli causes an increased rate of initiation leading to a 1.7- to 2.2-fold increase in chromosome copy number. A temperature shift-up without a reduction in polymerase activity induces only a transient non-scheduled initiation of chromosome replication caused by heat shock with no detectable effect on chromosome copy number.

Microcin B17, a novel tool for preparation of maxicells: identification of polypeptides encoded by the IncFII minireplicon pMccB17

The DNA replication inhibitor peptide microcin B17 is shown to be a useful tool for preparing Escherichia coli maxicells. To illustrate its usefulness, we have identified polypeptides synthesized from pMccB17 and R100 IncFII miniplasmids. After comparing the respective polypeptides and the miniplasmid restriction maps, we concluded that these plasmids share extensive homology in the basic replicon but are different for an adjacent region (parD) that is involved in plasmid stability and maintenance.

Identification of components of a new stability system of plasmid R1, ParD, that is close to the origin of replication of this plasmid

We provide evidence that a mutation which derepresses an autoregulated system that is located in the vicinity of the basic replicon of R1, stabilizes the ParA- and ParB- miniplasmid of R1 pKN1562, without increasing its copy number. The system, which we have called ParD, maps inside the 1.45-kb PstI-EcoRI fragment that is adjacent to the origin of replication of the plasmid. Two proteins whose expression is coordinated are components of the system. The sequence of the PstI-EcoRI fragment was obtained. The wild-type ParD system determines in cis a basal but detectable stability.

Genetic analysis of the parB+ locus of plasmid R1

Plasmid R1 in Escherichia coli carries two loci which independently contribute to the stable maintenance of the plasmid. A genetic analysis of one of these, parB+, was carried out, and it was shown that the minimal region exerting stabilizing activity comprises at most 580 bp. The nucleotide sequence of the parB+ locus was determined, and indicated the presence of two genes, of which one probably codes for a 52 amino acid polypeptide, whereas the other gene product may be an untranslated RNA. These suggestions, based on the nucleotide sequence information, were supported by gene expression studies employing lac fusions. An incompatibility phenotype connected to parB+ was localized to that part of the 580 bp parB+ region which seems to encode the untranslated RNA.

Identification and characterization of mutations responsible for a runaway replication phenotype of plasmid R1

Initiation of replication of the resistance plasmid R1 is carefully regulated by the two negatively acting factors, CopA and CopB. It is shown here that the temperature-dependent runaway-replication phenotype of an R1 plasmid mutant is caused by two point mutations in each of the promoters for the genes of these control factors. Expression of the two genes is affected in the following way: (1) one C-to-T transition in the putative -35 box of the copB-repA operon creates a two- to three-fold stronger promoter from which expression is temperature-dependent; (2) another C-to-T transition in a G + C-rich area immediately downstream from the -10 box of the copA promoter reduces expression of the copA gene three-fold. The phenotypic consequences of the two mutations are discussed in the light of the current model for R1 replication control.

Enhanced instability of IncFII basic replicon by the polA mutation

IncFII plasmids consisting of a basic replicon and of an additional fragment(s) unrelated to plasmid maintenance were all less stable in polA1 than in its wild type. Reversion to UV-resistance recovered stability and vice versa. UV irradiation promoted instability in polA1 cells. Larger plasmids showed a greater instability and a fewer number of copies in a same host. Surprisingly, polA1 cells with Tn3 on the plasmid showed a higher ampicillin resistance than the wild type, apparently suggesting that the polA1 mutation increases the copy number. The size-dependency of instability was less marked in polA1 than in its parent. Comparison of the generation times has suggested a detrimental effect exerted by a basic replicon in polA1 hosts.

