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Duggin IG, Bell SD. Termination structures in the Escherichia coli chromosome replication fork trap. J Mol Biol 2009; 387:532-9. [PMID: 19233209 DOI: 10.1016/j.jmb.2009.02.027] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2008] [Revised: 02/10/2009] [Accepted: 02/12/2009] [Indexed: 11/19/2022]
Abstract
The Escherichia coli chromosome contains two opposed sets of unidirectional DNA replication pause (Ter) sites that, according to the replication fork trap theory, control the termination of chromosome replication by restricting replication fork fusion to the terminus region. In contrast, a recent hypothesis suggested that termination occurs at the dif locus instead. Using two-dimensional agarose gel electrophoresis, we examined DNA replication intermediates at the Ter sites and at dif in wild-type cells. Two definitive signatures of site-specific termination--specific replication fork arrest and converging replication forks--were clearly detected at Ter sites, but not at dif. We also detected a significant pause during the latter stages of replication fork convergence at Ter sites. Quantification of fork pausing at the Ter sites in both their native chromosomal context and the plasmid context further supported the fork trap model.
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Affiliation(s)
- Iain G Duggin
- Medical Research Council Cancer Cell Unit, Hutchison-Medical Research Council Research Centre, Hills Road, Cambridge, UK.
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2
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Neylon C, Kralicek AV, Hill TM, Dixon NE. Replication termination in Escherichia coli: structure and antihelicase activity of the Tus-Ter complex. Microbiol Mol Biol Rev 2005; 69:501-26. [PMID: 16148308 PMCID: PMC1197808 DOI: 10.1128/mmbr.69.3.501-526.2005] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The arrest of DNA replication in Escherichia coli is triggered by the encounter of a replisome with a Tus protein-Ter DNA complex. A replication fork can pass through a Tus-Ter complex when traveling in one direction but not the other, and the chromosomal Ter sites are oriented so replication forks can enter, but not exit, the terminus region. The Tus-Ter complex acts by blocking the action of the replicative DnaB helicase, but details of the mechanism are uncertain. One proposed mechanism involves a specific interaction between Tus-Ter and the helicase that prevents further DNA unwinding, while another is that the Tus-Ter complex itself is sufficient to block the helicase in a polar manner, without the need for specific protein-protein interactions. This review integrates three decades of experimental information on the action of the Tus-Ter complex with information available from the Tus-TerA crystal structure. We conclude that while it is possible to explain polar fork arrest by a mechanism involving only the Tus-Ter interaction, there are also strong indications of a role for specific Tus-DnaB interactions. The evidence suggests, therefore, that the termination system is more subtle and complex than may have been assumed. We describe some further experiments and insights that may assist in unraveling the details of this fascinating process.
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Affiliation(s)
- Cameron Neylon
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom.
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3
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Postow L, Ullsperger C, Keller RW, Bustamante C, Vologodskii AV, Cozzarelli NR. Positive torsional strain causes the formation of a four-way junction at replication forks. J Biol Chem 2001; 276:2790-6. [PMID: 11056156 DOI: 10.1074/jbc.m006736200] [Citation(s) in RCA: 192] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The advance of a DNA replication fork requires an unwinding of the parental double helix. This in turn creates a positive superhelical stress, a (+)-DeltaLk, that must be relaxed by topoisomerases for replication to proceed. Surprisingly, partially replicated plasmids with a (+)-DeltaLk were not supercoiled nor were the replicated arms interwound in precatenanes. The electrophoretic mobility of these molecules indicated that they have no net writhe. Instead, the (+)-DeltaLk is absorbed by a regression of the replication fork. As the parental DNA strands re-anneal, the resultant displaced daughter strands base pair to each other to form a four-way junction at the replication fork, which is locally identical to a Holliday junction in recombination. We showed by restriction endonuclease digestion that the junction can form at either the terminus or the origin of replication and we visualized the structure with scanning force microscopy. We discuss possible physiological implications of the junction for stalled replication in vivo.
