Replication of colicin E1 plasmid DNA in vivo requires no plasmid-encoded proteins

Characterization of a minimal pKW2124 replicon from Weissella cibaria KLC140 and its application for the construction of the Weissella expression vector pKUCm1

A 2.1-kb plasmid was previously isolated from Weissella cibaria KLC140 in kimchi and cloned into pUC19 along with the slpA and gfp genes, resulting in an 8.6-kb pKWCSLGFP construct for use as a novel surface display vector. To reduce the size of the vector, the minimal replicon of pKW2124 was determined. The pKW2124 plasmid contains a putative origin of replication (ori), a potential ribosomal binding site (RBS), and the repA gene encoding a plasmid replication protein. To conduct the minimal replicon experiment, four different PCR products (MR1, ori+RBS+repA; MR2, RBS+repA; MR2’, repA; MR3, fragment of repA) were obtained and cloned into pUC19 (pKUCm1, pKUCm2, pKUCm2’, and pKUCm3, respectively) containing the chloramphenicol acetyltransferase (CAT) gene. These constructed vectors were electroporated into W. confusa ATCC 10881 with different transformation efficiencies of 1.5 × 10⁵ CFU/μg, 1.3 × 10¹ CFU/μg, and no transformation, respectively, suggesting that the putative ori, RBS, and repA gene are essential for optimum plasmid replication. Subsequent segregational plasmid stability testing of pKUCm1 and pKUCm2 showed that the vector pKUCm1 is highly stable up to 100 generations but pKUCm2 was completely lost after 60 generations, suggesting that the putative ori may be important for plasmid stability in the host strain. In addition, a host range test of pKUCm1 revealed that it has a broad host range spectrum including Weissella, Lactococcus, Leuconostoc, and even Lactobacillus. To verify the application of pKUCm1, the β-galactosidase gene and its promoter region from W. cibaria KSD1 were cloned in the vector, resulting in pKUGal. Expression of the β-galactosidase gene was confirmed using blue-white screening after IPTG induction. The small and stable pKUGal vector will be useful for gene transfer, expression, and manipulation in the Weissella genome and in other lactic acid bacteria.

A novel high-copy plasmid, pEC, compatible with commonly used Escherichia coli cloning and expression vectors

A 66164-bp cryptic plasmid, pEIB1, was isolated from strain Vibrio anguillarum MVM425 and sequenced. A plasmid carrying a 1089-bp fragment, containing the minimal replication region of pEIB1, a kanamycin-resistance marker and an L-arabinose promoter, designated pEC, was maintained as a high copy plasmid in E. coli and stably inherited in the absence of antibiotic selection. Significantly, pEC was compatible with the widely used ColE1, pSC101 and p15A replicons making it a useful tool for a dual-plasmid expression system.

Adenosine monophosphate-induced amplification of ColE1 plasmid DNA in Escherichia coli

ColE1 plasmid copy number was analyzed in relaxed (relA) and stringent (relA(+)) Escherichia coli cells after supplementation of culture media with adenosine monophosphate (AMP). When a relaxed E. coli strain bearing ColE1 plasmid was cultured in LB medium for 18 h and induced with AMP for 4h, the plasmid DNA yield was significantly increased, from 2.6 to 16.4 mgl(-1). However no AMP-induced amplification of ColE1 plasmid DNA was observed in the stringent host. Some plasmid amplification was observed in relA mutant cultures in the presence of adenosine, while adenine, ADP, ATP, ribose, potassium pyrophosphate and sodium phosphate caused a minor, if any, increase in ColE1 copy number. A mechanism for amplification of ColE1 plasmid DNA with AMP in relA mutant bacteria is suggested, in which AMP interferes with the aminoacylation of tRNAs, increases the abundance of uncharged tRNAs, and uncharged tRNAs promote plasmid DNA replication. According to this proposal, in relA(+) cells, the AMP induction could not increase ColE1 plasmid copy number because of lower abundance of uncharged tRNAs. Our results suggest that the induction with AMP can be used as an effective method of amplification of ColE1 plasmid DNA in relaxed strains of E. coli.

Processing of plasmid DNA with ColE1-like replication origin

With the increasing utilization of plasmid DNA as a biopharmaceutical drug, there is a rapidly growing need for high quality plasmid DNA for drug applications. Although there are several different kinds of replication origins, ColE1-like replication origin is the most extensively used origin in biotechnology. This review addresses problems in upstream and downstream processing of plasmid DNA with ColE1-like origin as drug applications. In upstream processing of plasmid DNA, regulation of replication of ColE1-like origin was discussed. In downstream processing of plasmid DNA, we analyzed simple, robust, and scalable methods, which can be used in the efficient production of pharmaceutical-grade plasmid DNA.

