Autoregulation of the DNA replication gene dnaA in E. coli K-12

Similarities in control of mini-F plasmid and chromosomal replication in Escherichia coli

In Escherichia coli, concentrations of a mini-F plasmid with two origins of replication (oriV and oriS) were 50% lower in fast-growing cells than in slow-growing cells. By contrast, a mini-F plasmid deleted for oriV maintained a uniform concentration in both fast- and slow-growing cells, and in this behavior the plasmid mimicked the control by the host of chromosomal origin (oriC) concentration.

Replication of mini-P1 plasmid DNA in vitro requires two initiation proteins, encoded by the repA gene of phage P1 and the dnaA gene of Escherichia coli

We have developed an in vitro DNA-replication system that replicates exogenously added mini-P1 plasmid DNA. The system consists of purified P1 RepA protein and a partially purified mixture of Escherichia coli replication proteins. It is essentially the same as that described for the replication of oriC plasmid DNA [Fuller, R.S., Kaguni, J.M. & Kornberg, A. (1981) Proc. Natl. Acad. Sci. USA 78, 7370-7374]. Mini-P1 DNA replication requires the E. coli DnaA initiation protein in addition to the P1 RepA initiation protein. The reaction is inhibited by rifampicin, novobiocin, and antibody to DnaB, suggesting the involvement of RNA polymerase, DNA gyrase, and DnaB protein. Replication is initiated in the region of the P1 origin of replication and proceeds unidirectionally as determined by electron microscopy. Thus, the in vitro system mimics the essential features of mini-P1 replication as suggested by genetic studies.

Stability and replication control of Escherichia coli minichromosomes

A stabilized minichromosome--a plasmid replicating from the chromosomal origin oriC--was constructed by cloning the sopA,B,C, genes from plasmid F. This minichromosome had a loss frequency of less than 10(-3), while that of the nonstabilized parental plasmid was 2 X 10(-2) to 4 X 10(-2). Both minichromosomes had the same average copy number per chromosomal origin, and the copy numbers were constant over an eightfold range of growth rates. Different mutations in the mioC gene and promoter, from which transcription enters oriC, were constructed, and their effects on minichromosome copy number and stability were tested. The results indicated that normal replication control at oriC was independent of the MioC protein and most of the sequences between the promoter and oriC, but required both transcription from the mioC promoter and probably also the presence of the DnaA box (DnaA protein-binding site) just upstream of the mioC promoter. Transcription from the mioC promoter was shown to be efficiently repressed in vivo after overproduction of DnaA protein and to be derepressed at the nonpermissive temperature in six different dnaA(Ts) mutants.

Overexpression of the dnaA gene in Escherichia coli B/r: chromosome and minichromosome replication in the presence of rifampin

The replication of chromosomes and minichromosomes in Escherichia coli B/r was examined under conditions in which the dnaA gene product was overproduced. Increased levels of the DnaA protein were achieved by thermoinduction of the dnaA gene, under the control of the lambda pL promoter, or by cellular maintenance of multicopy plasmids carrying the dnaA gene under the control of its own promoters. Previous work has shown that overproduction of DnaA protein stimulates replication of the chromosomal origin, oriC, but that the newly initiated forks do not progress along the length of the chromosome (T. Atlung, K. V. Rasmussen, E. Clausen, and F. G. Hansen, p. 282-297, in M. Schaechter, F. C. Neidhardt, J. L. Ingraham, and N. O. Kjeldgaard, ed., The Molecular Biology of Bacterial Growth, 1985). In the present study, it was found that overproduction of DnaA protein caused both a two- to threefold increase in the amount of residual chromosome replication and an extended synthesis of minichromosome DNA in the presence of rifampin. The amount of residual chromosome replication was consistent with the appearance of functional replication forks on the majority of the chromosomes. Since the rate of DNA accumulation and the cellular DNA/mass ratios were not increased significantly by overexpression of the dnaA gene, we concluded that the addition of rifampin either enabled stalled replication forks to proceed beyond oriC or enabled new forks to initiate on both chromosomes and minichromosomes, or both.

Transcripts within the replication origin, oriC, of Escherichia coli

Transcription start and termination sites were mapped in the E. coli replication origin, oriC. Outward transcription from within oriC (promoters Pori-r and Pori-l) was found to start in vivo at position 178 for Pori-l and at positions 294 and 304 for Pori-r, respectively. These transcripts were terminated after 100-150 bases, at terminators designated Tori-l and Tori-r. Transcription from the 16 kd promoter, which lies clockwise adjacent to oriC and promotes transcription toward oriC, started at position 757 and gave transcripts with 3' ends at several positions within and to the left of the minimal replication origin. However, the majority of transcripts traversed the whole oriC region, and were not terminated within the DNA segment tested. Transcription of the chromosomal 16 kd gene was negatively regulated by DnaA protein and positively affected by dam methylation. The possible function of these transcripts is discussed.