Partitioning of plasmid R1. Structural and functional analysis of the parA locus

The stability locus, parA+, of plasmid R1 is shown to be localized within a 1500 base-pair region of DNA on the largest EcoRI restriction fragment of plasmid R1. The nucleotide sequence of the region revealed the presence of two open reading frames, one of 320 codons, and another of 60 codons. The larger open reading frame encodes a polypeptide of 36,000 Mr. Deletions covering the promoter distal end of the 36,000 Mr reading frame give rise to synthesis of large amounts of truncated protein. Construction of promoter fusions between the parA+ promoter and the lacZ gene showed that the parA+ region encodes a factor that negatively regulates the expression of the 36,000 Mr protein. The locus exerting parA+-associated incompatibility, denoted incA+, was mapped to a 60 base-pair region covering the parA+ promoter. Most likely, this region is involved both in the negative regulation of the parA+ operon and in the parA+-associated incompatibility. Two explanations are suggested to explain this possible dual function of the parA+ promoter region. The parA+ region was cloned into an unstably inherited (par-) derivative of a mini-F derivative. The low copy number plasmid mini-F devoid of its own partition genes was stabilized more than 100-fold by carrying the parA+ genes. This observation is in accordance with the proposal that the parA+ locus specifies the true partition function of plasmid R1.

Incompatibility repressor in a RepA-like replicon of the IncFI plasmid ColV2-K94

The replication region Rep1 of the IncFI plasmid ColV2-K94 was cloned on self-replicating restriction fragments. Rep1 was structurally and functionally homologous to the RepA replicon of IncFII R plasmids. Despite this close relationship, these two replication systems were compatible with each other. The nucleotide sequence of the copA incompatibility-replication control gene of Rep1 was determined and compared with the copA sequence of RepA. Six base changes were found in a 24-base-pair span of the copA gene; these may result in the formation of a new, more stable, 49-base stem-loop structure in the potential CopA RNA repressor molecule. We postulate that these alterations weaken the interaction between RNA transcripts of the Rep1 and RepA replicons.

Purification and characterization of the CopB replication control protein, and precise mapping of its target site in the R1 plasmid

The CopB regulatory loop from plasmid R1 has been analyzed. The CopB protein was partially purified, but proteolytic activity in vitro resulted in the recovery of two molecular forms of the polypeptide. Both of these acted as repressors of the repA promoter and had identical activities. The smaller of the proteins was found to be the result of a specific cleavage in the normal in vivo translation product. The active form of the CopB protein is most likely a tetramer, which binds to a DNA region overlapping the repA promoter that also contains a stretch of dyad symmetry. Footprinting analysis and mutant analysis (including nucleotide sequence determination) identified this binding site within 20-25 base pairs. In agreement with in vivo results the binding between CopB and its target site is moderate compared with other operons like lac and trp.

Two functions of the E protein are key elements in the plasmid F replication control system

By using a plasmid carrying a translational fusion between the E gene of the IncFI plasmid F and the lacZ gene, we located the operator of the autogenously regulated E gene to an inverted repeat overlapping the E-gene promoter and showing perfect homology to part of the sequence found in all the direct repeats of two regions exerting an inhibitory effect on F replication, incB and incC. Excess E protein provided in trans to an F plasmid increased the replication frequency of the F plasmid. This stimulatory effect was counteracted by increased dosages of incB or incC. A model is proposed for the replication control system of F in which the key elements are autoregulation of E-gene expression and titration of E protein by incB and incC.

Incompatibility mutants of IncFII plasmid NR1 and their effect on replication control

DNA from the replication control region of plasmid NR1 or of the Inc- copy mutant pRR12 was cloned into a pBR322 vector plasmid. These pBR322 derivatives were mutagenized in vitro with hydroxylamine and transformed into Escherichia coli cells that harbored either NR1 or pRR12. After selection for the newly introduced pBR322 derivatives only, those cells which retained the unselected resident NR1 or pRR12 plasmids were examined further. By this process, 134 plasmids with Inc- mutations in the cloned NR1 or pRR12 DNA were obtained. These mutants fell into 11 classes. Two of the classes had plasmids with deletions or insertions in the NR1 DNA and were not examined further. Plasmids with apparent point mutations were classified by examining (i) their ability to reconstitute a functional NR1-derived replicon (Rep+ or Rep-), (ii) the copy numbers of the Rep+ reconstituted replicons, (iii) the cross-reactivity of incompatability among the various mutant classes and parental plasmids, and (iv) the trans effects of the mutants on the copy number and stable inheritance of a coresident plasmid.