Relatedness of chromosomal and plasmid DNAs of Erwinia pyrifoliae and Erwinia amylovora

The plant pathogen Erwinia pyrifoliae has been classified as a separate species from Erwinia amylovora based in part on differences in molecular properties. In this study, these and other molecular properties were examined for E. pyrifoliae and for additional strains of E. amylovora, including strains from brambles (Rubus spp.). The nucleotide composition of the internal transcribed spacer (ITS) region was determined for six of the seven 16S-23S rRNA operons detected in these species with a 16S rRNA gene probe. Each species contained four operons with a tRNA(Glu) gene and two with tRNA(Ile) and tRNA(Ala) genes, and analysis of the operons from five strains of E. amylovora indicated a high degree of ITS variability among them. One tRNA(Glu)-containing operon from E. pyrifoliae Ep1/96 was identical to one in E. amylovora Ea110, but three tRNA(Glu) operons and two tRNA(Ile) and tRNA(Ala) operons from E. pyrifoliae contained unique nucleotide changes. When groEL sequences were used for species-specific identification, E. pyrifoliae and E. amylovora were the closest phylogenetic relatives among a set of 12 bacterial species. The placement of E. pyrifoliae distinct from E. amylovora corroborated molecular hybridization data indicating low DNA-DNA similarity between them. Determination of the nucleotide sequence of plasmid pEP36 from E. pyrifoliae Ep1/96 revealed a number of presumptive genes that matched genes previously found in pEA29 from E. amylovora and similar organization for the genes and origins of replication. Also, pEP36 and pEA29 were incompatible with clones containing the reciprocal origin regions. Finally, the ColE1-like plasmid pEP2.6 from strain Ep1/96 contained sequences found in small plasmids in E. amylovora strains IL-5 and IH3-1.

ColE1-like plasmid pIP843 of Klebsiella pneumoniae encoding extended-spectrum beta-lactamase CTX-M-17

The resistance of Klebsiella pneumoniae BM4493, isolated in Ho Chi Minh City, Vietnam, to cefotaxime and aztreonam was due to production of a novel beta-lactamase, CTX-M-17. The bla(CTX-M-17) gene was borne by 7,086-bp plasmid pIP843, which was entirely sequenced and which was found to belong to the ColE1 family. The 876-bp bla(CTX-M-17) gene differed from bla(CTX-M-14) by 2 nucleotides, which led to the single amino acid substitution Glu289-->Lys. bla(CTX-M-17) was flanked upstream by an ISEcp1-like element and downstream by an insertion sequence (IS) IS903 variant designated IS903-C. The transcriptional start site of bla(CTX-M-17) was located 109 nucleotides upstream from the initiation codon in the ISEcp1-like element, which also provided the promoter sequences. Plasmid pIP843, which was non-self-transferable and nonmobilizable, contained five open reading frames transcribed in the same orientation. Regions homologous to sequences coding for putative RNA II and RNA I transcripts, a rom gene, which is involved in initiation of replication, and a cer-like gene, which is responsible for the stability of ColE1-like plasmids, were identified. Consensus sequences for putative replication (oriV) and transfer (oriT) origins were present. Results of primer extension experiments indicated that ISEcp1 provides the promoter for expression of bla(CTX-M-17) and may contribute to dissemination of this gene.

Replication of plasmids during bacterial response to amino acid starvation

Amino acid starvation of bacterial cells leads to expression of the stringent (in wild-type strains) or relaxed (in relA mutants) response (also called the stringent or relaxed control, respectively). The stringent control is a pleiotropic response which changes drastically almost the entire cell physiology. Although starvation is a rule rather than an exception in natural environments of bacteria, and DNA replication is a fundamental cell process, until recently our knowledge about regulation of DNA replication in amino acid-starved cells has been unexpectedly poor. Within recent years the stringent control of DNA replication has been investigated mainly on plasmid models. Several plasmid replicons have been studied, including oriC plasmids, ColE1-like replicons, pSC101, F, R1, RK2, and R6K, and plasmids derived from bacteriophages lambda and P1. However, molecular models of replication regulation in amino acid-starved cells have been proposed to date only for lambda plasmids and ColE1-like replicons. Although further extensive studies are necessary in the understanding of molecular mechanisms of the stringent and relaxed control of replication of other plasmids, the results obtained to date (summarized and discussed in this review) show that studies on DNA replication in amino acid-starved cells may provide new insights into the regulatory mechanisms and lead to more general conclusions.

Assessment of quantitative models for plasmid ColE1 copy number control

Two quantitative models of plasmid ColE1 copy number control are compared with respect to mathematical logic of derivation and application to experimental observations. Explanatory background material and clarifications are supplied for selected aspects of each model. Contrasting features are emphasized and experiments are suggested to distinguish between predictions of the models.

Regulation of replication of plasmid pBR322 in amino acid-starved Escherichia coli strains

The stringent response causes inhibition of replication of plasmid pBR322 in amino acid-starved Escherichia coli cells whereas in relaxed mutants the replication of this plasmid proceeds for several hours. On the basis of density shift experiments and pulse-labelling experiments we showed that most of the pBR322 molecules begin replication during the relaxed response and the rate of plasmid DNA synthesis in unstarved and isoleucine-starved relA- bacteria is similar. We found that the Rom function plays a key role in the stringent control of plasmid pBR322 replication, as insertional inactivation of the rom gene causes amplification of pBR322rom- in both relA- and relA+ strains during amino acid starvation. Moreover, pUC19, which is a pBR322-derived plasmid lacking the rom gene, behaves like pBR322rom-, whereas introduction of the rom gene into the pUC19 replicon drives it into the pBR322 mode of replication in amino acid-starved bacteria. A model for the regulation of pBR322 plasmid DNA replication by Rom protein in amino acid-starved Escherichia coli strains is proposed.

