Initiation of deoxyribonucleic acid replication in a temperature-sensitive mutant of B. subtilis: evidence for a transcriptional step

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.

The replicase sliding clamp dynamically accumulates behind progressing replication forks in Bacillus subtilis cells

The sliding clamp is an essential component of the replisome required for processivity of DNA synthesis and several other aspects of chromosome metabolism. However, the in vivo dynamics of the clamp are poorly understood. We have used various biochemical and cell biological methods to study the dynamics of clamp association with the replisome in Bacillus subtilis cells. We find that clamps form large assemblies on DNA, called "clamp zones." Loading depends on DnaG primase and is probably driven by Okazaki fragment initiation on the lagging strand. Unloading, which is probably regulated, only occurs after many clamps have accumulated on the DNA. On/off cycling allows chromosomal zones of about 200 accumulated clamps to follow the replisome. Since we also show that clamp zones recruit proteins bearing a clamp-binding sequence to replication foci, the results highlight the clamp as a central organizer in the structure and function of replication foci.

An RNA-DNA copolymer whose synthesis is correlated with the transcriptional requirement for chromosomal initiation in Bacillus subtilis contains ribosomal RNA sequences

During synchronous replication induced in a temperature-sensitive initiation mutant of Bacillus subtilis, we previously isolated an RNA covalently linked to DNA. This molecule was synthesized at specific times, correlated with the period of transcription that is required to initiate a new round of replication. In this paper, we show that both RNA and DNA components of the RNA-DNA molecule hybridized with the coding strand for ribosomal RNA. Competition hybridization experiments also demonstrated that ribosomal RNA sequences represent the great majority of the RNA that is linked to DNA. Both RNA and DNA components of the RNA-DNA molecule also hybridized with a region close to the origin of replication, in particular with E19 and E22, two restriction fragments that are replicated early. These fragments in fact form part of the ribosomal operon rrnO. The role of the RNA-linked DNA molecule in initiation in B. subtilis and the possibility that this molecule emanates directly from rrnO rather than from other ribosomal RNA genes are discussed.

Cell membrane and chromosome replication in Bacillus subtilis

This review covers studies of the structural and functional roles of the cell membrane on the replication of the Bacillus subtillis chromosome. A particular emphasis is placed on the essential roles of the membrane complex for the in vivo initiation and termination of the chromosome replication. A critical gene complex in B. subtillis for the role of membrane complex is the dnaB operon that most likely consists of four genes (dnaB, dnaI, ORFZ/ORF213, and ORF omega/ORF281). Detailed studies of these genes are currently available only for the dnaB and dnaI genes. The unique feature of the dnaB gene is that temperature-sensitive mutants of this gene simultaneously lose, at the nonpermissive temperature, chromosome attachment at oriC to the membrane as well as the new round of replication initiation at oriC. Further studies on the genes and their products of the dnaB operon are therefore essential for our understanding of the in vivo mechanism of the initiation of chromosome replication and its regulation. The role of the membrane on the termination and segregation of the daughter chromosomes has not been discovered, but an important clue comes from the terminus area of the B. subtillis chromosome being bound to the membrane in a high-salt resistant and DnaB-independent fashion.

A checkpoint involving RTP, the replication terminator protein, arrests replication downstream of the origin during the Stringent Response in Bacillus subtilis

Regulation of DNA replication in Bacillus subtilis involves a post-initiation mechanism which is subject to control by the Stringent System, an essential regulatory network, mediated by the alarmone, ppGpp. In detailed studies using DNA-DNA hybridization procedures, we have now shown that, following the induction of the Stringent Response, replication is blocked downstream of the origin, on the left, close to the hut marker (-175 kb) and on the right, beyond the soft10 marker (+199 kb). In addition, we provide evidence that inhibition of replication under these conditions requires the replication terminator protein (RTP). In a mutant lacking RTP, a protein normally involved in termination of chromosomal replication through recognition of specific terminator sequences, replication continues past the sites normally blocked by the Stringent Response. These data strengthen the argument that this second level of control of DNA replication occurs at specific sites, the Strigent Terminus (STer) sites, either side of orlC. Such sites are presumably related to the sequence involved in RTP recognition at the terminus, terC. We propose that the binding of RTP must be modulated, perhaps through the action of ppGpp, to recognize post-initiation control sequences during the Stringent Response, in order to block replisome movement. This, therefore, acts as a checkpoint in chromosome elongation.