DNA-protein interactions during replication of genetic elements of bacteria

Specific interactions of DNA with proteins are required for both the replication of deoxyribonucleic acid proper and its regulation. Genetic elements of bacteria, their extrachromosomal elements in particular, represent a suitable model system for studies of these processes at the molecular level. In addition to replication enzymes (DNA polymerases), a series of other protein factors (e.g. topoisomerases, DNA unwinding enzymes, and DNA binding proteins) are involved in the replication of the chromosomal, phage and plasmid DNA. Specific interactions of proteins with DNA are particularly important in the regulation of initiation of DNA synthesis. Association of DNAs with the cell membrane also plays an important role in their replication in bacteria.

Transcription and its regulation in the basic replicon region of plasmid R1

The transcriptional units in the basic replicon of plasmid R1 were defined by means of gene fusions. It was found that in the wild-type plasmid there is one large mRNA encoding both the control factor copB and the positive replication factor repA. A second, internal transcription initiation site, the repA promoter, is usually repressed by the copB protein, and is therefore only of significance in the absence of this control factor. By induction of the repA promoter through gradual dilution of the copB repressor it was shown that translation of repA-mRNA, controlled by the copA-RNA, is significantly increased only when the rate of repA transcription is above a certain level. No indication was found for a possible interference from convergent copA transcription on repA transcription.

Analysis of the individual regulatory components of the IncFII plasmid replication control system

Replication of the IncFII plasmid NR1 is controlled by regulating the amount of synthesis of the repA1 initiator protein at both the transcriptional and translational levels. We have examined mutations which have altered each of these levels of regulation, resulting in different plasmid copy numbers. The genes which encode each of the individual wild-type or mutant regulatory components from the replication control region of NR1 have been cloned independently into pBR322 vectors, and their effects in trans, either individually or in various combinations, on plasmid incompatibility, stability, copy number, and repA1 gene expression have been defined.

Stable inheritance of plasmid R1 requires two different loci

The largest EcoRI fragment from plasmid R1 mediates a stability phenotype which is required to ensure the stable inheritance of this low-copy-number plasmid. When covalently linked to small, unstable R1 derivatives, this fragment makes the plasmids as stable as the wild-type R1 plasmid. A genetic analysis showed that two independently acting stabilization functions are encoded by this EcoRI fragment, both of which have the potential of partial stabilization of mini-R1 plasmids. The two loci are located at opposite ends of the fragment. Stabilization was also obtained by inserting these regions in unrelated, unstable plasmids from the p15 group. One of the two functions was very efficient in stabilizing such foreign replicons. Besides the stability phenotype, these genes exert incompatibility in an allele-specific manner. The stability functions do not seem to interfere seriously with the copy number of the plasmid.