Replication of plasmids in gram-negative bacteria

Replication of plasmid deoxyribonucleic acid (DNA) is dependent on three stages: initiation, elongation, and termination. The first stage, initiation, depends on plasmid-encoded properties such as the replication origin and, in most cases, the replication initiation protein (Rep protein). In recent years the understanding of initiation and regulation of plasmid replication in Escherichia coli has increased considerably, but it is only for the ColE1-type plasmids that significant biochemical data about the initial priming reaction of DNA synthesis exist. Detailed models have been developed for the initiation and regulation of ColE1 replication. For other plasmids, such as pSC101, some hypotheses for priming mechanisms and replication initiation are presented. These hypotheses are based on experimental evidence and speculative comparisons with other systems, e.g., the chromosomal origin of E. coli. In most cases, knowledge concerning plasmid replication is limited to regulation mechanisms. These mechanisms coordinate plasmid replication to the host cell cycle, and they also seem to determine the host range of a plasmid. Most plasmids studied exhibit a narrow host range, limited to E. coli and related bacteria. In contrast, some others, such as the IncP plasmid RK2 and the IncQ plasmid RSF1010, are able to replicate in nearly all gram-negative bacteria. This broad host range may depend on the correct expression of the essential rep genes, which may be mediated by a complex regulatory mechanism (RK2) or by the use of different promoters (RSF1010). Alternatively or additionally, owing to the structure of their origin and/or to different forms of their replication initiation proteins, broad-host-range plasmids may adapt better to the host enzymes that participate in initiation. Furthermore, a broad host range can result when replication initiation is independent of host proteins, as is found in the priming reaction of RSF1010.

Replication of ColE2 and ColE3 plasmids: in vitro replication dependent on plasmid-coded proteins

We developed an in vitro replication system for ColE2 and ColE3 plasmids using cell extracts prepared from bacteria with or without these plasmids. DNA synthesis depended on host DNA polymerase I and was sensitive to rifampicin and chloramphenicol. Preincubation of the extracts with plasmid DNA, however, allowed replication of template DNA added subsequently in a plasmid-specific manner in the presence of rifampicin and chloramphenicol. The plasmid-specified trans-acting factor(s) was detected in cell extracts from bacteria carrying a recombinant plasmid with the region of ColE2 or ColE3 encoding the Rep protein. The plasmid-specified factor(s) consisted at least in part of protein, probably the Rep protein. In vitro replication started within a region of ColE2 or ColE3 containing the smallest cis-acting segment essential for in vivo replication and proceeded in a fixed direction.

Minimal region necessary for autonomous replication of pTAR

The native 44-kilobase-pair plasmid pTAR, discovered in a grapevine strain of Agrobacterium tumefaciens, contains a single origin of DNA replication confined to a 1.0-kilobase-pair region of the macromolecule. This region (ori) confers functions sufficient for replication in Agrobacterium and Rhizobium species but not in Pseudomonas solanacearum, Pseudomonas glumae, Pseudomonas syringae pv. savastanoi, Xanthomonas campestris pv. campestris, and Escherichia coli. ori contains a repA gene that encodes a 28,000-dalton protein required for replication. Nucleotide sequencing of repA and its promoter region revealed four 8-base-pair palindromic repeats upstream of the repA coding region. Deletion of these repeats alters repA expression and plasmid copy number. Downstream of repA are three additional repeats in a region essential for replication. A locus responsible for plasmid partitioning (parA) and a putative second locus regulating plasmid copy number are part of the origin region and are required for stable plasmid maintenance.

Replication of ColE2 and ColE3 plasmids: the regions sufficient for autonomous replication

We have localized the regions sufficient for autonomous replication on the genomes of the colicin E2 (ColE2) and colicin E3 (ColE3) plasmids and analyzed the replication functions carried by these regions. A 1.3 kb segment of each plasmid is sufficient for autonomous replication. Plasmids carrying this segment retain the replication properties of the original plasmid. The 1.3 kb segment consists of three functional portions. Firstly, a 0.9 kb region which specifies at least one trans-acting factor required for replication of each plasmid. Secondly, a 0.4 kb region located adjacent to one end of the 0.9 kb region, which is required for expression of the trans-acting factor(s) and probably contains the promoter. The region across the border of these two portions of ColE2 is involved in copy number control of the plasmid. The third portion is a 50 bp region adjacent to the other end of the 0.9 kb region, which contains a cis-acting site (origin) where replication initiates in the presence of the trans-acting factor(s). The action of the trans-acting factor(s) on the origin is plasmid specific. The 50 bp regions functioning as the origins of replication of ColE2 and ColE3 are the smallest among those in prokaryotic replicons so far identified and analyzed.