Post-initiation control of chromosomal replication in Bacillus subtilis: a mechanism for limiting over-replication or for duplicating key growth and sporulation genes?

We used the Bacillus subtilis dnaB37 mutant, which is defective in initiation, to synchronize DNA replication in order to identify the first fragments to be replicated following initiation and to study the control of this process under various conditions. We show by DNA/DNA hybridization analysis that, after returning the mutant from 45 degrees C to the permissive temperature (30 degrees C), the origin region relative to other sequences is over-replicated (approximately 2-fold) during the first round. This was confirmed by autoradiographic analysis. The over-replicated region is however limited to about 190 kb on the left and right arms. Replication apparently resumes from these positions during the following round of replication. We propose that, in B. subtilis, in addition to the first level of control at the origin, there is a second level or post-initiation control downstream of the origin which limits DNA replication resulting from premature initiation. We believe that these two levels of control are tightly coupled under conditions of balanced growth. Using the same system, we have now shown that DNA replication is subject to "stringent control", an important regulatory network in bacteria. These studies demonstrate that the inhibition of replication induced during the "stringent response" does not occur at the primary origin. In fact, by DNA/DNA hybridization, replication forks were found to be blocked at similar positions to the post-initiation control sites described above. Moreover, replication appears to resume from regions close to the stalled replisomes upon removal of the stringent response.(ABSTRACT TRUNCATED AT 250 WORDS)

The stringent response blocks DNA replication outside the ori region in Bacillus subtilis and at the origin in Escherichia coli

When the Bacillus subtilis dnaB37 mutant, defective in initiation, is returned to permissive temperature after growth at 45 degrees C, DNA replication is synchronized. Under these conditions, we have shown previously that DNA replication is inhibited when the Stringent Response is induced by the amino acid analogue, arginine hydroxamate. We have now shown, using DNA-DNA hybridization analysis, that substantial replication of the oriC region nevertheless occurs during the Stringent Response, and that replication inhibition is therefore implemented downstream from the origin. On the left arm, replication continues for at least 190 x 10(3) base-pairs to the gnt gene and for a similar distance on the right arm to the gerD gene. When the Stringent Response is lifted, DNA replication resumed downstream from oriC on both arms, confirming that DNA replication is regulated at a post-initiation level during the Stringent Response in B. subtilis. Resumption of DNA synthesis following the lifting of the Stringent Response did not require protein or RNA synthesis or the initiation protein DnaB. We suggest, therefore, that a specific control region, involving Stringent Control sites, facilitate reversible inhibition of fork movement downstream from the origin via modifications of a replisome component during the Stringent Response. In contrast, in Escherichia coli, induction of the Stringent Response appears to block initiation of DNA replication at oriC itself. No DNA synthesis was detected in the oriC region and, upon lifting the Stringent Response, replication occurred from oriC. Post-initiation control in B. subtilis therefore results in duplication of many key genes involved in growth and sporulation. We discuss the possibility that such a control might be linked to differentiation in this organism.

Overreplication of the origin region in the dnaB37 mutant of Bacillus subtilis: postinitiation control of chromosomal replication

When the Bacillus subtilis dnaB37 mutant, defective in initiation, is returned to permissive temperature after accumulation of initiation proteins at 45 degrees C, we have shown, by extensive DNA.DNA hybridization analysis, that the origin region is replicated in excess (approximately 2-fold). However, this replication is limited to a region of about 120-175 kilobases on either side of the origin. This has been confirmed by autoradiographic analysis of the overreplicated region. During the second round of synchronized replication at 30 degrees C, replication in fact appears to resume from the stalled forks on either side of the origin. We propose that in B. subtilis, in addition to a first level of control at the origin, a second level of control exists downstream of the origin in order to limit overreplication of the chromosome. These two controls might normally be tightly coupled. We suggest that the second level of control is exerted through the reversible inhibition of replisome movement at specific regions on either side of the origin.

