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Menikpurage IP, Woo K, Mera PE. Transcriptional Activity of the Bacterial Replication Initiator DnaA. Front Microbiol 2021; 12:662317. [PMID: 34140937 PMCID: PMC8203912 DOI: 10.3389/fmicb.2021.662317] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/19/2021] [Indexed: 11/13/2022] Open
Abstract
In bacteria, DnaA is the most conserved DNA replication initiator protein. DnaA is a DNA binding protein that is part of the AAA+ ATPase family. In addition to initiating chromosome replication, DnaA can also function as a transcription factor either as an activator or repressor. The first gene identified to be regulated by DnaA at the transcriptional levels was dnaA. DnaA has been shown to regulate genes involved in a variety of cellular events including those that trigger sporulation, DNA repair, and cell cycle regulation. DnaA's dual functions (replication initiator and transcription factor) is a potential mechanism for DnaA to temporally coordinate diverse cellular events with the onset of chromosome replication. This strategy of using chromosome replication initiator proteins as regulators of gene expression has also been observed in archaea and eukaryotes. In this mini review, we focus on our current understanding of DnaA's transcriptional activity in various bacterial species.
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Affiliation(s)
- Inoka P Menikpurage
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Kristin Woo
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Paola E Mera
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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2
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Riber L, Løbner‐Olesen A. Inhibition of Escherichia coli chromosome replication by rifampicin treatment or during the stringent response is overcome by de novo DnaA protein synthesis. Mol Microbiol 2020; 114:906-919. [PMID: 32458540 PMCID: PMC7818497 DOI: 10.1111/mmi.14531] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/13/2020] [Accepted: 05/16/2020] [Indexed: 12/15/2022]
Abstract
Initiation of Escherichia coli chromosome replication is controlled by the DnaA initiator protein. Both rifampicin-mediated inhibition of transcription and ppGpp-induced changes in global transcription stops replication at the level of initiation. Here, we show that continued DnaA protein synthesis allows for replication initiation both during the rifampicin treatment and during the stringent response when the ppGpp level is high. A reduction in or cessation of de novo DnaA synthesis, therefore, causes the initiation arrest in both cases. In accordance with this, inhibition of translation with chloramphenicol also stops initiations. The initiation arrest caused by rifampicin was faster than that caused by chloramphenicol, despite of the latter inhibiting DnaA accumulation immediately. During chloramphenicol treatment transcription is still ongoing and we suggest that transcriptional events in or near the origin, that is, transcriptional activation, can allow for a few extra initiations when DnaA becomes limiting. We suggest, for both rifampicin treated cells and for cells accumulating ppGpp, that a turn-off of initiation from oriC requires a stop in de novo DnaA synthesis and that an additional lack of transcriptional activation enhances this process, that is, leads to a faster initiation stop.
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Affiliation(s)
- Leise Riber
- Department of BiologyUniversity of CopenhagenCopenhagenDenmark
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The Stringent Response Inhibits DNA Replication Initiation in E. coli by Modulating Supercoiling of oriC. mBio 2019; 10:mBio.01330-19. [PMID: 31266875 PMCID: PMC6606810 DOI: 10.1128/mbio.01330-19] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
To survive bouts of starvation, cells must inhibit DNA replication. In bacteria, starvation triggers production of a signaling molecule called ppGpp (guanosine tetraphosphate) that helps reprogram cellular physiology, including inhibiting new rounds of DNA replication. While ppGpp has been known to block replication initiation in Escherichia coli for decades, the mechanism responsible was unknown. Early work suggested that ppGpp drives a decrease in levels of the replication initiator protein DnaA. However, we found that this decrease is not necessary to block replication initiation. Instead, we demonstrate that ppGpp leads to a change in DNA topology that prevents initiation. ppGpp is known to inhibit bulk transcription, which normally introduces negative supercoils into the chromosome, and negative supercoils near the origin of replication help drive its unwinding, leading to replication initiation. Thus, the accumulation of ppGpp prevents replication initiation by blocking the introduction of initiation-promoting negative supercoils. This mechanism is likely conserved throughout proteobacteria. The stringent response enables bacteria to respond to a variety of environmental stresses, especially various forms of nutrient limitation. During the stringent response, the cell produces large quantities of the nucleotide alarmone ppGpp, which modulates many aspects of cell physiology, including reprogramming transcription, blocking protein translation, and inhibiting new rounds of DNA replication. The mechanism by which ppGpp inhibits DNA replication initiation in Escherichia coli remains unclear. Prior work suggested that ppGpp blocks new rounds of replication by inhibiting transcription of the essential initiation factor dnaA, but we found that replication is still inhibited by ppGpp in cells ectopically producing DnaA. Instead, we provide evidence that a global reduction of transcription by ppGpp prevents replication initiation by modulating the supercoiling state of the origin of replication, oriC. Active transcription normally introduces negative supercoils into oriC to help promote replication initiation, so the accumulation of ppGpp reduces initiation potential at oriC by reducing transcription. We find that maintaining transcription near oriC, either by expressing a ppGpp-blind RNA polymerase mutant or by inducing transcription from a ppGpp-insensitive promoter, can strongly bypass the inhibition of replication by ppGpp. Additionally, we show that increasing global negative supercoiling by inhibiting topoisomerase I or by deleting the nucleoid-associated protein gene seqA also relieves inhibition. We propose a model, potentially conserved across proteobacteria, in which ppGpp indirectly creates an unfavorable energy landscape for initiation by limiting the introduction of negative supercoils into oriC.
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Abstract
Genes of the Rel/Spo homolog (RSH) superfamily synthesize and/or hydrolyse the modified nucleotides pppGpp/ ppGpp (collectively referred to as (p)ppGpp) and are prevalent across diverse bacteria and in plant chloroplasts. Bacteria accumulate (p)ppGpp in response to nutrient deprivation (generically called the stringent response) and elicit appropriate adaptive responses mainly through the regulation of transcription. Although at different concentrations (p)ppGpp affect the expression of distinct set of genes, the two well-characterized responses are reduction in expression of the protein synthesis machinery and increase in the expression of genes coding for amino acid biosynthesis. In Escherichia coli, the cellular (p)ppGpp level inversely correlates with the growth rate and increasing its concentration decreases the steady state growth rate in a defined growth medium. Since change in growth rate must be accompanied by changes in cell cycle parameters set through the activities of the DNA replication and cell division apparatus, (p)ppGpp could coordinate protein synthesis (cell mass increase) with these processes. Here we review the role of (p)ppGpp in bacterial cell cycle regulation.