Analysis of Agrobacterium tumefaciens plasmid pTiC58 replication region with a novel high-copy-number derivative

The origin of replication, ori, of the nopaline tumor-inducing plasmid, pTiC58, mapped in a region that shares sequence homology with octopine plasmids pTiAch5 and pTiB6. Within this region, the minimum amount of DNA necessary for maintaining autonomous replication was a 2.6-kilobase region, which also comprised the incompatibility function inc. pTiC58 derivatives containing inc were incompatible with Agrobacterium tumefaciens plasmids pTiC58, pTiD1439, pTiAch5, pTi15955, and pTiA5 and were compatible with A. rhizogenes plasmid pRi12. Situated adjacent to the origin region was a 1.5-kilobase par segment involved in stable inheritance of pTiC58 under nonselective growth conditions. When par was present, plasmid maintenance approached that of the wild-type pTiC58. Rapid loss from the cell population was observed for plasmids not containing this locus. Another 1.5-kilobase region, cop, positively regulated pTiC58 copy number, enabling certain pTiC58 derivatives to exist at a copy number up to 80 times higher than that of wild-type pTiC58. Deletions within the cop locus resulted in reduced copy number. The ori/inc regions were flanked on either side by the par and cop loci.

Construction of Co1E1 RNA1 mutants and analysis of their function in vivo

We have carried out experiments designed to investigate the relationship between structure and function for the Co1E1 RNA1 species. RNA1 is a small RNA (108 nucleotides) that has been implicated in copy number control of the multicopy plasmid Co1E1. In vitro, RNA1 inhibits the processing of the primer precursor required for initiation of DNA replication. The RNA1 gene is entirely complementary to the 5'-terminal region of the primer. We have functionally separated these 2 RNA species by cloning the RNA1 gene downstream from the S. marcescens trp promoter. When cloned in a Co1E1-compatible plasmid, a trp-RNA1 fusion has been shown to mediate Co1E1-type incompatibility in vivo. The construction scheme described here also generates mutant RNA1 species with altered sequences at the 5' terminus of RNA1 which have been assayed for function in vivo. These experiments have indicated that sequences at the 5' terminus play a critical role in RNA1 function.

Effects of point mutations on formation and structure of the RNA primer for ColE1 DNA replication

We report mutations affecting several steps of CoIE1 primer formation. Primer precursor forms the hybrid with the template DNA and is cleaved by RNAase H to form the primer. Point mutations at positions -264, -265, -268, and -308 (base pairs upstream of the replication origin) reduce efficiency of hybrid formation. A suppressor mutation at -18 increases the efficiency for a mutant transcript and reduces that for a wild-type transcript. Therefore, hybrid formation probably starts after transcription passes this position. A mutation at -10 affects the site of cleavage by RNAase H. The site appears to be determined by the distance from a stem-loop structure immediately upstream. A double mutation at -186 and -188 results in formation of an RNA secondary structure that prevents use of an RNAase H-cleaved transcript as primer.

Enzymology of DNA in replication in prokaryotes

This review stresses recent developments in the in vitro study of DNA replication in prokaryotes. New insights into the enzymological mechanisms of initiation and elongation of leading and lagging strand DNA synthesis in ongoing studies are emphasized. Data from newly developed systems, such as those replicating oriC containing DNA or which are dependent on the lambda, O, and P proteins, are presented and the information compared to existing mechanisms. Evidence bearing on the coupling of DNA synthesis on both parental strands through protein-protein interactions and on the turnover of the elongation systems are analyzed. The structure of replication origins, and how their tertiary structure affects recognition and interaction with the various replication proteins is discussed.

Isolation and complementation of temperature-sensitive replication mutants of Staphylococcus aureus plasmid pC194

Temperature-sensitive replication (Tsr) mutants have been isolated from the Staphylococcus aureus plasmid pC194. For three of the four mutant plasmids tested (pSAO801, pSAO802, and pSAO804) the segregation kinetics suggested a complete block of plasmid replication at 43 degrees C. The replication defects of three mutant plasmids: pSAO802, pSAO803, and pSAO804 could be complemented by recombinant plasmids carrying a segment from either the wild type or the other mutant, pSAO801. There was no complementation when the segment carried by the recombinant plasmid was derived from one of the three complementable mutants. These data were taken as evidence for the involvement of a diffusible, plasmid-encoded product, RepH, in pC194 replication. The complementation of the fourth Tsr mutant, pSAO801, could not be tested due to an abnormal susceptibility of this mutant to the incompatibility expressed by recombinants carrying segments derived from pC194 or its mutants. A single mutation was found to be responsible for both pSAO801 instability and its altered incompatibility properties but the nature of the defect has not yet been elucidated.

