Studies on the regulation of initiation of chromosome replication in Escherichia coli

Open Questions about the Roles of DnaA, Related Proteins, and Hyperstructure Dynamics in the Cell Cycle

The DnaA protein has long been considered to play the key role in the initiation of chromosome replication in modern bacteria. Many questions about this role, however, remain unanswered. Here, we raise these questions within a framework based on the dynamics of hyperstructures, alias large assemblies of molecules and macromolecules that perform a function. In these dynamics, hyperstructures can (1) emit and receive signals or (2) fuse and separate from one another. We ask whether the DnaA-based initiation hyperstructure acts as a logic gate receiving information from the membrane, the chromosome, and metabolism to trigger replication; we try to phrase some of these questions in terms of DNA supercoiling, strand opening, glycolytic enzymes, SeqA, ribonucleotide reductase, the macromolecular synthesis operon, post-translational modifications, and metabolic pools. Finally, we ask whether, underpinning the regulation of the cell cycle, there is a physico-chemical clock inherited from the first protocells, and whether this clock emits a single signal that triggers both chromosome replication and cell division.

Fundamental principles in bacterial physiology-history, recent progress, and the future with focus on cell size control: a review

Bacterial physiology is a branch of biology that aims to understand overarching principles of cellular reproduction. Many important issues in bacterial physiology are inherently quantitative, and major contributors to the field have often brought together tools and ways of thinking from multiple disciplines. This article presents a comprehensive overview of major ideas and approaches developed since the early 20th century for anyone who is interested in the fundamental problems in bacterial physiology. This article is divided into two parts. In the first part (sections 1-3), we review the first 'golden era' of bacterial physiology from the 1940s to early 1970s and provide a complete list of major references from that period. In the second part (sections 4-7), we explain how the pioneering work from the first golden era has influenced various rediscoveries of general quantitative principles and significant further development in modern bacterial physiology. Specifically, section 4 presents the history and current progress of the 'adder' principle of cell size homeostasis. Section 5 discusses the implications of coarse-graining the cellular protein composition, and how the coarse-grained proteome 'sectors' re-balance under different growth conditions. Section 6 focuses on physiological invariants, and explains how they are the key to understanding the coordination between growth and the cell cycle underlying cell size control in steady-state growth. Section 7 overviews how the temporal organization of all the internal processes enables balanced growth. In the final section 8, we conclude by discussing the remaining challenges for the future in the field.

Studies on the alteration of chromosome copy number and cell division potential in a dnaA mutant of Escherichia coli

The dnaA167 mutant of Escherichia coli, N167, maintains, on the average, two replicating chromosomes per cell at the permissive growth temperature of 30 degrees C and only one per cell at the higher permissive growth temperature of 38 degrees C. When the growth temperature of this mutant is changed from 30 degrees to 38 degrees C the cells rapidly readjust their chromosome copy number from two to one. I have examined the kinetics of this transition with reference to DNA replication and cell division. My results indicate that this mutant uncouples cell division from chromosome duplication to achieve the appropriate copy number, suggesting that the dnaA gene product may be involved in the coordination between these two cellular events.

Control of cyclic chromosome replication in Escherichia coli

The biochemical basis for cyclic initiation of bacterial chromosome replication is reviewed to define the processes involved and to focus on the putative oscillator mechanism which generates the replication clock. The properties required for a functional oscillator are defined, and their implications are discussed. We show that positive control models, but not negative ones, can explain cyclic initiation. In particular, the widely accepted idea that DnaA protein controls the timing of initiation is examined in detail. Our analysis indicates that DnaA protein is not involved in the oscillator mechanism. We conclude that the generations of a single leading to cyclic initiation is separate from the initiation process itself and propose a heuristic model to focus attention on possible oscillator mechanisms.

Chromosome replication in Escherichia coli induced by oversupply of DnaA

Overexpression of DnaA protein from a multicopy plasmid accompanied by a shift to 42 degrees C causes initiation of one extra round of replication in a dnaA+ strain grown in glycerol minimal medium. This extra round of replication does not lead to an extra cell division, such that cells contain twice the normal number of chromosomes.

Transcriptional repression of the dnaA gene of Escherichia coli by dnaA protein

The promoter region of the dnaA gene and of a gene which encodes a 16 kDa protein contain sites which are recognized and bound by dnaA protein. Using assays of run-off transcription of restriction fragments, purified dnaA protein specifically repressed transcription from both dnaA promoters and from the promoter for the 16 KD gene to almost undetectable levels. This repressive effect was observed at levels of dnaA protein required for specific binding of dnaA protein to restriction fragments containing the promoters for these genes. These results indicate that transcription of these genes is regulated by binding of dnaA protein to the promoter regions of these genes.