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Affiliation(s)
- L Postow
- Department of Molecular and Cell Biology, University of California, Berkeley 94720, USA
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4
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Andersen PA, Griffiths AA, Duggin IG, Wake RG. Functional specificity of the replication fork-arrest complexes of Bacillus subtilis and Escherichia coli: significant specificity for Tus-Ter functioning in E. coli. Mol Microbiol 2000; 36:1327-35. [PMID: 10931283 DOI: 10.1046/j.1365-2958.2000.01945.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The Escherichia coli replication terminator TerB was inserted in its two alternate orientations into a Bacillus subtilis fork-arrest assay plasmid. After transferring these new plasmids into B. subtilis, which could overproduce the E. coli terminator protein Tus, it was shown that the E. coli Tus-TerB complex could cause polar replication fork arrest, albeit at a very low level, in B. subtilis. A new B. subtilis-E. coli shuttle plasmid was designed to allow the insertion of either the Terl (B. subtilis) or TerB (E. coli) terminator at the same site and in the active orientation in relation to the approaching replication fork generated in either organism. Fork-arrest assays for both terminator-containing plasmids replicating in both organisms which also produced saturating levels of either the B. subtilis terminator protein (RTP) or Tus were performed. The efficiency of the Tus-TerB complex in causing fork arrest was much higher in E. coli than in B. subtilis. The efficiency of the B. subtilis RTP-Terl complex was higher in B. subtilis than in E. coli, but the effect was significantly less. Evidently a specificity feature in E. coli operates to enhance appreciably the fork-arrest efficiency of a Tus-Ter complex. The specificity effect is of less significance for an RTP-Ter complex functioning in B. subtilis.
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Affiliation(s)
- P A Andersen
- Department of Biochemistry, University of Sydney, NSW, Australia
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5
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Autret S, Levine A, Vannier F, Fujita Y, Séror SJ. The replication checkpoint control in Bacillus subtilis: identification of a novel RTP-binding sequence essential for the replication fork arrest after induction of the stringent response. Mol Microbiol 1999; 31:1665-79. [PMID: 10209741 DOI: 10.1046/j.1365-2958.1999.01299.x] [Citation(s) in RCA: 30] [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
We have shown previously that induction of the stringent response in Bacillus subtilis resulted in the arrest of chromosomal replication between 100 and 200 kb either side of oriC at distinct stop sites, designated LSTer and RSTer, left and right stringent terminators respectively. This replication checkpoint was also shown to involve the RTP protein, normally active at the chromosomal terminus. In this study, we show that the replication block is absolutely dependent upon RelA, correlated with high levels of ppGpp, but that efficient arrest at STer sites also requires RTP. DNA-DNA hybridization data indicated that one or more such LSTer sites mapped to gene yxcC (-128 kb from oriC). A 7.75 kb fragment containing this gene was cloned into a theta replicating plasmid, and plasmid replication arrest, requiring both RelA and RTP, was demonstrated. This effect was polar, with plasmid arrest only detected when the fragment was orientated in the same direction with respect to replication, as in the chromosome. This LSTer2 site was further mapped to a 3.65 kb fragment overlapping the next40 probe. Remarkably, this fragment contains a 17 bp sequence (B'-1) showing 76% identity with an RTP binding site (B sequence) present at the chromosomal terminus. This B'-1 sequence, located in the gene yxcC, efficiently binds RTP in vitro, as shown by DNA gel retardation studies and DNase I footprinting. Importantly, precise deletion of this sequence abolished the replication arrest. We propose that this modified B site is an essential constituent of the LSTer2 site. The differences between arrest at the normal chromosomal terminus and arrest at LSTer site are discussed.