Accumulation of ColE1 early replicative intermediates catalyzed by extracts of Escherichia coli dnaG mutant strains

To investigate the events occurring at the replication forks during DNA synthesis, we studied the replication of plasmid ColE1 DNA in vivo and in vitro, using strains of Escherichia coli carrying either the dnaG3(Ts) or dnaG308(Ts) mutation. Extracts of both mutant strains supported in vitro DNA synthesis, but the amount of [3H]TMP incorporated into DNA was always less for mutant extracts than for extracts of revertant strains, which were able to grow at 42 degrees C. Sucrose gradient analysis, Southern blot analysis, and electron microscopy showed that mutant extracts synthesize a large number of early replicative intermediates containing one or two (one on each template strand) fragments at the origin of replication and some completed molecules, either open circles or covalently closed circles. The revertant extracts synthesized more completed molecules although the fraction of templates used was about the same, 0.27 for mutant extracts and 0.21 for revertant extracts. Our results show that a mutation in dnaG causes a block in the synthesis of both leading and lagging strands after initiation, which results in the accumulation of early replicative intermediates. The average size of the newly replicated region in the early replicative intermediates is 730 bases as measured from electron micrographs of early replicative intermediates. We conclude that the DnaG protein functions in lagging strand synthesis and may be necessary for the continuation of leading strand synthesis as well.

DNA fusion product of phage P2 with plasmid pBR322: a new phasmid

The chromosome of the temperate bacteriophage P2 and that of the plasmid pBR322 have been joined in vitro after treatment with restriction endonuclease EcoRI. The fusion product - a phasmid - can behave as a plasmid, as a phage and as a prophage. It can replicate its DNA under the control of either the specific replication mechanism of the parent phage in a polA mutant or that of the parent plasmid in a rep mutant. Several interesting interactions between the two replication modes are indicated. In particular, phage particles may be produced even when the phage mode of DNA replication is blocked, and this throws new light on the involvement of the early gene A in the regulation of late gene expression in phage P2.

The plasmid as a tool for plasmid genetics. II. Isolation of point mutations that affect replication of a ColE1-related plasmid

The insertion of a high-copy-number plasmid into a lambdoid phage chromosome which lacks a functional repressor gene confers on the hybrid ‘phasmid’ the capacity to grow on an immune lysogen. This was found to be due to titration of repressor because of plasmid replication. We have exploited this property in order to isolate mutants that affect plasmid replication. These mutants have been mapped in a region that was previously characterized as necessary for plasmid replication and incompatibility properties. Some of the mutations could revert at frequencies characteristic of single-base-pair change mutations.

Isolation of the origin of replication of the IncW-group plasmid pSa

The origin of replication of the IncW plasmid pSa has been cloned and the function of this origin in Escherichia coli examined. A 1.9-kb region of DNA is required for efficient autonomous replication, and a 0.47-kb fragment within this region can initiate replication only in the presence of an autonomously replicating derivative of pSa. An Mr 35,000 protein (repA) is encoded adjacent to the origin and is required for efficient initiation of replication. The derivatives examined provide information suggesting a direct role of partition factors in plasmid replication and incompatibility.

Replication and incompatibility properties of plasmid pE194 in Bacillus subtilis

pE194, a 3.5-kilobase multicopy plasmid, confers resistance to the macrolide-lincosamide-streptogramin B antibiotics in Bacillus subtilis. By molecular cloning and deletion analysis we have identified a replication segment on the physical map of this plasmid, which consists of about 900 to 1,000 base pairs. This segment contains the replication origin. It also specifies a trans-acting function (rep) required for the stable replication of pE194 and a negatively acting copy control function which is the product of the cop gene. The target sites for the rep and cop gene products are also within this region. Two incompatibility determinants have been mapped on the pE194 genome and their properties are described. One (incA) resides within the replication region and may be identical to cop. incB, not located in the replication region, expresses incompatibility toward a copy control mutant (cop-6) but not toward the wild-type replicon.

Functional origin of replication of pT181 plasmid DNA is contained within a 168-base-pair segment

We have used a recently developed in vitro replication system from Staphylococcus aureus to determine the origin and direction of replication of pT181 plasmid DNA. The origin was located to within 168 base pairs by two methods: (i) sequential labeling of restriction endonuclease fragments after synchronous initiation in vitro in the presence of various amounts of dideoxy-TTP and (ii) by constructing in vitro deletions of pT181 DNA close to the origin of replication and testing for their ability to replicate in vitro pT181 plasmid was found to replicate unidirectionally and anticlockwise, as the map is conventionally drawn. The nucleotide sequence of the region containing the origin of replication has been determined and found to be partially or entirely contained within the coding sequence for the repC protein, which is uniquely required for pT181 plasmid replication. Preliminary evidence suggesting that pT181 replicates by a rolling circle mechanism is discussed.