Overproduction of DnaA protein stimulates initiation of chromosome and minichromosome replication in Escherichia coli

Increased synthesis of DnaA protein, obtained with plasmids carrying the dnaA gene controlled by the heat inducible lambda pL promoter, stimulated initiation of replication from oriC about threefold. The overinitiation was determined both as an increase in copy number of a minichromosome and as an increase in chromosomal gene dosage of oriC proximal DNA. The additional replication forks which were initiated on the chromosome did not lead to an overall increase in DNA content. DNA/DNA hybridization showed an amplification encompassing less than a few hundred kilobases on each side of oriC. Kinetic studies showed that the overinitiation occurred very rapidly after the induction, and that the initiation frequency then decreased to a near normal frequency per oriC. The results indicate that the DnaA protein is one important factor in regulation of initiation of DNA replication from oriC.

The adjacent dnaZ and dnaX genes of Escherichia coli are contained within one continuous open reading frame

The dnaZ and dnaX loci of Escherichia coli have been genetically defined as separate genes, both of which are essential for DNA replication (1). The 2.1 kb region of DNA that complements mutations in both genes has a maximum coding capacity of approximately 80,000 daltons. Two protein products are produced from this region with molecular weights of 77,000 and 52,000 (2,3). We have sequenced a 2.7 kb fragment containing the dnaZ and dnaX genes and determined that it contains only one open reading frame of sufficient length to encode either of these proteins. This open reading frame may encode a protein of 71,147 daltons or of 68,451 daltons depending on which potential translational initiation codon is utilized. There are two transcriptional promoters preceding the gene as well as a ribosome binding site preceding the two potential initiation codons. Both the promoters and ribosome binding sites are predicted to be weak, perhaps contributing to the low expression of these genes.

Regulation of transcription of the chromosomal dnaA gene of Escherichia coli

By comparative S1 analysis we investigated the in vivo regulation of transcription of the chromosomal dnaA gene coding for a protein essential for the initiation of replication at the chromosomal origin. Inactivation of the protein in dnaA mutants results in derepression, whereas excess DnaA protein (presence of a DnaA overproducing plasmid) leads to repression of dnaA transcription. Both dnaA promoters are subject to autoregulation allowing modulation of transcriptional efficiency by at least 20-fold. Increasing the number of oriC sequences (number of DnaA binding sites) in the cell by introducing oriC plasmids leads to a derepression of transcription. Autoregulation and binding to oriC suggest that the DnaA protein exerts a major role in the regulation of the frequency of initiation at oriC. The efficiency of transcription of the dnaA2 promoter is reduced in the absence of dam methylation, which is involved in the regulation of oriC replication.

Enhancement of bacterial gene expression by insertion elements or by mutation in a CAP-cAMP binding site

The regulatory region (bglR) of the cryptic bgl operon was characterized by DNA sequence analysis and transcription mapping. Bgl(-)-specific transcription was found to occur in both the wild-type Bgl- and mutant Bgl+ cells. However, the steady-state level of bgl RNA was much higher in the Bgl+ mutant than in the wild-type. Activation of the bgl operon by insertion sequence-mediated bglR mutations or point mutations in bglR is therefore the result of increased transcription. The ethylmethane sulfonate-induced point mutations in bglR are alterations in a single base in the cAMP binding protein (CAP) binding site, leading to a stronger binding of the CAP-cAMP complex. The IS1 and IS5-mediated bglR mutations analyzed show that the insertion sequences can activate the bgl operon by integration 78 to 125 base-pairs upstream from the transcription initiation site. The role of the insertion sequences in activation of the bgl operon is discussed.

Sequence-specific interaction between the replication initiator protein of plasmid pT181 and its origin of replication

The replication of the pT181 plasmid is dependent on the plasmid-encoded initiator protein RepC. We have previously shown that RepC protein has sequence-specific endonuclease and topoisomerase-like activities. In this paper we demonstrate that this initiator protein has sequence-specific DNA-binding properties. Based on filter binding of plasmid restriction fragments, RepC protein specifically recognizes only the pT181 origin region. Using DNase I and neocarzinostatin "footprinting" techniques, we show that RepC protein specifically binds to a 32-base-pair sequence within the origin that is part of the initiator cistron. Using dimethyl sulfate as a chemical probe, we have identified the purine residues that interact with the initiator protein. The features of the DNA region that interacts with RepC protein include sequences with the potential to form Z DNA and/or hairpin structures. The specific DNA-protein interaction at the origin may be critical in the initiation of pT181 DNA replication by RepC protein in association with other host initiation proteins.

Host participation in plasmid maintenance: dependence upon dnaA of replicons derived from P1 and F

Nonparticipation of the bacterial dnaA gene in plasmid replication has been assumed to be the general rule. In conditional dnaA mutants of Escherichia coli, only plasmid pSC101 has been shown to have a dnaA requirement. Experiments with dnaA null mutants of E. coli, presented here, show that dnaA plays a critical and direct role in the replication of miniplasmids derived from P1 and F as it does in the initiation of bacterial replication. Evidence is also presented for the existence of a dnaA-independent secondary replicon of P1 that is able to drive bacterial chromosome replication but is inadequate to support the maintenance of P1 as a plasmid in E. coli.