Chromosomal initiation in Bacillus subtilis may involve two closely linked origins

When the dnaB37 initiation mutant of Bacillus subtilis is returned to a permissive temperature following a period at 45 degrees C, a synchronous round of DNA replication immediately ensues. Using this system we have been able to analyse the first fragments to be replicated while avoiding the use of thymine starvation or inhibitors of DNA replication. Such treatments are necessary to achieve even modest synchrony in germinating spores. Our results showed that the first fragment to be replicated was a 4 kb BamHI-SalI restriction fragment, BS6. In contrast, when the analysis was performed out in the presence of novobiocin, an inhibitor of DNA gyrase, replication from BS6 was inhibited and the first fragment to be replicated was BS5, a 5.6 kb fragment located 1.7 kb to the right of BS6. Replication from both putative origins was suppressed by rifamycin and was dependent upon dnaB. The results are discussed in relation to previous attempts to identify the first replicating fragment in germinating spores. We also discuss the possibility that B. subtilis contains two origins and suggest that either can act as the primary origin under certain conditions, or alternatively that both origins may act in concert in normal bidirectional replication, each site being required for the leading strand in each direction.

Physiological properties of cold-sensitive suppressor mutations of a temperature-sensitive dnaZ mutant of Escherichia coli

Suppressors of a temperature-sensitive dnaZ polymerization mutant of Escherichia coli have been identified by selecting temperature-insensitive revertants. Those suppressed strains which concomitantly became cold sensitive were chosen for further study. Intragenic suppressor mutations, which caused cold-sensitive defects in DNA polymerization, were located in dnaZ by transduction with lambda dnaZ+ phages. Extragenic suppressor mutations were mapped within the initiation gene dnaA. These suppressor-containing strains were defective in initiation at low temperature as determined by measurements of DNA synthesis in vivo and in toluene-treated cells. The occurrence of suppressor mutations of dnaZ(Ts) within the dnaA gene is considered evidence that the dnaA and dnaZ products interact in vivo. A second indication of a dnaA-dnaZ protein-protein interaction was provided by the observation that the introduction of additional copies of the dnaZ+ gene into a strain carrying the dnaA suppressor mutation was lethal [whether the strain was dnaZ+ or dnaZ(Ts)].

Interaction of the Escherichia coli dnaA initiation protein with the dnaZ polymerization protein in vivo

To define in vivo interactions of Escherichia coli DNA replication components, extragenic suppressors of a dnaZ(TS) mutant were isolated. A temperature-sensitive dnaZ mutant, which is defective in polymerization, was placed at 39 degrees C to select temperature-insensitive revertants. Some of these revertants also were cold sensitive, a phenotypic property that facilitated study of the suppressor. Mapping of the cold sensitivity indicated that some of the suppressor mutations are intragenic but others are located within the initiation gene, dnaA. The dnaA mutations that suppress the dnaZ(TS) defect are designated dnaA(SUZ, CS). The dnaA(SUZ, CS) strains have a defect in DNA synthesis at low temperature that is typical of an initiation defect. These data suggest that the dnaA product, an initiation factor, interacts in vivo with the dnaZ protein, a polymerization factor.

Possible involvement of DNA-linked RNA in the initiation of Bacillus subtilis chromosome replication

After thermal denaturation, an in vivo-labeled RNA was found in a temperature-sensitive initiation mutant of Bacillus subtilis (dna-37) associated with high-molecular-weight DNA. This RNA could be clearly distinguished from other RNA species by different techniques of separation, such as Sepharose 2B filtration, chromatography on nitrocellulose, and equilibrium centrifugation in density gradient. It was obtained even when HCHO was present during denaturation and chilling of nucleic acids and was still detected after a second denaturation as well as after incubation with proteinase K. Properties of the complex were not altered by prior treatment with RNase H. A control experiment using two samples of the complex treated either with pancreatic DNase or with pancreatic RNase, denatured together and centrifuged in the same density gradient, showed that no artifactual associations occur between the DNA and the RNA components of the complex. These results demonstrate that the DNA and RNA in the complex are associated by neither hydrogen bonds nor proteins, but are indicative of a DNA-RNA covalent linkage. In addition, during synchronous replication after a previous period at a nonpermissive temperature, DNA-linked RNA synthesis took place at specific times which coincided with the appearance of rifampin resistance of the first and the second replication cycles. A possible involvement of this RNA in the initiation of chromosome replication is discussed.