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Affiliation(s)
- S Autret
- Institut de Génétique et Microbiologie, URA CNRS 2225, Université Paris XI, Orsay, France
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6
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Coskun-Ari FF, Hill TM. Sequence-specific interactions in the Tus-Ter complex and the effect of base pair substitutions on arrest of DNA replication in Escherichia coli. J Biol Chem 1997; 272:26448-56. [PMID: 9334221 DOI: 10.1074/jbc.272.42.26448] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Arrest of DNA replication in Escherichia coli is mediated by specific interactions between the Tus protein and terminator (Ter) sequences. Binding of Tus to a Ter site forms a asymmetric protein-DNA complex that arrests DNA replication in an orientation-dependent fashion. In this study, mutant Ter sites carrying single base pair substitutions at 16 different positions were examined for their ability to bind purified Tus protein and arrest DNA replication. In vitro competition assays demonstrated that base pair substitutions at positions 8-19 had significant effects on the free energy of Tus binding (DeltaDeltaG0 of 1.5 to >4. 0 kcal/mol). Concomitant with loss of binding affinity, mutations at these positions also showed significantly lower or undetectable replication arrest activities in vivo. Substitutions at positions 6, 20, and 21 had moderate effects on Tus-Ter interactions, suggesting that these base pairs contribute to, but are not absolutely critical for, Tus binding. Even though the effects on binding were minimal, these Ter mutants were not as efficient as wild type Tus-TerB complexes at arresting replication forks. Three new potential Ter sites, referred to as TerH, TerI, and TerJ, were identified by searching the E. coli genome for sequence similarity to a consensus Ter site sequence.
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Affiliation(s)
- F F Coskun-Ari
- Department of Microbiology and Immunology, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58202-9037, USA
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7
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Skokotas A, Hiasa H, Marians KJ, O'Donnell L, Hill TM. Mutations in the Escherichia coli Tus protein define a domain positioned close to the DNA in the Tus-Ter complex. J Biol Chem 1995; 270:30941-8. [PMID: 8537350 DOI: 10.1074/jbc.270.52.30941] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
A new genetic screen for mutations in the tus gene of Escherichia coli has been devised that selects for Tus proteins with altered ability to arrest DNA replication. We report here the characterization of three such mutants: TusP42S, TusE49K, and TusH50Y. TusP42S and TusE49K arrest DNA replication in vivo at 36% of the efficiency of wild-type Tus, whereas TusH50Y functions at 78% efficiency. The loss of replication arrest activity did not correlate with changes in the stability of the Tus-TerB complexes formed by the mutant proteins. TusE49K formed a more stable protein-DNA complex than wild-type Tus (t1/2 of 178 versus 149 min, respectively) and TusP42 had a 9-min half-life, yet these two mutants showed identical efficiencies for replication arrest. When tested in vitro using a helicase assay or an oriC replication system, we observed a general, but imperfect, correlation between the in vivo and in vitro assays. Finally, the half-lives of the mutant protein-DNA complexes suggested that the domain of Tus where these mutations are located is positioned close to the DNA in the Tus-Ter complex.
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Affiliation(s)
- A Skokotas
- Department of Bioscience and Biotechnology, Drexel University, Philadelphia, Pennsylvania 19104, USA
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8
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Skokotas A, Wrobleski M, Hill T. Isolation and characterization of mutants of Tus, the replication arrest protein of Escherichia coli. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)32013-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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9
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Bierne H, Ehrlich SD, Michel B. Flanking sequences affect replication arrest at the Escherichia coli terminator TerB in vivo. J Bacteriol 1994; 176:4165-7. [PMID: 8021197 PMCID: PMC205617 DOI: 10.1128/jb.176.13.4165-4167.1994] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
We have analyzed the effect of flanking sequences on Tus-induced replication arrest. pBR322 plasmid derivatives which carry the Escherichia coli replication terminator TerB at different locations were used. Efficiency of the replication arrest was estimated from the plasmid copy number and transformation frequency of tus+ cells. We found that flanking sequences do affect replication arrest efficiency, a weak arrest being correlated with the presence of an AT-rich region which is replicated just before TerB. Some sequences located after the replication terminator can also affect replication termination. We propose that the AT-rich regions might impair binding of the Tus protein to the TerB sequence or facilitate helicase-induced unwinding of DNA and Tus displacement from the TerB site.
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Affiliation(s)
- H Bierne
- Laboratoire de Génétique Microbienne, Institut National de la Recherche Agronomique, Jouy-en-Josas, France
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10
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Sharma B, Hill TM. TerF, the sixth identified replication arrest site in Escherichia coli, is located within the rcsC gene. J Bacteriol 1992; 174:7854-8. [PMID: 1447156 PMCID: PMC207506 DOI: 10.1128/jb.174.23.7854-7858.1992] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
We report the existence of a sixth replication arrest site, TerF, that is located within the coding sequences of the rcsC gene, a negative regulator of capsule biosynthesis. The TerF site is oriented to allow transcription of the rcsC gene but prevent DNA replication in the terminus-to-origin direction. Our results demonstrate that the TerF site is functional in both chromosomal and plasmid environments and that the stability of the Tus-TerF protein-DNA complex more closely resembles the plasmid R6K Ter sites than the chromosomal TerB site.