Trimethoprim-produced F-specific insertion mutations in Escherichia coli K-12

Besides producing thymine-requiring mutants (thy), trimethoprim (TMP) cured the mini-ColE1 replicon pML21 at an appreciable frequency. The cured Escherichia coli K-12 cells behaved like polA mutants by failing to support the stable maintenance of the ColE1 plasmid. The mini-F replicon pSC138, which was lacking all three insertion sequences (IS3, gammadelta, and IS2) normally used for F-specific integration and excision, was not cured by TMP. Instead, it integrated into specific regions of the E. coli chromosome and thus caused auxotrophic mutations in operons which were always localized on either side of oriC (origin of chromosomal replication). The incompatibility and replication functions of the integrated plasmid in auxotrophs were retained, and the plasmid DNAs recovered from spontaneously occurring revertants did not show any alterations in their contour lengths as determined by electron microscopy. The F replicon (fragment 5) contained in plasmid pSC138 carried two origins of replication, the primary origin, oriV(1) at 42.6F and the secondary origin, oriV(2), at 44.1F. Another mini-F plasmid pMF21, deleted of the primary origin of replication (oriV(1)), was still capable of autonomous replication but failed to integrate onto the chromosome after TMP treatment. Furthermore, the composite plasmid pRS5, which normally uses only the replication origin and functions of the pSC101 component, was also insensitive to TMP. On the basis of these results, we propose a new scheme of F integration via the functional oriV(1) and suggest the involvement of a similar mechanism in the formation of Hfr strains by integrative suppression.

Cloning vectors derived from bacterial plasmids

A wide variety of plasmid cloning vectors, most of which utilize the basic Co1E1I replicon have been constructed. Utilizing these vectors, in conjunction with the newly developed techniques of gene isolation and oligonucleotide synthesis, essentially any gene which can be identified can be cloned. We anticipate that future work in this area will be directed at improving techniques for the regulated expression of cloned genes and the further development of plasmid replicons in which the copy number can be readily controlled.

Complementation of replication-deficient deletion derivatives of plasmid mini-F

Deleted mini-F plasmids with defects in replication were constructed and tested to see whether they could be rescued through complementation by a helper plasmid. This allowed us to identify two genetic loci determining trans-acting functions required for stable maintenance of plasmid mini-F, one encoded by the PstI fragment from 45.7 to 47.3 F-coordinates (F) and the other most probably located in the region from 43.1 to 43.8 F. The smallest mini-F plasmid that could be established through complementation consists of the PstI fragment 44.0 to 45.7 F, encoding origin II and the incB locus.

Replication of plasmid pT181 DNA in vitro: requirement for a plasmid-encoded product

PT181 is a naturally occurring 4.5-kilobase Staphylococcus aureus plasmid encoding resistance to tetracycline. The plasmid has a copy number of about 20 per cell; a mutant, cop-608, that has a copy number of 800-1000 has been isolated. A cell-free extract has been developed that carries out complete replication of this plasmid. Extracts made from a strain containing the mutant have much greater replication activity than do extracts of strains containing pT181. In an extract from which endogenous DNA has been removed, DNA synthesis is dependent upon the addition of exogenous plasmid DNA. The replication system is specific for pT181 and related plasmids but it is inactive with other S. aureus plasmids. Furthermore, pT181 DNA does not replicate in extracts made from plasmid-negative strains or strains containing other plasmids. The results suggest that a specific plasmid-encoded substance is required for the replication of pT181 DNA.

Identification of mutations affecting replication control of plasmid Clo DF13

The bacteriocinogenic plasmid Clo DF13, originally isolated from Escherichia cloacae, is stably maintained in Escherichia coli to the extent of about 10 copies per cell. Its replication resembles that of many other small, multicopy plasmids; plasmid-encoded protein is not required but plasmid-specific genetic information is involved in regulation of replication as both conditional and nonconditional copy-number mutants of Clo DF13, and transcomplementable copy-number mutants of plasmid Col E1 have been described. The sequences essential for replication of Col E1 (refs 16, 17) and Clo DF13 (refs 18, 19) have been identified within a region surrounding the replication origin. Initiation of Col E1 replication is preceded by transcription of the origin region, providing the RNA primer at the origin. However, transcription in the opposite direction results in a small transcript of approximately 100 nucleotides (RNA-100) for both Col E1 (refs 21, 22) and Clo DF13 (ref. 23). Data suggest that Col E1 RNA-100 acts as a negative control element for the initiation of replication. We show here that single base transitions in the RNA-100 cistron of Clo DF13 can result in a nonconditional increase in plasmid copy-number. Also, sequence analysis has revealed that a specific base transition in a DNA region, apparently involved in both termination and initiation of transcription towards the replication origin, results in a thermosensitive plasmid copy-number.

Replication of plasmids from Staphylococcus aureus in Escherichia coli

Plasmid pBR322 derives from plasmid ColE1 and does not replicate in Escherichia coli strains lacking DNA polymerase I. Hybrids between pBR322 and a plasmid isolated from Staphylococcus aureus, pC194, replicate in such E. coli strains, provided that the pC194 replication region is intact. Inactivation of the pBR322 replication region does not interfere with the replication of hybrids in E. coli. Hybrids between pBR322 and two other plasmids from S. aureus, pT127 and pUB112, and replicate at the restrictive temperature in E. coli having thermosensitive DNA polymerase I. Similar hybrids involving pC221 and pHV400, plasmids from S. aureus and Bacillus subtilis, respectively, do not replicate under such conditions. These results show that some plasmids from a Gram-positive bacterium, S. aureus, can replicate in a Gram-negative one, E. coli.