Cloning and characterization of dnaA(Cs), a mutation which leads to overinitiation of DNA replication in Escherichia coli K-12

The product of the dnaA gene is essential for the initiation of chromosomal DNA replication in Escherichia coli K-12. A cold-sensitive mutation, dnaA(Cs), was originally isolated as a putative intragenic suppressor of the temperature sensitivity of a dnaA46 mutant (G. Kellenberger-Gujer, A. J. Podhajska, and L. Caro, Mol. Gen. Genet. 162:9-16, 1978). The cold sensitivity of the dnaA(Cs) mutant was attributed to a loss of replication control resulting in overinitiation of DNA replication. We cloned and sequenced the dnaA gene from the dnaA(Cs) mutant and showed that it contains three point mutations in addition to the original dnaA46(Ts) mutation. The dnaA(Cs) mutation was dominant to the wild-type allele. Overproduction of the DnaA(Cs) protein blocked cell growth. In contrast, overproduction of wild-type DnaA protein reduced the growth rate of cells but did not stop cell growth. Thus, the effect of elevated levels of the DnaA(Cs) protein was quite different from that of the wild-type protein under the same conditions.

Comparison of dnaA nucleotide sequences of Escherichia coli, Salmonella typhimurium, and Serratia marcescens

The dnaA genes of Salmonella typhimurium and Serratia marcescens, which complemented the temperature-sensitive dnaA46 mutation of Escherichia coli, were cloned and sequenced. They were very homologous to the dnaA gene of E. coli. The 63 N-terminal amino acids and the 333 C-terminal amino acids of the corresponding DnaA proteins were identical. The region in between, corresponding to 71 amino acids in E. coli, exhibited a number of changes. This variable region coincided with a nonhomologous region found in the comparison of E. coli dnaA and Bacillus subtilis "dnaA" genes. The regions upstream of the genes were also homologous. The ribosome-binding area, one of the promoters, the DnaA protein-binding site, and many GATC sites (Dam methyltransferase-recognition sequence) were conserved in these three enteric bacteria.

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.

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.

Initiation of chromosome replication in Escherichia coli after induction of dnaA gene expression from a lac promoter

Escherichia coli HB282 carries a dnaA46(Ts) allele on the chromosome, a wild-type dnaA allele under the control of the lacUV5 promoter on the multicopy plasmid pBC32, and an overproducing lac repressor allele on an F' factor. When the plasmid dnaA gene is repressed, the strain is thermosensitive. After a temporary deficiency in active dnaA protein at nonpermissive temperature, the addition of isopropyl-beta-D-thiogalactopyranoside to the culture was found to produce a burst of initiations within 5 to 10 min at 30% of the origins in 90% of the cells. Initiations then continued at a rate slightly faster than the mass-doubling time such that after 2 h the origin-to-mass ratio of the control culture was restored.

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

The dnaA gene in E. coli K-12 is required for the initiation of DNA replication. Although the specific function of the dnaA protein is unknown, it has been suggested that it is a regulator of the frequency of initiation. In this paper we report that the expression of both a dnaA-lacZ translational fusion and a dnaA-trpA-lacZ transcriptional fusion in vivo are sensitive to changes in the level of functional dnaA protein. Overproduction of the dnaA gene product leads to a reduction in expression from both fusions while introduction of dnaA- alleles results in an increased expression. Results from a deletion analysis of the dnaA promoter/regulatory region suggest that both dnaA promoters are regulated by the dnaA gene product and that a site between the two promoters is responsible for the regulation. DNAase protection experiments showed that the dnaA protein binds to DNA in the region of the two dnaA promoters. Our results indicate that the dnaA gene product regulates its own synthesis by inhibiting transcription from both of its promoters.

Expression of accumulated capacity for initiation of chromosome and minichromosome replication in dnaA mutants of Escherichia coli

Chromosome and minichromosome replication were examined in temperature-sensitive dnaA mutants of Escherichia coli growing at temperatures between permissive and nonpermissive. Periodicities in [14C]thymidine uptake were detected as cultures incubated at intermediate temperatures approached late exponential-early stationary phase of growth. Exposure of the cultures to a nutritional shift-up caused a stimulation of chromosome replication associated with a rapid initiation of new rounds of replication, very similar to that observed after exposure to chloramphenicol. Addition of rifampin also caused a stimulation, but to a much lesser extent. The induced initiations of chromosome replication took place in two waves, as was the case when the cultures were simply shifted to permissive temperature. Minichromosomes were also stimulated to replicate by the addition of chloramphenicol at intermediate temperatures, providing further evidence that the chromosomal region which responded to the chloramphenicol treatment was in the vicinity of oriC. The findings are consistent with the conclusion that the initiations induced by chloramphenicol are consequences of the involvement of the dnaA gene product in a transcriptional step at initiation, as suggested by Orr et al. The results also suggest that the activity of the dnaA gene product is not normally involved in controlling the frequency of initiation of chromosome replication.