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Abstract
Recent advancements in fluorescence imaging have shown that the bacterial nucleoid is surprisingly dynamic in terms of both behavior (movement and organization) and structure (density and supercoiling). Links between chromosome structure and replication initiation have been made in a number of species, and it is universally accepted that favorable chromosome structure is required for initiation in all cells. However, almost nothing is known about whether cells use changes in chromosome structure as a regulatory mechanism for initiation. Such changes could occur during natural cell cycle or growth phase transitions, or they could be manufactured through genetic switches of topoisomerase and nucleoid structure genes. In this review, we explore the relationship between chromosome structure and replication initiation and highlight recent work implicating structure as a regulatory mechanism. A three-component origin activation model is proposed in which thermal and topological structural elements are balanced with trans-acting control elements (DnaA) to allow efficient initiation control under a variety of nutritional and environmental conditions. Selective imbalances in these components allow cells to block replication in response to cell cycle impasse, override once-per-cell-cycle programming during growth phase transitions, and promote reinitiation when replication forks fail to complete.
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Ferullo DJ, Lovett ST. The stringent response and cell cycle arrest in Escherichia coli. PLoS Genet 2008; 4:e1000300. [PMID: 19079575 PMCID: PMC2586660 DOI: 10.1371/journal.pgen.1000300] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2008] [Accepted: 11/07/2008] [Indexed: 11/18/2022] Open
Abstract
The bacterial stringent response, triggered by nutritional deprivation, causes an accumulation of the signaling nucleotides pppGpp and ppGpp. We characterize the replication arrest that occurs during the stringent response in Escherichia coli. Wild type cells undergo a RelA-dependent arrest after treatment with serine hydroxamate to contain an integer number of chromosomes and a replication origin-to-terminus ratio of 1. The growth rate prior to starvation determines the number of chromosomes upon arrest. Nucleoids of these cells are decondensed; in the absence of the ability to synthesize ppGpp, nucleoids become highly condensed, similar to that seen after treatment with the translational inhibitor chloramphenicol. After induction of the stringent response, while regions corresponding to the origins of replication segregate, the termini remain colocalized in wild-type cells. In contrast, cells arrested by rifampicin and cephalexin do not show colocalized termini, suggesting that the stringent response arrests chromosome segregation at a specific point. Release from starvation causes rapid nucleoid reorganization, chromosome segregation, and resumption of replication. Arrest of replication and inhibition of colony formation by ppGpp accumulation is relieved in seqA and dam mutants, although other aspects of the stringent response appear to be intact. We propose that DNA methylation and SeqA binding to non-origin loci is necessary to enforce a full stringent arrest, affecting both initiation of replication and chromosome segregation. This is the first indication that bacterial chromosome segregation, whose mechanism is not understood, is a step that may be regulated in response to environmental conditions.
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Affiliation(s)
- Daniel J. Ferullo
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Susan T. Lovett
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
- * E-mail:
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Dasgupta S, Løbner-Olesen A. Host controlled plasmid replication: Escherichia coli minichromosomes. Plasmid 2005; 52:151-68. [PMID: 15518873 DOI: 10.1016/j.plasmid.2004.08.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2004] [Revised: 08/06/2004] [Indexed: 11/26/2022]
Abstract
Escherichia coli minichromosomes are plasmids replicating exclusively from a cloned copy of oriC, the chromosomal origin of replication. They are therefore subject to the same types of replication control as imposed on the chromosome. Unlike natural plasmid replicons, minichromosomes do not adjust their replication rate to the cellular copy number and they do not contain information for active partitioning at cell division. Analysis of mutant strains where minichromosomes cannot be established suggest that their mere existence is dependent on the factors that ensure timely once per cell cycle initiation of replication. These observations indicate that replication initiation in E. coli is normally controlled in such a way that all copies of oriC contained within the cell, chromosomal and minichromosomal, are initiated within a fairly short time interval of the cell cycle. Furthermore, both replication and segregation of the bacterial chromosome seem to be controlled by sequences outside the origin itself.
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Affiliation(s)
- Santanu Dasgupta
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Box 596, SE-751 24, Sweden
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Su'etsugu M, Emoto A, Fujimitsu K, Keyamura K, Katayama T. Transcriptional control for initiation of chromosomal replication in Escherichia coli: fluctuation of the level of origin transcription ensures timely initiation. Genes Cells 2003; 8:731-45. [PMID: 12940821 DOI: 10.1046/j.1365-2443.2003.00671.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND During the cell cycle, the initiation of chromosomal replication is strictly controlled. In Escherichia coli, the initiator DnaA and the replication origin oriC are major targets for this regulation. Here, we assessed the role of transcription of the mioC gene, which reads through the adjacent oriC region. This mioC-oriC transcription is regulated in coordination with the replication cycle so that it is activated after initiation and repressed before initiation. RESULTS We isolated a strain bearing a mioC promoter mutation that causes constitutive mioC-oriC transcription from the chromosome. A quantitative S1 nuclease assay indicated that in this mutant, the level of transcription does not fluctuate. Introduction of this mutation suppressed the growth defect of an overinitiation-type dnaAcos mutant, and severely inhibited the growth of initiation-defective dnaA mutants at semipermissive temperatures in a dnaA allele-specific manner. These results suggest that mioC-oriC transcription inhibits initiation at oriC. Indeed, flow cytometry analysis and quantification of DNA replication in synchronized cultures revealed that the mioC promoter mutation alters the control of the initiation of chromosomal replication, for instance by delaying replication within the cell cycle. CONCLUSIONS These results suggest that the transcriptional regulation of the mioC gene is required for cell cycle-coordinated initiation of chromosomal replication.