IncFII plasmid incompatibility product and its target are both RNA transcripts

The region of DNA coding for incompatibility (inc) and copy number control (cop) of the IncFII plasmid NR1 is transcribed in both the rightward and leftward directions. The rightward transcripts serve as mRNA for the repA1 protein, which is required for replication. A small, 91-base leftward transcript is synthesized from the opposite DNA strand and is complementary to a portion of the rightward mRNA near its 5' end. A 262-base-pair Sau3A restriction fragment that encodes the small leftward transcript, but does not include the rightward transcription promoters, was cloned into the vector pBR322 or pUC8. The same fragment was cloned from an Inc- mutant of NR1 that does not make the small leftward transcript. Transcription through the cloned fragments in these derivatives was under control of the tetracycline resistance gene in pBR322 or the lac promoter-operator in pUC8. In one orientation of the inserted DNA, a hybrid transcript containing rightward NR1 RNA sequences was synthesized. In the other orientation, a hybrid transcript containing leftward NR1 RNA sequences was synthesized. These plasmids were used to vary the intracellular levels of the rightward or leftward NR1 RNA transcripts and to test their effects in trans on various coresident derivatives of NR1. An excess of rightward NR1 RNA in trans stimulated expression of the essential repA1 gene and caused an increase in the copy number of a coresident NR1 plasmid. An excess of leftward NR1 RNA in trans inhibited the expression of the repA1 gene and lowered the coresident NR1 copy number, thereby causing incompatibility. A pBR322 derivative with no transcription through the cloned NR1 DNA had no effect in trans. These results suggest that the small leftward transcript is the incompatibility inhibitor of NR1 and that its target is the complementary portion of the rightward mRNA.

Control of replication of bacterial plasmids: genetics, molecular biology, and physiology of the plasmid R1 system

Plasmids are autonomously replicating DNA molecules that are present in defined copy numbers in bacteria. This number may for some plasmids be very low (2-5 per average cell). In order to be stably inherited, replication and partitioning of the plasmid have to be strictly controlled. Plasmids carry genetic information for both processes. In the present paper we summarize what is known about the replication control system of one low-copy-number plasmid, R1, belonging to the FII incompatibility group. We do so because the FII group seems to be one of the best understood examples with respect to genetics, molecular biology, and physiology of the replication control system. The paper is not a classical review, but rather an essay in which we discuss the aspects of replication control that we regard as being important.

Initiation of plasmid R1 replication in vitro is independent of transcription by host RNA polymerase

A Sau3A fragment containing most of the repA gene of plasmid R1 has been cloned in the BamH1 site of the expression vector pAS1. One of the recombinants, pSO1, codes for a fused RepA' protein which is efficiently synthesized both in vivo and in vitro from transcriptional and translational signals of the vector. It is shown that following pSO1 promoted accumulation of RepA' in cell-free extracts of E. coli, in vitro replication of the R1 miniplasmid pKN182 can initiate and proceed uncoupled from further protein synthesis. Using this uncoupled system and also a M13mp9 based ori-R1 recombinant, pRD95, it is also shown that RepA' acts at the origin region of R1 to promote initiation of replication that is independent on transcription by host RNA polymerase. This is indicated by the insensitivity of pRD95 and pKN182 replication to rifampicin as well as to RNA polymerase antibodies. The properties of the uncoupled in vitro replication system are further described.

How the R1 replication control system responds to copy number deviations

The copy number of R1 and of a repA-lacZ gene fusion was increased above normal by coupling to a plasmid which is present at a fivefold higher copy number at 30 degrees C. This carrier plasmid is deficient in replication at 42 degrees C, and it was thus possible after a temperature shift to analyze the response to the increased plasmid concentration of the R1 replication control system. Both the frequency of replication per plasmid molecule and the rate of repA expression per gene copy were reduced under these conditions, and the data strongly suggest that there is an inverse proportionality between the specific rate of plasmid replication viz repA expression and the copy number/gene dosage of the plasmid.

Copy mutants of plasmid R1: effects of base pair substitutions in the copA gene on the replication control system

Five different copA copy mutants of plasmid R1 have been identified by nucleotide sequencing. Independent measurements of the activities of the mutant inhibitor RNA and of the mutant target properties were carried out using several different methods. Correlation of these measurements with the location of th nucleotide substitutions resulted in the following conclusions: (1) The copy number of plasmid R1 is controlled primarily by interaction between the CopA RNA molecule and its target, the RepA mRNA. (2) The binding of th inhibitor to its target is based on nucleotide interactions within two complementary sequences of ten nucleotides and dependent on the secondary structure of the active site. (3) The secondary structure of both the CopA target and the CopA RNA is a stem-loop structure. Mutations in the loop region interfere with binding affinity between inhibitor and target, whereas mutations in the upper stem mainly interfere with secondary structure. Mutations in the latter region create temperature-dependent copy number phenotypes.