Inhibition of deoxyribonucleic acid replication in Bacillus brevis by ribonucleic acid polymerase inhibitors

The incorporation of [3H]thymidine into deoxyribonucleic acid by exponentially growing cells of Bacillus brevis was inhibited by streptolydigin and rifampin in the same concentration range in which these drugs inhibit ribonucleic acid synthesis. Complete inhibition occurred within one-third generation time after drug addition, suggesting an effect on deoxyribonucleic acid chain elongation.

Suppression of the DnaA phenotype by mutations in the rpoB cistron of ribonucleic acid polymerase in Salmonella typhimurium and Escherichia coli

A class of mutations that confer resistance to rifampin in Salmonella typhimurium and Escherichia coli also suppresses the thermosensitivity of chromosome initiation in dnaA mutants. Ribonucleic acid polymerase is resistant to rifampin in vitro in these suppressive mutants, and the suppressors of dnaA cannot be separated from the rpoB mutations by transduction. It is concluded, therefore, that certain rpoB mutations may suppress the DnaA phenotype.

NOVEL Escherichia coli dnaB mutant: direct involvement of the dnaB252 gene product in the synthesis of an origin-ribonucleic acid species during initiaion of a round of deoxyribonucleic acid replication

The initiation process of deoxyribonucleic acid (DNA) replication in Escherichia coli has been studied using the thermoreversible dna initiation mutant E. coli HfrHl65/120/6 dna-252. This dna mutation was incorrectly classed as a dnaA mutation. Biochemical and genetic evidence suggests that the dna-252 mutant is a novel dnaB mutant, possessing phenotypic properties which distinguish it from other dnaB mutants. Sensitivity of reinitiation in the dna-252 mutant to specific inhibitors of protein, ribonucleic acid (RNA), and DNA synthesis was studied. Reinitiation is shown to be sensitive to rifampin and streptolydigin but not to cholramphenicol. Thus, the dna-252 gene product appears to be required during the initiation process for a step occurring either before or during synthesis of an RNA species (origin-RNA). Using reversible inhibition of RNA synthesis by streptolydigin of a streptolydigin-sensitive derivative of the dna-252 mutant, the dna-252 gene product is shown to be directly involved in the synthesis of an orgin-RNA species. These results are included in a schematic model presented in the accompanying paper of the temporal sequence of events occurring during the initiation process.

Temporal sequence of events during the initiation process in Escherichia coli deoxyribonucleic acid replication: roles of the dnaA and dnaC gene products and ribonucleic acid polymerase

Three thermosensitive deoxyribonucleic acid (DNA) initiation mutants of Escherichia coli exposed to the restrictive temperature for one to two generations were examined for the ability to reinitiate DNA replication after returning to the permissive temperature in the presence of rifampin, chloramphenicol, or nalidixic acid. Reinitiation in the dnaA mutant was inhibited by rifampin but not by chloramphenicol, whereas renitiation was not inhibited by rifampin but not by chloramphenicol, whereas reinitiation was not inhibited in two dnaC mutants by either rifampin or chloramphenicol. To observe the rifampin inhibition, the antibiotic must be added at least 10 min before return to the permissive temperature. The rifampin inhibition of reinitiation was not observed when a rifampin-resistant ribonucleic acid ((RNA) polymerase gene was introduced into the dnaA mutant, demonstrating that RNA polymerase synthesizes one or more RNA species required for the initation of DNA replication (origin-RNA). Reinitiation at 30 degrees C was not inhibited by streptolydigin in a stretolydigin-sensitive dnaA muntant. Incubation in the presence of nalidixic acid prevented subsequent reinitiation in the dnaC28 mutant but did not inhibit reinitiation in the dnaA5 muntant. These results demonstrate that the dnaA gene product acts before or during the synthesis of an origin-RNA, RNA polymerase synthesizes this origin RNA, and the dnaC gene product is involved in a step after this RNA synthesis event. Furthermore, these results suggest that the dnaC gene product is involved in the first deoxyribounucleotide polymerization event wheareas the dnaA gene product acts prior to this event. A model is presented describing the temporal sequence of events that occur during initiation of a round of DNA replication, based on results in this and the accompanying paper.