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Affiliation(s)
- Masayuki Su'etsugu
- Department of Molecular Biology, Kyushu University Graduate School of Pharmaceutical Sciences, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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Bates DB, Boye E, Asai T, Kogoma T. The absence of effect of gid or mioC transcription on the initiation of chromosomal replication in Escherichia coli. Proc Natl Acad Sci U S A 1997; 94:12497-502. [PMID: 9356478 PMCID: PMC25015 DOI: 10.1073/pnas.94.23.12497] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Despite the widely accepted view that transcription of gid and mioC is required for efficient initiation of cloned oriC, we show that these transcriptions have very little effect on initiation of chromosome replication at wild-type chromosomal oriC. Furthermore, neither gid nor mioC transcription is required in cells deficient in the histone-like proteins Fis or IHF. However, oriC that is sufficiently impaired for initiation by deletion of DnaA box R4 requires transcription of at least one of these genes. We conclude that transcription of mioC and especially gid is needed to activate oriC only under suboptimal conditions. We suggest that either the rifampicin-sensitive step of initiation is some other transcription occurring from promoter(s) within oriC, or the original inference of transcriptional activation derived from the rifampicin experiments is incorrect.
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Affiliation(s)
- D B Bates
- Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
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Tesfa-Selase F, Drabble WT. Specific binding of DnaA protein to a DnaA box in the guaB gene of Escherichia coli K12. EUROPEAN JOURNAL OF BIOCHEMISTRY 1996; 241:411-6. [PMID: 8917437 DOI: 10.1111/j.1432-1033.1996.00411.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Expression of the guaBA operon of Escherichia coli is regulated by the DNA replication-initiating protein, DnaA. Two DnaA boxes, which are potential binding sites for DnaA, are present in the gua operon. One box (with 8/9 match to the DnaA box consensus sequence) is at the gua promoter; the other box, which has a consensus sequence, is on the non-transcribed strand within the guaB coding region approximately 200 bp downstream of the initiation codon. The binding in vitro of purified DnaA protein to these boxes was investigated by filter retention and gel retardation analysis, and by deoxyribonuclease I footprinting, using restriction fragments of gua operon DNA. DnaA protein was shown to bind specifically only to the fragment carrying the consensus sequence DnaA box, and to protect this box from deoxyribonuclease I. Transcription termination resulting from the binding of DnaA to this box within the guaB gene explains repression by DnaA of the gua operon in vivo.
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Affiliation(s)
- F Tesfa-Selase
- Department of Biochemistry, University of Southampton, England
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12
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Bogan JA, Helmstetter CE. mioC transcription, initiation of replication, and the eclipse in Escherichia coli. J Bacteriol 1996; 178:3201-6. [PMID: 8655499 PMCID: PMC178071 DOI: 10.1128/jb.178.11.3201-3206.1996] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The potential role of mioC transcription as a negative regulator of initiation of chromosome replication in Escherichia coli was evaluated. When initiation was aligned by a shift of dnaC2(Ts) mutants to nonpermissive temperature (40 degrees C), mioC transcript levels measured at the 5' end or reading through oriC disappeared within one mass doubling. Upon return to permissive temperature (30 degrees C), the transcripts reappeared coordinately about 15 min after the first synchronized initiation and then declined sharply again 10 min later, just before the second initiation. Although these observations were consistent with the idea that mioC transcription might have to be terminated prior to initiation, it was found that the interval between initiations at permissive temperature, i.e., the eclipse period, was not influenced by the time required to shut down mioC transcription, since the eclipse was the same for chromosomes and minichromosomes which lacked mioC transcription. This finding did not, in itself, rule out the possibility that mioC transcription must be terminated prior to initiation of replication, since it might normally be shut off before initiation, and never be limiting, even during the eclipse. Therefore, experiments were performed to determine whether the continued presence of mioC transcription during the process of initiation altered the timing of initiation. It was found that minichromosomes possessing a deletion in the DnaA box upstream of the promoter transcribed mioC continuously and replicated with the same timing as those that either shut down expression prior to initiation or lacked expression entirely. It was further shown that mioC transcription was present throughout the induction of initiation by addition of chloramphenicol to a dnaA5(Ts) mutant growing at a semipermissive temperature. Thus, transcription through oriC emanating from the mioC gene promoter is normally inhibited prior to initiation of replication by the binding of DnaA protein, but replication can initiate with the proper timing even when transcription is not shut down; i.e., mioC does not serve as a negative regulator of initiation. It is proposed, however, that the reappearance and subsequent disappearance of mioC transcription during a 10-min interval at the end of the eclipse serves as an index of the minimum time required for the establishment of active protein-DNA complexes at the DnaA boxes in the fully methylated origin region of the chromosome. On this basis, the eclipse constitutes the time for methylation of the newly formed DNA strands (15 to 20 min at 30 degrees C) followed by the time for DnaA protein to bind and activate oriC for replication (10 min).
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Affiliation(s)
- J A Bogan
- Department of Biological Sciences, Florida Institute of Technology, Melbourne, 32901, USA
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13
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Sakakibara Y. Rifampin-induced initiation of chromosome replication in dnaR-deficient Escherichia coli cells. J Bacteriol 1996; 178:1242-7. [PMID: 8631698 PMCID: PMC177795 DOI: 10.1128/jb.178.5.1242-1247.1996] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The dnaR130 mutant of Escherichia coli, which was thermosensitive in initiation of chromosome replication, was capable of thermoresistant DNA synthesis in the presence of rifampin at a low concentration that allowed almost normal RNA synthesis. The DNA synthesis in the presence of the drug depended on protein synthesis at the high temperature. The protein synthesis in the dnaR-deficient cells provided a potential for thermoresistant DNA synthesis to be induced at a high dose of the drug that almost completely prevented RNA synthesis. The induced synthesis was synchronously initiated from oriC and proceeded semiconservatively toward terC. The replication depended on the dnaA function, which was essential for normal initiation of replication from oriC. The capability for drug-induced replication was abolished by certain rifampin resistance mutations in the beta subunit of RNA polymerase. Thus, the drug can induce the dnaA-dependent initiation of replication in the dnaR-deficient cells through its effect on RNA polymerase. This result implies that the dnaR product is involved in the transcription obligatory for the initiation of replication of the bacterial chromosome.
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Affiliation(s)
- Y Sakakibara
- Department of Biochemistry and Cellular Biology, National Institute of Health, Tokyo, Japan
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14
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Levine A, Autret S, Séror SJ. A checkpoint involving RTP, the replication terminator protein, arrests replication downstream of the origin during the Stringent Response in Bacillus subtilis. Mol Microbiol 1995; 15:287-95. [PMID: 7746150 DOI: 10.1111/j.1365-2958.1995.tb02243.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
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.