Low-copy-number plasmid-cloning vectors amplifiable by derepression of an inserted foreign promoter

By insertion of a DNA fragment, containing the phage lambda pR promoter and the pM-promoted cI857 allele of the lambda repressor gene, in plasmid R1 upstream of the replication control genes, cloning vectors have been constructed which are present in one copy per chromosome at temperatures below 37 degrees C, and which display uncontrolled replication at 42 degrees C. Derivatives have been made which carry the R1 par region, stabilizing the plasmid at low temperature when grown in the absence of selection pressure. Cells harbouring these plasmids stop growing after 1-2 h incubation at 42 degrees C, and at this time 50% of the total DNA in the cells is plasmid DNA corresponding to more than 1000 plasmid molecules per cell. Concomitant with plasmid amplification at the high temperature, synthesis of plasmid-coded gene products is amplified, and these vectors can therefore be utilized for obtaining greatly enhanced yields of gene products that may be detrimental to the host cell when present in large amounts.

Replication of the broad host range plasmid RSF1010: requirement for three plasmid-encoded proteins

Cloning of specific regions of plasmid RSF1010, in conjunction with in vitro replication studies, has revealed three novel genes: repA, repB, and repC. They are clustered in one region of the plasmid, separated from the origin of replication by regions that are not essential for plasmid viability in an Escherichia coli host. In vivo, a 2.1-kilobase segment of the plasmid, bearing the replication origin, can establish itself as an autonomous replicon if the DNA region carrying the three rep genes is present in the same cell on an independent plasmid. In vitro, RSF1010 DNA is efficiently replicated by an ammonium sulfate fraction from the E. coli extract, provided the extracts are prepared from cells that can supply the required rep gene products. Using cells containing the cloned rep gene region as a source of elevated levels of the rep proteins, we have partially purified these proteins in functional form. When added to an enzyme fraction derived from plasmid-free cells, they specifically promote the replication of plasmid DNA bearing the RSF1010 origin.

Definition of oriR, the minimum DNA segment essential for initiation of R1 plasmid replication in vitro

The 3.6-kilobase Bgl II-EcoRI fragment from R1 plasmid containing copA, repA, and the replication origin (ori) was inserted into the ColE1-type plasmid pUC8. The resulting hybrid plasmid replicates in extracts prepared from both polA- and polA+ cells, whereas pUC8 replicates only in a polA+ extract. This characteristic provides a method for assaying the repA and ori functions. Hybrid plasmids that were either repA- or ori- were unable to replicate in a polA- cell extract. Replication of the repA- ori+ plasmid was restored by complementation of the repA defect by a repA+ ori- plasmid in vitro. Successful complementation of the repA function in vitro provides a method for assaying the repA protein. In order to define the minimum DNA segment with origin function (oriR), deletions were introduced starting from either side of the insert, and the replication properties of the plasmids carrying these deletions were examined in a polA- cell extract. The right end of oriR was located at position 1,611 in the nucleotide coordinates defined previously [Ryder, T., Rosen, J., Armstrong, K., Davidson, D. & Ohtsubo, E. (1981) in The Initiation of DNA Replication: ICN-UCLA Symposia on Molecular and Cellular Biology, ed. Ray, D.S. (Academic, New York), Vol. 22, 91-111]. By complementing repA- ori+ plasmids with the repA+ ori- plasmid, the left end of oriR was localized at position 1,424. Therefore, the oriR sequence, localized within a region of 188 base pairs, is separate from the repA gene. A hybrid plasmid carrying the 206-base-pair segment between positions 1,406 and 1,611 also replicates in a polA- cell extract when the repA function is supplied in trans. Removal of an additional 66 base pairs (positions 1,406-1,471) inactivates the function of the minimal oriR segment.