A new mutant of Bacillus subtilis altered in the initiation of chromosome replication

We have isolated a new mutant of Bacillus subtilis temperature sensitive in DNA replication; its properties are those of an initiation mutant. When liquid cultures are shifted to 48 degrees DNA replication is the first macromolecular synthesis that stops, but only after synthesis of the amount of DNA predicted for the completion of one replication round. When spores of the mutant are germinated and shifted to 48 degrees at subsequent times, one round of DNA replication is observed only when the shift occurs between 60 and 100 min; earlier shifts do not allow replication to start, later shifts allow more than one replication. The DNA replicated after a shift to high temperature is enriched in markers close to the terminus. The reinitiation of DNA replication stopped by the high temperature, takes place following a shift to a permissive temperature only if protein synthesis is allowed. Examination of DNA replication following toluene treatment shows that the elongation of DNA chains is not affected at the non-permissive temperature. This mutant is shown by PBS-1 mapping to correspond to a new gene denominated dna P, which is located between the thy A and fur A genes and is distinct from all the mapped dna and rec genes of Bacillus subtilis. The mutation confers to the cells also a deficiency in the ability to be transformed, to be transfected with SPP1 phage DNA, and to survive treatment with methyl-methane sulfonate. These deficiencies, observed at the permissive temperature, are no more temperature dependent than in the parental strain. The ability to perform homologous and heterologous transduction with PBS-1 phage and the sensitivity to ultraviolet radiation or mitomycin C are normal.

Alterations of the rate of movement of deoxyribonucleic acid replication forks

Antibiotics that inhibit ribonucleic acid (RNA) or protein synthesis are often used in studies of deoxyribonucleic acid (DNA) synthesis. The experiments presented here demonstrate that the rate of movement of DNA replication forks can be influenced by such antibotics. Addition of either chloramphenicol, which inhibits movement of ribosomes along messenger RNA, or streptolydigin, which inhibits movement of RNA polymerase, leads to a decrease in the rate of fork movement. Rifampin, which inhibits initiation of RNA synthesis, reverses the effects of chloramphenicol or streptolydigin. The slowed movement of DNA replication forks is discussed in terms of obstruction of fork movement by transcription complexes temporarily immobilized on the DNA template.

Role of ribonucleic acid synthesis in replication of deoxyribonucleic acid

An experiment previously interpreted to show a ribonucleic acid requirement for propagation of deoxyribonucleic replication is reexamined and the earlier interpretation is shown to be incorrect.

F deoxyribonucleic acid transferred to recipient cells in the presence of rifampin

When Escherichia coli F+ cells resistant to rifampin and streptomycin are mated with F- cells sensitive to the antibiotics, a large fraction of F factor deoxyribonucleic acid (DNA), which is transferred to the recipient cells in the presence of either of the antibiotics, can be recovered as covalently closed, circular double-stranded DNA, as in the control mating in the absence of antibiotic. Similar results were obtained in the presence of chloramphenicol or chloramphenicol plus rifampin. It is suggested that the transferred single-stranded F DNA can be converted to the covalently closed, circular double-stranded form in the absence of protein synthesis, and that rifampin-sensitive transcription is not required for the conversion.