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Affiliation(s)
- A Levine
- Institut de Génétique et Microbiologia, URA CNRS 1354, Université Paris XI, Orsay, France
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15
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Wu F, Levchenko I, Filutowicz M. Binding of DnaA protein to a replication enhancer counteracts the inhibition of plasmid R6K gamma origin replication mediated by elevated levels of R6K pi protein. J Bacteriol 1994; 176:6795-801. [PMID: 7961437 PMCID: PMC197046 DOI: 10.1128/jb.176.22.6795-6801.1994] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Replication of the gamma origin of Escherichia coli plasmid R6K requires pi protein, encoded by the R6K pir gene, and many host factors, including DnaA protein. Pi has dual roles, activating replication at low levels and inhibiting replication at high levels. The inhibitory function of pi is counteracted by integration host factor and a specific sequence of the origin called the enhancer. This 106-bp DNA segment contains a binding site for DnaA protein (DnaA box 1). In this study, we mutated this site to determine if it was required for the enhancer's function. Using gamma origin derivative plasmids with the DnaA box 1 altered or deleted, we show that this site is necessary to protect the origin against levels of wild-type pi protein that would otherwise inhibit replication. To show that the base substitutions in DnaA box 1 weakened the binding of DnaA, we developed a new application of the agarose gel retardation assay. This quick and easy assay has broad applicability, as shown in binding studies with DNA fragments carrying a different segment of the R6K origin, the chromosomal origin (oriC), or the pUC origin. The gel retardation assay suggests a stoichiometry of DnaA binding different from that deduced from other assays.
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Affiliation(s)
- F Wu
- Department of Bacteriology, University of Wisconsin--Madison 53706
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16
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Skarstad K, Boye E. The initiator protein DnaA: evolution, properties and function. BIOCHIMICA ET BIOPHYSICA ACTA 1994; 1217:111-30. [PMID: 8110826 DOI: 10.1016/0167-4781(94)90025-6] [Citation(s) in RCA: 141] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- K Skarstad
- Department of Biophysics, Institute for Cancer Research, Montebello, Oslo, Norway
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17
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Theisen PW, Grimwade JE, Leonard AC, Bogan JA, Helmstetter CE. Correlation of gene transcription with the time of initiation of chromosome replication in Escherichia coli. Mol Microbiol 1993; 10:575-84. [PMID: 7968535 DOI: 10.1111/j.1365-2958.1993.tb00929.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Transcriptional levels of the Escherichia coli mioC and gidA genes, which flank the chromosomal origin of replication (oriC) and the dnaA gene, were correlated with the time of initiation of chromosome replication. The transcripts were measured either in dnaC2(ts) mutants that had been aligned for initiation of chromosome replication by a temperature shift or in synchronous cultures of cells obtained using the baby machine technique. In both types of experiments, mioC transcription was inhibited prior to initiation of chromosome replication and resumed several minutes after initiation. Conversely, gidA and dnaA transcription were both inhibited after initiation of replication, coincident with the period of hemimethylation of oriC DNA. It is proposed that mioC transcription prevents initiation of chromosome replication, and must terminate before replication can begin. It is further proposed that the eclipse period between rounds of replication, i.e. the minimum interval between successive initiations, encompasses the time required to methylate GATC sequences in newly replicated oriC plus the time required to terminate mioC transcription. Conversely, the active transcription of gidA and dnaA prior to initiation is consistent with their positive effects on initiation, and their shutdown after initiation could serve to limit premature reinitiation.
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Affiliation(s)
- P W Theisen
- Department of Biological Sciences, Florida Institute of Technology, Melbourne 32901
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18
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Løbner-Olesen A, Boye E. Different effects of mioC transcription on initiation of chromosomal and minichromosomal replication in Escherichia coli. Nucleic Acids Res 1992; 20:3029-36. [PMID: 1620598 PMCID: PMC312433 DOI: 10.1093/nar/20.12.3029] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The mioC gene, which neighbors the chromosomal origin of replication (oriC) in Escherichia coli, has in a number of studies been implicated in the control of oriC initiation on minichromosomes. The present work reports on the construction of cells carrying different mioC mutations on the chromosome itself. Flow cytometry was employed to study the DNA replication control and growth pattern of the resulting mioC mutants. All parameters measured (growth rate, cell size, DNA/cell, number of origins per cell, timing of initiation) were the same for the wild type and all the mioC mutant cells under steady state growth and after different shifts in growth medium and after induction of the stringent response. It may be concluded that the dramatic effects of mioC mutations reported for minichromosomes are not observed for chromosomal replication and that the mioC gene and gene product is of little importance for the control of initiation. The data demonstrate that a minichromosome is not necessarily a valid model for chromosomal replication.
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Affiliation(s)
- A Løbner-Olesen
- Department of Microbiology, Technical University of Denmark, Lyngby, Copenhagen
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19
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Tam JE, Davis CH, Thresher RJ, Wyrick PB. Location of the origin of replication for the 7.5-kb Chlamydia trachomatis plasmid. Plasmid 1992; 27:231-6. [PMID: 1513879 DOI: 10.1016/0147-619x(92)90025-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The hypothetical origin of replication for the 7.5-kb plasmid common to Chlamydia trachomatis is believed to be in a region of the plasmid that contains four 22-bp tandem repeats preceded by an A-T-rich region. To test this hypothesis, replication of plasmid DNA in metabolically active reticulate bodies of the Lymphogranuloma venereum biovar of C. trachomatis was examined by electron microscopy. The results presented show that the origin of replication appears to be near the tandem repeats of pCHL2. In addition, replication of the 7.5-kb plasmid is unidirectional, and the copy number during replication is 7-10. The evidence presented suggests that C. trachomatis has a homologue to the Escherichia coli dnaA gene and that this homologue might be involved in replication of the C. trachomatis 7.5-kb plasmid.