Gene fusion vectors based on the gene for staphylococcal protein A

Two plasmid vectors, containing the gene coding for staphylococcal protein A and adapted for gene fusion, have been constructed. These vectors will allow fusion of any gene to the protein A gene, thus giving hybrid proteins which can be purified, in a one-step procedure, by IgG affinity chromatography. As an example of the practical use of such vectors, the protein A gene has been fused to the lacZ gene of Escherichia coli. E. coli strains containing such plasmids produce hybrid proteins with both IgG binding and beta-galactosidase activities. The hybrid protein(s) can be immobilized on IgG-Sepharose by its protein A moiety with high efficiency without losing its enzymatic activity and they can be eluted from the column by competitive elution with pure protein A. The fused protein(s) also binds to IgG-coated microtiter wells which means that the in vivo product can be used as an enzyme conjugate in ELISA tests.

Further studies on the inviability of Escherichia coli K12 rho mutant strains carrying IncFII plasmids

Previous results (Baumberg and Lovett 1977) showed that many conjugative plasmids, most notably those of the IncFII group, were only transferable to Escherichia coli K12 rho mutants at very low frequencies, and that this appeared to be due to a lethal interaction between plasmid and rho- allele. Experiments reported here were designed to examine this phenomenon further, and in particular to test the possibility that uncontrolled plasmid replication in the presence of the rho mutant allele occurs. The rifampicin resistance allele rpo203 antagonizes the effect of rho201 on conjugal plasmid transfer; since the former is known to counteract the latter's effect on transcription termination, this result indicates that the plasmid-rho interaction stems directly from the lack of transcription termination caused by a rho mutant allele. Direct estimation of Rldrd19 replication after conjugal transfer to rho+ and rho201 recipients showed no difference according to rho status. Also, cotransduction of rho101 and 201 with ilv::Tn5 into recipients carrying miniplasmid derivatives of R1, which retain a restriction fragment containing all the DNA known to be involved in plasmid replication, was normal and the rho- transductants retained the miniplasmids. It therefore appears that the lethal interaction between the Inc FII plasmids and rho mutant alleles does not involve plasmid replication functions.

Replication of plasmid R1: Meselson-Stahl density shift experiments revisited

Meselson-Stahl density shift experiments have been used extensively to study selection and timing of plasmid replication. Experiments with plasmid R1 were previously performed and the conclusion was that this plasmid replicates one copy at a time and that there is an eclipse period after each replication during which no further replications can take place in the cell (Nordström et al., Plasmid 1, 187-203 (1978)). However, this interpretation is in conflict with other data, mainly with those obtained in copy number shift experiments (Gustafsson and Nordström, J. Bacteriol. 141, 106-110 (1980)). However, the density shift experiments have now been reinterpreted such that there no longer is any conflict with the copy number shift experiments. There does not seem to be any such eclipse period, but newly replicated plasmid molecules are not available for a second replication for about 20% of a generation time.

The incompatibility product of IncFII R plasmid NR1 controls gene expression in the plasmid replication region

The incompatibility properties of IncFII R plasmid NR1 were compared with those of two of its copy number mutants, pRR12 and pRR21. pRR12 produced an altered incompatibility product and also had an altered incompatibility target site. The target site appeared to be located within the incompatibility gene, which is located more than 1,200 base pairs from the plasmid origin of replication. The incompatibility properties of pRR21 were indistinguishable from those of NR1. Lambda phages have been constructed which contain the incompatibility region of NR1 or of one of its copy mutants fused to the lacZ gene. In lysogens constructed with these phages, beta-galactosidase was produced under the control of a promoter located within the plasmid incompatibility region. Lysogens containing prophages with the incompatibility regions from pRR12 and pRR21 produced higher levels of beta-galactosidase than did lysogens containing prophages with the incompatibility region from the wild-type NR1. The introduction into these inc-lac lysogens of pBR322 plasmids carrying the incompatibility regions of the wild-type or mutant plasmids resulted in decreased levels of beta-galactosidase production. For a given lysogen, the decrease was greater when the pBR322 derivative expressed a stronger incompatibility toward the plasmid from which the fragment in the prophage was derived. This suggested that the incompatibility product acts on its target to repress gene expression in the plasmid replication region.