Initiation of DNA replication in a ColE1-type plasmid: isolation of mutations in the ori region

We have constructed a plaque-forming hybrid phage, lambda SN4, which behaves as a composite replicon of the lambda phage and a mini-ColE1 plasmid. From the hybrid phage, plaque-type mutants altered in the ability to replicate as a ColE1 replicon were isolated. These mutations were designated as cer, signifying ColE1 replication defective. One of such mutants, lambda SN4cer6, was studied further. The mutant DNA was unable to replicate in vivo if expression and function of its lambda replicon were inhibited. The defect could not be complemented in trans. DNA sequence determination of the mutant phage revealed a single base pair (bp) alteration, C-G to T-A, at 160 bp upstream from the ori site of its ColE1 replicon. From lambda SN4cer6, revertants were obtained that had regained function of the ColE1 replicon, and they could be classified into two groups that showed a full and a partial recovery in the rates of ColE1-driven DNA synthesis. DNA sequence determination of revertant DNA indicated that the former group contained true revertants, T-A to C-G, at the cer6 site, whereas one of the partial revertants was found to sustain a secondary-site mutation, G-C to A-T at 187 bp upstream of the ori site. It was possible to construct a hairpin structure that starts by hydrogen bonding of bases at the site -160 and -187.

Genes and sites involved in replication and incompatibility of an R100 plasmid derivative based on nucleotide sequence analysis

The nucleotide sequence of the entire region required for autonomous replication and incompatibility of an R100 plasmid derivative, pSM1, has been determined. This region includes the replication region and all plasmid encoded information required for replication. Numerous reading frames for possible proteins can be found in this region. The existence of one of these proteins called RepA1 (285 amino acids; 33,000 daltons) which is encoded within the region known by cloning analysis to be required for replication is supported by several lines of evidence. These include an examination of the characteristic sequences on the proximal and distal ends of the coding region, a comparison of the sequence of the replication regions of pSM1 and the highly related R1 plasmid derivative Rsc13 as well as other biochemical and genetic evidence. The existence of two other proteins, RepA3 (64 amino acis; 7000 daltons) and RepA2 (103 amino acids; 11,400 daltons) is also consistent with most of the criteria mentioned above. However, the region encoding RepA3, which by cloning analysis is within the region responsible for both replication and incompatibility, has never been demonstrated to produce a 7,000 dalton polypeptide. Since a large secondary structure can be constructed in this region, it is possible that the region contains structure or other information that is responsible for incompatibility. RepA2, encoded entirely within the region identified by cloning analysis to be responsible for incompatibility but not for replication can be visualized in vivo and in vitro. However, the nucleotide sequence of the region encoding RepA2 is completely different in mutually incompatible plasmid derivatives of R1 and R100. It is therefore unlikely that RepA2 plays a major role in incompatibility. Thus, we predict that RepA2 is required to initiate DNA synthesis at the replication origin and that the region proximal to RepA2 either encodes a gene product or structure information that is responsible for incompatibility.

Functional relationship between parts of the replication region of plasmid ColE1

The inhibition of plasmid ColE1 replication caused by a deletion of the ColE1 plasmid replication origin has been previously reported (T. Hashimoto-Gotoh and J. Inselburg, J. Bacteriol. 139:597-619). Evidence is presented showing that restoration of the deleted nucleotide sequence in the precise relationship it normally has to the rest of the replication region is essential for restoration of ColE1 replication capability to the deletion mutant.

Nucleotide sequence of the region required for maintenance of colicin E1 plasmid

Plasmids carrying various portions of colicin E1 plasmid (ColE1) DNA have been isolated in an attempt to determine the regions of ColE1 DNA which are required for maintenance of the plasmid in bacteria. To construct the plasmids, the DNA of a ColE1 derivative that contains a gene which controls ampicillin resistance was cleaved by the restriction endonuclease HaeII. The digestion products were joined by T4 DNA ligase and then used to transform bacteria to ampicillin resistance. The plasmid derivatives obtained in this way were always composed of certain HaeII segments. These contain approximately 10% of the ColE1 genome and include the origin of replication of ColE1. We presume that the region of ColE1 which is common to all these derivatives is required for maintenance of the plasmid. After a description of these results, the nucleotide sequence of this region is presented, and possible roles of the region in plasmid replication and maintenance are discussed.

Role of plasmid-coded RNA and ribonuclease III in plasmid DNA replication

An in vitro replication system has been used to study the control of DNA replication of the relaxed plasmids Col E1 and RSF1030. An RNA transcript approximately 100 nucleotides long is synthesized during the in vitro DNA replication reaction. This RNA is synthesized approximately 450 bp away from the origin of replication. A small insertion in the coding sequence for the RNA made from Col E1 DNA leads to a larger RNA species and simultaneously to an increase in plasmid copy number. Revertants missing the specific insertion show shorter RNA transcripts and wild-type copy number. Although plasmids Col E1 and RSF1030 have no extensive sequence homology, the RNA synthesized during RSF1030 replication has almost the same mobility as the Col E1 RNA on polyacrylamide gels and hybridizes to the Col E1 origin region. Extracts prepared from mutants of Escherichia coli deficient in ribonuclease III do not replicate RSF1030 or Col E1 plasmids in vitro. When supplemented with homogeneous RNAase III, such extracts do support DNA replication on these templates, indicating that RNAase III is required for DNA replication. We propose that the 100 nucleotide RNA species is involved in regulating the initiation of DNA replication of these plasmids, and that RNAase III may be involved in processing this RNA.