Suppression of the Escherichia coli dnaA46 mutation by amplification of the groES and groEL genes

A lambda hybrid phage (lambda Sda1), containing an 8.1 kb EcoRI DNA fragment from the Escherichia coli chromosome, was selected on the basis of its ability to suppress bacterial thermosensitivity caused by the dnaA46 mutation. We have shown that this suppression is due to a recA+-dependent amplification of the 8.1 kb fragment; consistent with this observation, cloning of the 8.1 kb fragment into a high copy number plasmid (pBR325) leads also to suppression of dnaA46. In the suppressed strains growing at high temperature, bidirectional replication starts in or near the oriC region and requires the presence of the DnaA polypeptide. These findings suggest that the overproduction of a gene product(s), encoded by the cloned 8.1 kb fragment, can restore dnaA-dependent initiation of replication at high temperature in the oriC region. Genetic mapping shows that the groES (mopB) and groEL (mopA) genes are located on the 8.1 kb suppressor fragment. Further analysis, including in vitro mutagenesis and subcloning, demonstrates that the amplification of the groES and groEL genes is both necessary and sufficient to suppress the temperature sensitive phenotype of the dnaA46 mutation.

A DNA fragment containing the groE genes can suppress mutations in the Escherichia coli dnaA gene

An 8.2 kb fragment of E. coli chromosomal DNA, when cloned in increased copy number, suppresses the dnaA46 mutation, and an abundant protein of about 68 kd (60 kd when measured by us), encoded by the fragment, is essential for the suppression (Takeda and Hirota 1982). Mapping experiments show that the fragment originates from the 94 min region of the chromosome. It encodes several proteins but only one abundant polypeptide of the correct size, the product of the groEL gene. Suppression by the fragment is allele specific; those mutations which map to the centre of the gene are suppressed. Other initiation mutants including dnaA203, dnaA204, dnaA508, dnaAam, dnaC, dnaP and dnaB252 are not suppressed. Most suppressed strains are cold-sensitive suggesting an interaction between the mutant proteins (or their genes) and the suppressing protein or proteins.

DNA methylation differentially enhances the expression of one of the two E. coli dnaA promoters in vivo and in vitro

The promoter/regulatory region of the dnaA gene, whose gene product is required for the initiation of DNA replication in Escherichia coli K-12, contains an unusually large number of Dam methylation sites. In this paper we report that the expression of the dnaA gene is decreased in Dam- strains of E. coli. The decrease in the expression of dnaA was measured in vivo using a dnaA-lacZ gene fusion. In vivo S1 nuclease mapping demonstrated that the decrease was due to a differential decrease in expression from the more proximal of the two dnaA promoters, dnaA2P. Comparison of the strengths of the two dnaA promoters in an in vitro transcription system using methylated and unmethylated DNA templates suggests that the effect of methylation on dnaA2P is probably at the level of RNA polymerase/DNA interaction. We suggest that this effect of methylation may be important in controlling the expression of dnaA during the E. coli cell cycle.

Autoregulation of the dnaA gene of Escherichia coli K12

Regulation of the dnaA gene, which codes for an essential factor for the initiation of replication from the chromosomal origin, was studied in vivo using transcriptional and translational gene fusions. We found that the dnaA gene was autoregulated over a 30-fold range by the activity of dnaA protein. Expression from the dnaA promoter region of a dnaA"lacZ fusion was inhibited up to sevenfold by surplus dnaA protein and was stimulated up to fivefold upon thermoinactivation of the mutant protein in five different dnaA(Ts) strains. The autoregulation was found to be exerted at transcription from the major dnaA promoter and was eliminated by deletion of sequences around position -65 of this promoter where a 9-bp sequence, which is also found four times in the chromosomal origin, is located.

cDNA cloning of mRNAS which increase rapidly in human lymphocytes cultured with concanavalin-A and cycloheximide

To induce or "superexpress" genes involved in the entry of cultured GO lymphocytes into the G1-phase of the cell cycle, the cells were treated for 2 hours with a lectin (concanavalin-A) and a protein synthesis inhibitor (cycloheximide). A cDNA library was generated from small quantities of RNA by the high efficiency method of Gubler & Hoffman (1). 30,000 colonies were screened for differential hybridization to cDNA corresponding to treated cultures, but not to cDNA corresponding to control cultures. 50 recombinants were identified on this basis. One recombinant (#7) corresponded to mRNA (2150 base pairs) which was increased by cycloheximide alone, but was not increased by concanavalin A. Another recombinant (#19) corresponded to 2 mRNAs (980 and 1120 base pairs) one or both of which were increased either by concanavalin-A or by cycloheximide. It is speculated that the latter mRNAs are products of a locus which is activated when the concentration of a repressor is decreased by concanavalin-A or cycloheximide.