Reinitiation of deoxyribonucleic acid synthesis by deoxyribonucleic acid initiation mutants of Escherichia coli: role of ribonucleic acid synthesis, protein synthesis, and cell division

The dnaA and dnaC genes are thought to code for two proteins required for the initiation of chromosomal deoxyribonucleic acid replication in Escherichia coli. When a strain carrying a mutation in either of these genes is shifted from a permissive to a restrictive temperature, chromosome replication ceases after a period of residual synthesis. When the strains are reincubated at the permissive temperature, replication again resumes after a short lag. This reinitiation does not require either protein synthesis (as measured by resistance to chloramphenicol) or ribonucleic acid synthesis (as measured by resistance to rifampin). Thus, if there is a requirement for the synthesis of a specific ribonucleic acid to initiate deoxyribonucleic acid replication, this ribonucleic acid can be synthesized prior to the time of initiation and is relatively stable. Furthermore, the synthesis of this hypothetical ribonucleic acid does not require either the dnaA of dnaC gene products. The buildup at the restrictive temperature of the potential to reinitiate deoxyribonucleic acid synthesis at the permissive temperature shows rather complex kinetics the buildup roughly parallels the rate of mass increase of the culture for at least the first mass doubling at the restrictive temperature. At later times there appears to be a gradual loss of initiation potential despite a continued increase in mass. Under optimal conditions the increase in initiation potential can equal, but not exceed, the increase in cell division at the restrictive temperature. These results are most easily interpreted according to models that postulate a relationship between the initiation of deoxyribonucleic acid synthesis and the processes leading to cell division.

Characteristics of a Bacillus subtilis W23 mutant temperature sensitive for initiation of chromosome replication

A temperature-sensitive mutant of Bacillus subtilis W23, dna-20 (Ts), has been isolated and shown to be defective in initiation of rounds of chromosome replication at the nonpermissive temperature. Upon transfer of dna-20(Ts) from 30 to 45 C, deoxyribonucleic acid synthesis, as measured by [3H]thymine incorporation, gradually ceases. The distribution of genetic markers among unreplicated and replicated deoxyribonucleic acid, isolated from dna-20(Ts) after a period at 43 C in a medium containing 5-bromouracil, and fractionated in a CsCl gradient, shows that the cessation of initiation at the higher temperature is immediate. On the other hand, ribonucleic acid and protein synthesis continues at elevated or unaltered rates for some time after the shift to 45 C. Marker frequency analysis shows that all rounds of replication in progress at the time of the temperature shift terminate rapidly (within 40 min), even when chromosomes are replicating dichotomously in rich media. dna-20(Ts) remains 100% viable for at least 2 h at 45 C. Over a 5-h period at 45 C the nuclear bodies remain compact; a small number (less than 5%) of deoxyribonucleic acid-less cells are produced, but there is no morphological distortion of the cells. When the cells are returned to 30 C after 2 h at 45 C, chromosome replication is initiated rapidly at the normal origin and then proceeds in the normal established sequence. However, a second round of replication is initiated soon after the first. dna-20(Ts) has been shown to map as a B-group mutation, the major class of initiation mutants identified in B. subtillus 168.

Control of deoxyribonucleic acid synthesis in a Bacillus subtilis mutant temperature sensitive for initiation of chromosome replication

We used a Bacillus subtilis mutant described previously, which is temperature sensitive for initiation of replication. The inhibition of deoxyribonucleic acid synthesis occurring at 45 C was shown to be reversed when the temperature is lowered even in the absence of protein synthesis. If the bacteria are returned to 30 C, after a prior period at 45 C, they are able to initiate the first round of replication in the presence of chloramphenicol, but the initiation of the second round still requires protein synthesis. This paper shows that the proteins necessary to initiate the second round of replication can be present in bacteria long before this round is initiated. In addition, the appearance of these proteins seems to be influenced by the length of the previous 45 C period. Although similar reinitiation kinetics are observed at 30 C after prior 45 C periods of 30 or 65 min, the ability to initiate the second round without further protein synthesis appears much earlier after a longer exposure at 45 C. To explain these results, a hypothesis is presented which assumes that two different proteins are both necessary for initiation. Only one of these proteins could be accumulated at 45 C during the inhibition of deoxyribonucleic acid synthesis. A peculiarity of initiation material in mutant Ts 37 is that it may be active at 45 C if it has been exposed previously at 30 C.