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Affiliation(s)
- J E Tam
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill 27514
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20
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Asai T, Chen CP, Nagata T, Takanami M, Imai M. Transcription in vivo within the replication origin of the Escherichia coli chromosome: a mechanism for activating initiation of replication. MOLECULAR & GENERAL GENETICS : MGG 1992; 231:169-78. [PMID: 1736090 DOI: 10.1007/bf00279788] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Within the replication origin, oriC, of the Escherichia coli chromosome, novel in vivo transcripts were detected which proceeded rightward and whose production was activated by DnaA protein. In contrast, DnaA protein repressed the previously described ori-L leftward transcription. The former should introduce negative supercoiling, and the latter positive supercoiling, into the 13-mers. The effects of transcription on the initiation of replication were also investigated by making constructs with promoters placed near oriC. Transcription was found to enhance the origin activity only when it was oriented in such a way as to introduce negative supercoiling into the 13-mers. From these results, we propose that transcription within oriC regulates replication initiation by altering the topology of the 13-mer region.
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Affiliation(s)
- T Asai
- Institute for Virus Research, Kyoto University, Japan
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21
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Tesfa-Selase F, Drabble WT. Regulation of the gua operon of Escherichia coli by the DnaA protein. MOLECULAR & GENERAL GENETICS : MGG 1992; 231:256-64. [PMID: 1736096 DOI: 10.1007/bf00279799] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The guaBA operon determines production of the two enzymes required to convert hypoxanthine to guanine at the nucleotide level during guanine nucleotide biosynthesis. Two DnaA boxes, binding sites for the DNA replication-initiating DnaA protein, are present in the gua operon, one at the gua promoter (guaP) and the other within the guaB coding sequence. Regulation of the guaBA operon by DnaA protein was studied using strains carrying chromosomal gua-lacZ fusions. In these strains beta-galactosidase acts as a reporter enzyme for transcription initiated at guaP. When the intracellular levels of DnaA were increased (by induction of a multicopy plasmid carrying the dnaA gene fused to the tac promoter) transcription from the gua promoter was repressed. Reducing the intracellular level of DnaA, either by sequestration with an oriC plasmid or by placing a temperature-sensitive dnaA mutant at the restrictive temperature, resulted in increased transcription from guaP. Thus the transcriptional activity of the gua operon is coupled, through the DnaA protein, to the DNA replication cycle. Repression of guaP by DnaA was dependent on the presence of both boxes in the gua-lacZ fusion; constructs containing only the box at guaP were unaffected by DnaA.
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Affiliation(s)
- F Tesfa-Selase
- Department of Biochemistry, University of Southampton, UK
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22
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Vassilev LT, DePamphilis ML. Guide to identification of origins of DNA replication in eukaryotic cell chromosomes. Crit Rev Biochem Mol Biol 1992; 27:445-72. [PMID: 1473351 DOI: 10.3109/10409239209082569] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Several experimental approaches for identification of origins of DNA replication have been developed recently that allow, for the first time, unique initiation sites in mammalian chromosomes to be mapped at single-copy loci. A brief description of the rationale, advantages, and limitations has been provided for each approach, as well as information that can help the reader choose the method(s) most suitable for a particular system. The various methods are divided into three groups: (1) analysis of nascent DNA strands, (2) analysis of DNA structures, and (3) analysis of origin activity (i.e., ability to support autonomous replication). It is hoped that this information will serve as a practical guide for identifying new origins of replication.
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Affiliation(s)
- L T Vassilev
- Department of Cell and Developmental Biology, Roche Research Center, Nutley, NJ 07110
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23
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Filutowicz M, Ross W, Wild J, Gourse RL. Involvement of Fis protein in replication of the Escherichia coli chromosome. J Bacteriol 1992; 174:398-407. [PMID: 1309527 PMCID: PMC205730 DOI: 10.1128/jb.174.2.398-407.1992] [Citation(s) in RCA: 111] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
We report evidence indicating that Fis protein plays a role in initiation of replication at oriC in vivo. At high temperatures, fis null mutants form filamentous cells, show aberrant nucleoid segregation, and are unable to form single colonies. DNA synthesis is inhibited in these fis mutant strains following upshift to 44 degrees C. The pattern of DNA synthesis inhibition upon temperature upshift and the requirement for RNA synthesis, but not protein synthesis, for resumed DNA synthesis upon downshift to 32 degrees C indicate that synthesis is affected in the initiation phase. fis mutations act synergistically with gyrB alleles known to affect initiation. oriC-dependent plasmids are poorly established and maintained in fis mutant strains. Finally, purified Fis protein interacts in vitro with sites in oriC. These interactions could be involved in mediating the effect of Fis on DNA synthesis in vivo.
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Affiliation(s)
- M Filutowicz
- Department of Bacteriology, University of Wisconsin-Madison 53706
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24
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Wende M, Quinones A, Diederich L, Jueterbock WR, Messer W. Transcription termination in the dnaA gene. MOLECULAR & GENERAL GENETICS : MGG 1991; 230:486-90. [PMID: 1766443 DOI: 10.1007/bf00280306] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The termination of transcription in the dnaA gene of E. coli was analyzed using transcriptional fusions to the galactokinase gene, S1 nuclease mapping and quantification of translation products by Western blots. The majority of transcripts originating from dnaA promoters terminated at several positions within a 200 bp region inside the dnaA reading frame.
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Affiliation(s)
- M Wende
- Max-Planck-Institut für molekulare Genetik, Berlin, FRG
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25
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Ogawa T, Okazaki T. Concurrent transcription from the gid and mioC promoters activates replication of an Escherichia coli minichromosome. MOLECULAR & GENERAL GENETICS : MGG 1991; 230:193-200. [PMID: 1745229 DOI: 10.1007/bf00290668] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The origin of replication of the Escherichia coli chromosome (oriC) is located in an intercistronic region between the gidA and the mioC genes. The possibility that transcription from the promoters of these two genes is involved in minichromosome replication was examined. Inactivation of the gid promoter led to a reduction in transformation frequency with an oriC plasmid but inactivation of the mioC promoter did not. The decrease in transformation frequency was most pronounced when both promoters were inactive. Under conditions that selected for plasmid-harboring cells, mutation of the gid promoter caused efficient multimerization or integration of oriC plasmids into the chromosomal oriC region and loss of free plasmid molecules. These changes in plasmid structure were also observed, albeit less frequently, with some plasmids defective in mioC promoter activity. In an in vitro DNA replication system for oriC DNA, plasmids with a defective gid promoter had greatly reduced template activity and essentially no replication occurred when both promoters were inactive. These results suggest that coupled transcription starting from the gid as well as the mioC promoter activates initiation of plasmid replication, the major contribution being made by gid transcription. These two promoters are suggested to be under stringent control.