The sites of action of the two copy number control functions of plasmid R1

Two negatively acting functions - the CopA-RNA and the CopB protein - are involved in the control of replication of plasmid R1. They both act as inhibitors of expression of a gene, repA, which seems to be positively required for autonomous plasmid replication. Here we show that the two control functions act separately and independently. The CopB protein represses initiation of transcription of the repA gene, and its target site lies within a 60 base pair region containing the repA promoter. The CopA-RNA acts downstream of the repA promoter in the leader sequence containing the copA gene itself, preceding the repA structural gene. Measurements of RepA-beta-galactosidase expression from wild-type and a copA mutant fusion hybrid in the presence of extra copies of the respective copA genes show that a point mutation affecting the activity of the CopA-RNA can also affect CopA target properties. It is therefore concluded that the target site for the CopA-RNA resides within the copA gene in a small region encoding the loop of a stem-loop structure in the CopA-RNA. In addition, the data indicate a direct nucleic acid-nucleic acid interaction as the basis for the CopA inhibitor activity.

Expression of a copy number control gene (copB) of plasmid R1 is constitutive and growth rate dependent

The copy number control gene copB from plasmid R1 was fused to the lacZ gene in vitro, resulting in expression of a fused polypeptide consisting of the first 53 amino acids of the CopB polypeptide and the beta-galactosidase polypeptide minus its first 8 amino acids. Based on measurements of specific activities of this fused protein under various conditions, it was concluded that expression of copB is gene dosage dependent, unregulated by plasmid-coded functions, and proportional to growth rate between 0.4 and 2.0 doublings per h. The rate of expression of the copB gene is surprisingly high compared with other known cases of regulatory proteins.

Molecular cloning and functional characterization of a copy number control gene (copB) of plasmid R1

Deletions or insertions in the copB gene of plasmid R1 result in a copy mutant phenotype. The wild-type copB gene has been cloned on various plasmid vectors. The presence of such chimeric plasmids reduced the copy number of R1 copB mutant plasmids to normal or subnormal levels, indicating the expression of a trans-acting inhibitor activity from the copB chimeras. However, the cloned copB gene did not affect the copy number of wild-type R1, and no incompatibility was exerted by the cloned copB gene against wild-type R1 (or R100). Although the copB gene is not normally required for the incompatibility exerted by copA, it is shown that the CopB function is required for expression of incompatibility by the copA gene from some types of chimeric plasmids. Mutant plasmids that have lost both Cop functions replicate in an uncontrolled fashion.

Coding sequence for the pT181 repC product: a plasmid-coded protein uniquely required for replication

pT181 is a 4.4-kilobase plasmid from Staphylococcus aureus specifying tetracycline resistance and present in about 20 copies per cell. The existence of a diffusible pT181 product required for plasmid replication has been proposed on the basis of trans-complementable thermosensitive mutants defective in plasmid maintenance (phenotype Tsr). In this report, the Tsr mutants are shown to have primary replication defects, and the genetic complementation data are confirmed biochemically. All of five mutations are in a single cistron, the repC cistron; interruption of the plasmid DNA molecule at any of three neighboring restriction sites inactivates repC function. Analysis of the DNA sequence in this region reveals an open reading frame of 939 base pairs which encodes the repC product, a 313-amino acid protein. pT181 replication has been demonstrated in cell-free extracts to require specifically a pT181-coded protein of approximately the same size, and it is proposed that this protein is, indeed, the repC product. Preliminary evidence is discussed suggesting that the pT181 replication rate is controlled at the level of synthesis of the repC protein.