Studies on the expression of outer membrane protein 2 in escherichia coli

The relative level of protein 2 expressed in the outer membrane of strains of Escherichia coli K-12 lysogenized with bacteriophage PA-2 was found to be influenced by both the growth temperature and lc+ gene dosage. An increase in either of these parameters was accompanied by an increase in the level of protein 2 up to an apparent saturation level. Any increase in the amount of protein 2 was accompanied by a concomittant decrease in the amount of OmpF and OmpC porins. This inverse relationship led to the maintenance of an approximately constant protein mass per unit of peptidoglycan. Our results are discussed in light of recent genetic studies on the regulation of the OmpF and OmpC porins and can be explained through the competition of these three matrix proteins for a common export or insertion site.

Continuous synthesis of the dnaA gene product of Escherichia coli in the cell cycle

The dnaA gene product of Escherichia coli, identified as a weakly basic protein of about 48,000 daltons (Yuasa and Sakakibara 1980), can be separated from other cellular proteins by means of two-dimensional gel electrophoresis. Synthesis of the dnaA protein took place continuously during a cell growth cycle. The newly synthesized dnaA protein persisted stably for one generation. Thermosensitive dnaA protein produced by the dnaA167 mutant was stable at 30 degrees C, but was disintegrated at 42 degrees C. The amount of intact dnaA protein present in the mutant exposed to the high temperature for 60 min was less than a quarter of the amount at the time of the shift. The cells having the reduced amount of intact dnaA protein were capable of initiating a new round of chromosome replication at the low temperature without de novo synthesis of the dnaA protein. The potential of the mutant for initiation of DNA replication decreased with reduction in the amount of the thermoreversible dnaA protein. The mutations dnaA167 and dnaA46 had no significant effect on the syntheses of the dnaA mRNA and the protein product at the low and high temperatures.

Regulation of DNA synthesis and capacity for initiation in DNA temperature sensitive mutants of Escherichia coli. II. Requirements for acquisition and expression of initiation capacity

This paper deals with the conditions that are necessary for the acquisition and expression of initiation potential in dnaA temperature sensitive mutants after they have been held for periods of time at nonpermissive temperature and then returned to permissive temperature in the presence of chloramphenicol. The following conditions were found to be essential: (1) 40-60 min at nonpermissive temperature during which time protein synthesis must occur; this period must be followed by (2) return to permissive temperature under which conditions active dnaA product is present, and (3) protein synthesis must be blocked during the first 10-20 min immediately after return to permissive temperature (when initiation takes place). In order for expression of the initiation potential (4) the chloramphenicol must be removed to allow the progression of the replication forks which had been initiated to occur and (5) the recA+ phenotype appears to be required for acquisition or expression (or both) of the initiation potential.

Isolation and characterization of amber mutations in gene dnaA of escherichia coli K-12

Amber mutants with defects in the dnaA gene of Escherichia coli K-12 were isolated after localized mutagenesis of the tna-dnaA region of the chromosome. We isolated 36 mutants defective in the initiation of deoxyribonucleic acid replication as determined by their dependence upon integrative suppression by a P2 sig5 prophage. Three of the 36 mutants were shown to contain amber mutations through the use of a temperature-sensitive amber suppressor. These mutations, which mapped between gyrB and tna, were characterized genetically and biochemically as amber mutations in dnaA.

Temperature dependent release of beta-beta' subunits of DNA dependent RNA polymerase from the folded chromosome of a dnaAts mutant of Escherichia coli

DNA-dependent RNA polymerase has been found to be preferentially released at 43 degrees C from the folded nucleoids of an E. coli dnaAts mutant when compared with the same nucleoids at 30 degrees C or with nucleoids of a dnaA+ strain at either 30 degrees or 43 degrees C. The polypeptides released are identical in molecular weight with those of the beta and beta' constituent polypeptides of the core enzyme of a known E. coli RNA polymerase. In addition, these polypeptides are precipitated by specific anti-RNA polymerase rabbit IgG. The implications of the interactions of RNA polymerase with the dnaA gene product are discussed.