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Affiliation(s)
- T Ogawa
- Department of Molecular Biology, School of Science, Nagoya University, Japan
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26
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Pavco PA, Steege DA. Characterization of elongating T7 and SP6 RNA polymerases and their response to a roadblock generated by a site-specific DNA binding protein. Nucleic Acids Res 1991; 19:4639-46. [PMID: 1891355 PMCID: PMC328703 DOI: 10.1093/nar/19.17.4639] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
As a means of generating homogeneous populations of elongation complexes with the RNA polymerases encoded by phages T7 and SP6, transcription has been carried out in vitro on templates associated with the Gln-111 mutant of EcoRI endonuclease. The Gln-111 protein, as a result of a single amino acid substitution at position 111, lacks cleavage function yet shows higher than wild-type affinity for the EcoRI recognition sequence GAATTC. On a series of linear and circular templates associated with Gln-111 protein, blockage of the phage RNA polymerase elongation complex is observed. The 3' endpoint of the major blocked-length RNA species, just 3 bp upstream from the GAATTC, reveals an extremely close approach of polymerase's leading edge to essential contacts between Gln-111 protein and its binding site. In contrast to E. coli RNA polymerase, which is blocked stably and quantitatively by Gln-111 protein (Pavco, P.A. and Steege, D. A. (1990) J. Biol. Chem. 265, 9960-9969), the phage polymerases show substantial levels of readthrough transcription beyond the protein block.
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Affiliation(s)
- P A Pavco
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710
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27
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Abstract
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.
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Affiliation(s)
- H Bremer
- Program in Molecular and Cell Biology, University of Texas at Dallas, Richardson 75083
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28
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Séror SJ, Levine A, Vannier F. Post-initiation control of chromosomal replication in Bacillus subtilis: a mechanism for limiting over-replication or for duplicating key growth and sporulation genes? Res Microbiol 1991; 142:861-7. [PMID: 1784824 DOI: 10.1016/0923-2508(91)90066-j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
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)
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Affiliation(s)
- S J Séror
- Institut de Génétique et de Microbiologie, URA-CNRS, Université Paris XI, Orsay, France
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29
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Levine A, Vannier F, Dehbi M, Henckes G, Séror SJ. The stringent response blocks DNA replication outside the ori region in Bacillus subtilis and at the origin in Escherichia coli. J Mol Biol 1991; 219:605-13. [PMID: 1905358 DOI: 10.1016/0022-2836(91)90657-r] [Citation(s) in RCA: 85] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
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.
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Affiliation(s)
- A Levine
- Institut de Génétique et de Microbiologie, Université Paris XI, Orsay, France
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30
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In vitro apolipoprotein B mRNA editing: identification of a 27S editing complex. Proc Natl Acad Sci U S A 1991; 88:1489-93. [PMID: 1996349 PMCID: PMC51044 DOI: 10.1073/pnas.88.4.1489] [Citation(s) in RCA: 91] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Specific apolipoprotein B (apoB) mRNA editing can be performed in vitro on apoB RNA substrates. Native gels and glycerol gradient sedimentation have been used to determine the physical properties of the in vitro editing activity in rat liver cytosolic S100 extracts. ApoB RNA substrates were progressively assembled as 27S complexes for 3 hr with similar kinetics as seen for the accumulation of edited RNA. Assembly was not observed on RNAs from apoB deletion constructs that did not support editing. The 27S complex contained both edited and unedited RNA sequences. Inhibition of 27S complex assembly by vanadyl-ribonucleoside complexes was accompanied by inhibition of editing. Based on these data, we propose that the 27S complex is the in vitro "editosome," A "mooring sequence" model for RNA recognition and editosome assembly has been proposed involving RNA sequences flanking the edited nucleotide.
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31
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Asai T. [Factors for activation of the replication origin of the E. coli chromosome]. IDENGAKU ZASSHI 1991; 66:85-107. [PMID: 2064802 DOI: 10.1266/jjg.66.85] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- T Asai
- Institute for Virus Research, Kyoto University, Japan
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32
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Wegrzyn G, Neubauer P, Krueger S, Hecker M, Taylor K. Stringent control of replication of plasmids derived from coliphage lambda. MOLECULAR & GENERAL GENETICS : MGG 1991; 225:94-8. [PMID: 1825694 DOI: 10.1007/bf00282646] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The first events of lambda plasmid replication in vivo, which probably regulate this process, are the transcriptional activation of the origin of replication by RNA polymerase and the binding of the initiator protein, lambda O, to this nucleotide sequence. The lambda O protein is known for its rapid proteolytic degradation; hence amino acid starvation of Escherichia coli should result in inhibition of lambda plasmid replication caused by inhibition of protein synthesis. However, contrary to this prediction, we found that lambda plasmid replication, as measured by the increase in plasmid content per bacterial mass, proceeds for hours in an amino acid-starved, relaxed mutant, whereas it is inhibited in its wild-type stringent partner. lambda plasmid replication in amino acid-starved, relaxed cells reveals absolute lambda O dependence and is not inhibited by chloramphenicol at 200 micrograms/ml. This process also occurs in wild-type cells treated with chloramphenicol. We conclude that lambda plasmid replication is under stringent control, probably as a result of the action of ppGpp, the indirect product of the relA gene, on RNA polymerase. The problem of stability of the lambda O initiator protein is discussed.
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Affiliation(s)
- G Wegrzyn
- Department of Molecular Biology, University of Gdańsk, Poland
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33
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Abstract
A DNA structure is defined as paranemic if the participating strands can be separated without mutual rotation of the opposite strands. The experimental methods employed to detect paranemic, unwound, DNA regions is described, including probing by single-strand specific nucleases (SNN), conformation-specific chemical probes, topoisomer analysis, NMR, and other physical methods. The available evidence for the following paranemic structures is surveyed: single-stranded DNA, slippage structures, cruciforms, alternating B-Z regions, triplexes (H-DNA), paranemic duplexes and RNA, protein-stabilized paranemic DNA. The problem of DNA unwinding during gene copying processes is analyzed; the possibility that extended paranemic DNA regions are transiently formed during replication, transcription, and recombination is considered, and the evidence supporting the participation of paranemic DNA forms in genes committed to or undergoing copying processes is summarized.