Characterization of an improved in vitro DNA replication system for Escherichia coli plasmids

A modified in vitro replication system has been characterized and used to catalogue the host proteins required for the replication of plasmid RSF1030. These extracts differ from systems described previously in that endogenous DNA is removed. Replication in vitro therefore requires an exogenouos RSF1030. Synthesis in the in vitro system faithfully mimics in vivo replication with respect to the products synthesized, effects of specific inhibitors, and requirements for RNA polymerase and DNA polymerase I. In addition, we find that proteins encoded by dnaB, dnaC, dnaG, dnaI, dnaP and polC (DNA polymerase III), are required for in vitro plasmid synthesis. The product of dnaA is not required. Extracts prepared from E. coli mutants deficient in in vitro replication can be complemented by addition of purified proteins or of extracts carrying the wild type protein.

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.

Nucleotide sequence of small ColE1 derivatives: structure of the regions essential for autonomous replication and colicin E1 immunity

A small ColE1 derivative, pAO2, which replicates like the original ColE1 and confers immunity to colicin E1 on its host cell has been constructed from a quarter region of ColE1 DNA (Oka, 1978). The entire nucleotide sequence of pAO2 (1,613 base pairs) was determined based on its fine cleavage map. The sequence of a similar plasmid, pAO3, carrying additional 70 base pairs was also deduced. The sequence in the region covering the replication initiation site on these plasmids was consistent with those reported for ColE1 by Tomizawa et al. (1977) and by Bastia (1977). DNA sequences indispensable for autonomous replication were examined by constructing plasmids from various restriction fragments of pAO2 DNA. As a result, a region of 436 base pairs was found to contain sufficient information to permit replication. The occurrence of initiation and termination codons and of the ribosome-binding sequence on pAO2 DNA suggests that a polypeptide chain consisting of 113 amino acid residues may be encoded by the region in which the colicin E1 immunity gene has been mapped.

Cell-free synthesis of proteins coding for mobilisation functions of ColE1 and transposition functions of Tn3

A hybrid plasmid, pJC74, carrying the large (3.35 Md) EcoRI-PstI fragment of ColE1, the 1.3 and 1.8 Md PstI fragments of plasmid R1 drd19 (containing a part of Tn3 and known to specify transpostion functions), and a part of gamma bacteriophage DNA carrying the fused cohesive ends of gamma (cos) was constructed. Supercoiled DNA of pJC74 and a series of deletions (series pJC75) were used in a cell-free coupled transcription-translation system. Analysis of the proteins produced allowed the identification of a 28 to 30 kd protein and/or a 3 kd protein responsible for mobilisation of the plasmids in sex-factor-promoted conjugation. Furthermore, three protein bands of 12, 12.5 and 13 kd were correlated with the presence of a portion of the Tn3 transposon previously shown to code for transposition functions which can complement in trans. These latter and the 30 kd beta-lactamase were the only proteins identified as Tn3-specific by comparison of ColE1 with RSF2124.

Plasmid replication functions. II. Cloning analysis of the repA replication region of antibiotic resistance plasmid R6-5

R6-5 is a low copy number, conjugative, FII incompatibility group plasmid that has a molecular length of 102 kb and that specifies resistance against several antibiotics (chloramphenicol, fusidic acid, kanamycin, streptomycin and sulphonamide) and mercury salts. By means of in vitro cloning procedures, mini plasmids have been generated that contain a DNA segment from the essential region of R6-5 that is only 2.6 kb in length. This DNA segment, which consists of two PstI fragments that are adjacent in the parent plasmid, carries all genes and sequences required for the regulated replication and incompatibility properties of R6-5, including its origin of replication, OriV, an essential function that has been designated RepA, and the copy control function, Cop. Three different polypeptides, having monomer molecular weights of 23,000, 10,000 and 9,500 daltons, are synthesized in detectable quantities by minicells carrying pBR322 hybrid plasmids that contain DNA segments from the R6-5 essential region. A spontaneous deletion derivative of a pBR322 hybrid plasmid that carries the R6-5 origin of replication was isolated. Heteroduplex analysis of this derivative plasmid indicates that the deleted DNA segment carries the R6-5 replication origin and that its termini consist of short inverted repeat sequences.

Structural and functional analysis of cloned DNA segments containing the replication and incompatibility regions of a miniplasmid derived from a copy number mutant of NR1

A 1.45-megadalton segment of DNA cloned from a miniplasmid derived in vivo from a copy number mutant of the R plasmid NR1 has been shown to contain all functions essential for incompatibility and autonomous plasmid replication in Escherichia coli. Specific endonuclease cleavage sites within this DNA segment that localize functions required for replication have been mapped. A 0.45-megadalton fragment that specifies the FII incompatibility of NR1 has been identified within the replication region, and DNA fragments containing this incompatibility region, but lacking other functions required for replication, have been cloned.