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MESH Headings
- Animals
- Base Sequence
- Chromosomes/ultrastructure
- DNA/drug effects
- DNA/metabolism
- DNA/ultrastructure
- DNA Helicases/metabolism
- DNA Replication
- DNA Topoisomerases, Type I/metabolism
- DNA Topoisomerases, Type II/metabolism
- DNA, Single-Stranded/drug effects
- DNA, Single-Stranded/metabolism
- DNA, Single-Stranded/ultrastructure
- DNA, Superhelical/drug effects
- DNA, Superhelical/metabolism
- DNA, Superhelical/ultrastructure
- DNA-Binding Proteins/metabolism
- Endonucleases/metabolism
- Models, Genetic
- Molecular Sequence Data
- Nucleic Acid Conformation/drug effects
- Nucleic Acid Denaturation
- Plasmids
- Transcription, Genetic
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Affiliation(s)
- G Yagil
- Department of Cell Biology, Weizmann Institute of Science, Rehovot, Israel
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34
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35
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Analysis of bacterial genome organization and replication using pulsed-field gel electrophoresis. Methods 1990. [DOI: 10.1016/s1046-2023(05)80131-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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36
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Pavco PA, Steege DA. Elongation by Escherichia coli RNA polymerase is blocked in vitro by a site-specific DNA binding protein. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(19)38764-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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37
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Chiaramello AE, Zyskind JW. Coupling of DNA replication to growth rate in Escherichia coli: a possible role for guanosine tetraphosphate. J Bacteriol 1990; 172:2013-9. [PMID: 1690706 PMCID: PMC208699 DOI: 10.1128/jb.172.4.2013-2019.1990] [Citation(s) in RCA: 85] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Two promoters for the Escherichia coli operon that contains the four genes dnaA, dnaN, recF, and gyrB were found to be growth rate regulated and under stringent control. Transcript abundance relative to total RNA increased with the growth rate. Changes in transcription from the dnaAp1 and dnaAp2 promoters that were induced by amino acid starvation and chloramphenicol and were relA dependent were correlated with the stringent response. The abundance of these transcripts per total RNA also decreased in spoT mutants as the severity of the mutation increased (guanosine 5'-diphosphate 3'-diphosphate [ppGpp] basal levels increased). Because expression of these promoters appears to be inhibited by ppGpp, it is proposed that one mechanism for coupling DNA replication to the growth rate of bacteria is through ppGpp synthesis at the ribosome.
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Affiliation(s)
- A E Chiaramello
- Department of Biology, San Diego State University, California 92182
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38
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Eberle H, Van de Merwe W, Madden K, Kampo G, Wright L, Donlon K. The nature of an intragenic suppressor of the Escherichia coli dnaA508 temperature-sensitive mutation. Gene 1989; 84:237-45. [PMID: 2558967 DOI: 10.1016/0378-1119(89)90497-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Escherichia coli strain E508 (dnaA508) is temperature-sensitive for dnaA function. A mutant with an intragenic suppressor of the dnaA508 mutation, called PR1, has been isolated. The suppressor mutation(s) allow initiation of DNA synthesis at 42 degrees C and, like dnaA cold-sensitive mutants, PR1 grows poorly at 32 degrees C. Two-dimensional gel analysis indicates that DnaA protein is overproduced in PR1. Transcriptional analysis indicates two to three times the number of dnaA and dnaN transcripts in PR1, as compared to a wild-type dnaA+ strain. The dnaA gene from PR1 has been cloned and found to complement the original dnaA508 mutation, as well as dnaA46, but not dnaA5. Sequencing of the dnaAPR1 gene reveals three separate base changes, two of which result in nonconservative amino acid substitutions and the third is a change in the start codon from GTG to ATG.
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Affiliation(s)
- H Eberle
- Department of Biophysics, University of Rochester School of Medicine, NY 14642
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39
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Abstract
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.
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40
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41
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Chiaramello AE, Zyskind JW. Expression of Escherichia coli dnaA and mioC genes as a function of growth rate. J Bacteriol 1989; 171:4272-80. [PMID: 2546917 PMCID: PMC210201 DOI: 10.1128/jb.171.8.4272-4280.1989] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The synthesis of specific cellular components related to the initiation process of DNA replication was correlated with changes in growth rate. The concentrations of DnaA protein and mioC mRNA were determined for cells grown at six different growth rates; both increased relative to either total protein or total RNA, respectively, as the growth rate increased. Expression from the chromosomal mioC promoter, which contains a DnaA protein-binding site, was not repressed when the DnaA protein concentration was increased and was not derepressed in a dnaA46 mutant at 42 degrees C. The mioC transcript had a characteristic mRNA-type half-life of 1.51 min.
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Affiliation(s)
- A E Chiaramello
- Department of Biology, San Diego State University, California 92182
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42
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Pierucci O, Rickert M, Helmstetter CE. DnaA protein overproduction abolishes cell cycle specificity of DNA replication from oriC in Escherichia coli. J Bacteriol 1989; 171:3760-6. [PMID: 2544554 PMCID: PMC210122 DOI: 10.1128/jb.171.7.3760-3766.1989] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Initiation of DNA replication from oriC in Escherichia coli takes place at a specific time in the cell division cycle, whether the origin is located on a chromosome or a minichromosome, and requires participation of the product of the dnaA gene. The effects of overproduction of DnaA protein on the cell cycle specificity of the initiation event were determined by using minichromosome replication as the assay system. DnaA protein was overproduced by inducing the expression of plasmid-encoded dnaA genes under control of either the ptac or lambda pL promoter. Induction of DnaA protein synthesis caused a burst of minichromosome replication in cells at all ages in the division cycle. The magnitude of the burst was consistent with the initiation of one round of replication per minichromosome in all cells. The replication burst was followed by a period of reduced minichromosome replication, with the reduction being greater at 30 than at 41 degrees C. The results support the idea that the DnaA protein participates in oriC replication at a stage that is limiting for initiation. Excess DnaA protein enabled all cells to achieve the state required for initiation of DNA polymerization by either effecting or overriding the normal limiting process.
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Affiliation(s)
- O Pierucci
- Department of Experimental Biology, Roswell Park Memorial Institute, Buffalo, New York 14263
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43
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Weinberger M, Helmstetter CE. Inhibition of protein synthesis transiently stimulates initiation of minichromosome replication in Escherichia coli. J Bacteriol 1989; 171:3591-6. [PMID: 2661526 PMCID: PMC210099 DOI: 10.1128/jb.171.7.3591-3596.1989] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Replication of oriC-dependent minichromosomes was found to be transiently stimulated when protein synthesis was inhibited by the addition of chloramphenicol. Initiation of replication was also induced by amino acid starvation of relA mutant strains and a nutritional upshift. The results are explained on the basis that these treatments rendered RNA polymerase more available for participation in the initiation process. As a consequence, the oriC duplex may be transcriptionally activated to an open form, a necessary prerequisite for DNA polymerization.
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Affiliation(s)
- M Weinberger
- Department of Experimental Biology, Roswell Park Memorial Institute, Buffalo, New York 14263
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44
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Ohki M, Smith CL. Tracking bacterial DNA replication forks in vivo by pulsed field gel electrophoresis. Nucleic Acids Res 1989; 17:3479-90. [PMID: 2657661 PMCID: PMC317790 DOI: 10.1093/nar/17.9.3479] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The location of chromosomal DNA replication forks was identified in synchronously replicating E. coli cultures by pulse labeling DNA at specific times with 14C-thymidine and following incorporation of radionucleotide into genomic Not I restriction fragments. This technique could be used to characterize chromosomal DNA replication, to characterize mutations which affect this process, to identify the location of DNA replication origins and termini as well as aid in the construction of macrorestriction maps. Here, we further characterize the DNA replication mutations divE and dnaK and preliminary characterize the genomic organization of E. coli isolate 15.
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Affiliation(s)
- M Ohki
- Biology Division, National Cancer Center Research Institute, Tokyo, Japan
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Masters M, Paterson T, Popplewell AG, Owen-Hughes T, Pringle JH, Begg KJ. The effect of DnaA protein levels and the rate of initiation at oriC on transcription originating in the ftsQ and ftsA genes: in vivo experiments. MOLECULAR & GENERAL GENETICS : MGG 1989; 216:475-83. [PMID: 2546042 DOI: 10.1007/bf00334393] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The DnaA protein of Escherichia coli, essential for initiation at oriC, binds at a defined sequence which occurs at the chromosomal origin, near plasmid replication origins and in the promoters of the dnaA and mioC genes. This sequence also occurs at many other sites on the E. coli chromosome including three sites within the essential cell division genes ftsQ and A. Using an fts-lac fusion phage, lambda JFL100, we show here that fts gene expression responds both to reduced and increased intracellular levels of DnaA protein in a manner consistent with the hypothesis that DnaA protein regulates fts gene expression. Experiments using dnaC and dnaB-ts strains, however, suggest that DnaA control of fts transcription may be indirect, at least in part, with fts responding to the rate of initiation at oriC as well as to changes in DnaA protein level per se. It differs in this respect from dnaA gene expression which is unaffected when initiation of replication is inhibited by DnaB or DnaC inactivation. Strains integratively suppressed with pKN500 behave anomalously; neither fts nor dnaA transcription is significantly increased when DnaA is inactivated in these strains.
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Affiliation(s)
- M Masters
- Department of Molecular Biology, University of Edinburgh, Scotland
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Messer W, Seufert W, Schaefer C, Gielow A, Hartmann H, Wende M. Functions of the DnaA protein of Escherichia coli in replication and transcription. BIOCHIMICA ET BIOPHYSICA ACTA 1988; 951:351-8. [PMID: 2850012 DOI: 10.1016/0167-4781(88)90106-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The function of DnaA protein as a replisome organizer in the initiation of DNA replication is reviewed. A model is presented showing the construction of two basic types of DnaA-dependent replication origin. New data demonstrate that the dnaA box-DnaA protein complex is a transcription terminator. Only one orientation of the dnaA box results in termination of transcription. Mutation of the dnaA box within the dnaA reading frame shows that DnaA-mediated transcription termination has a role in the autoregulation of the dnaA gene.
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Affiliation(s)
- W Messer
- Max-Planck-Institut für molekulare Genetik, Berlin, F.R.G
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Gielow A, Kücherer C, Kölling R, Messer W. Transcription in the region of the replication origin, oriC, of Escherichia coli: termination of asnC transcripts. MOLECULAR & GENERAL GENETICS : MGG 1988; 214:474-81. [PMID: 2464126 DOI: 10.1007/bf00330483] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Transcription from the asnC promoter was found to proceed through the replication origin, oriC, into the gidA gene of Escherichia coli. Between 10% and 20% of asnC transcripts reached oriC in vivo. Termination sites in the intergenic region between asnC and mioC and within mioC were determined in vivo and in vitro using S1 mapping. Only about 10% of the transcripts terminated at the asnC terminator in vivo. DnaA protein dependent termination was observed close to the binding site, dnaA box, for DnaA protein. In the in vitro replication system asnC transcripts did not reach oriC, suggesting that asnC transcripts are not involved in the initiation of replication, contrary to mioC transcripts. We suggest that oriC and mioC might have been transposed during evolution into an asnC regulation.
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Affiliation(s)
- A Gielow
- Max-Planck-Institut für Molekulare Genetik, Berlin, Federal Republic of Germany
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Baker TA, Kornberg A. Transcriptional activation of initiation of replication from the E. coli chromosomal origin: an RNA-DNA hybrid near oriC. Cell 1988; 55:113-23. [PMID: 2458841 DOI: 10.1016/0092-8674(88)90014-1] [Citation(s) in RCA: 201] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Transcription by RNA polymerase preceding the initiation of replication from the E. coli chromosomal origin (oriC) in vitro enables dnaA protein to open the DNA duplex under conditions when its action alone is insufficient. The RNA polymerases of phages T7 and T3 are as effective as the E. coli enzyme in activating initiation. The persistent RNA transcript hybridized to the template creates an R-loop that is responsible for activation. The activating RNA need not cross oriC, but must be less then 500 bp away. Transcripts lacking a 3' OH group are effective, proving that priming of DNA synthesis is not involved in the activation. Thus, transcription activates the origin of an otherwise inert plasmid by altering the local DNA structure, facilitating its opening by dnaA protein during the assembly of replication forks.
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Affiliation(s)
- T A Baker
- Department of Biochemistry, Stanford University Medical School, California 94305
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Nozaki N, Okazaki T, Ogawa T. In vitro transcription of the origin region of replication of the Escherichia coli chromosome. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)68202-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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