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Affiliation(s)
- B Sharma
- Department of Bioscience and Biotechnology, Drexel University, Philadelphia, Pennsylvania 19104
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11
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Smith MT, Wake RG. Definition and polarity of action of DNA replication terminators in Bacillus subtilis. J Mol Biol 1992; 227:648-57. [PMID: 1404381 DOI: 10.1016/0022-2836(92)90214-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The first stage in termination of chromosome replication in Bacillus subtilis involves arrest of the clockwise fork at the inverted repeat region (IRR), comprising the opposed IRI and IRII sequences, adjacent to the upstream region of the rtp gene, which encodes the replication terminator protein RTP. RTP binds to IRI and IRII. The ability of the IRR and its components to function as terminators, in conjunction with RTP, and their polarity of action have now been tested by the use of plasmids replicating in B. subtilis as unidirectional theta structures and into which potential terminator sequences were inserted in alternate orientations relative to fork movement. When the complete IRR was inserted into such plasmids and the new plasmids transferred into a B. subtilis strain overproducing RTP, it was able to block movement of a replication fork approaching from either direction. IRI and IRII were shown to function as polar terminators, each blocking movement of a fork when it approached from one particular direction but not the other. Furthermore, the polarity of action was in accordance with the IRR being able to operate as a replication fork trap. Thus, a fork approaching the IRR would pass through the first terminator encountered (IRI or IRII) and be halted by the second. The previously observed nonfunctioning of a particular orientation of chromosomal IRR as a fork arrest site probably reflects a limiting level of RTP in the cell. Interestingly, a 21 base-pair core sequence spanning a single RTP binding site within IRI (the 47 base-pair IRI contains 2 binding sites) was unable to arrest a fork approaching from either direction in the plasmid system. This suggests that both binding sites within an IR must be filled in order to function as an arrest site. It is possible that co-operative interaction between adjacent dimers within IRI or IRII provides the necessary conformation for causing fork arrest.
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Affiliation(s)
- M T Smith
- Department of Biochemistry, University of Sydney, N.S.W., Australia
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12
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Lee E, Kornberg A. Features of replication fork blockage by the Escherichia coli terminus-binding protein. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(19)50346-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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13
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Uzest M, Ehrlich SD, Michel B. The Escherichia coli terB sequence affects maintenance of a plasmid with the M13 phage replication origin. J Bacteriol 1991; 173:7695-7. [PMID: 1938965 PMCID: PMC212539 DOI: 10.1128/jb.173.23.7695-7697.1991] [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: 12/29/2022] Open
Abstract
Replication initiated at the bacteriophage M13 origin can be affected by interaction of a properly oriented termination signal terB and the Tus protein. The effect can be alleviated by overproduction of the M13 replication gene protein II.
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Affiliation(s)
- M Uzest
- Laboratoire de Génétique Microbienne, Institut National de la Recherche Agronomique, Jouy en Josas, France
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14
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Takenaka S, Ihara T, Takagi M. Cleavage of double helical DNA by Cu2+ ion in the presence of bisintercalator containing penta(ethylene glycol) connector chain. J Mol Recognit 1990; 3:156-62. [PMID: 2278732 DOI: 10.1002/jmr.300030404] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In designing new DNA recognizing and cleaving reagents, we introduce herein a bisacridine derivative (referred to as bisacridine) in which two acridine heterocycles are connected by a penta(ethylene glycol) bridging chain. This compound offers two possible functions: 1, stabilization of DNA bisacridine intercalator complex by metal ion. The penta(ethylene glycol) chain stabilizes metal ions binding to the phosphate site of DNA, where the penta(ethylene glycol) chain constitutes a part of a pseudomacrocyclic ligand for metal binding; and 2, enhancement of metal-assisted hydrolytic cleavage of DNA by means of a metal concentration effect by the pseudomacrocyclic ethereal chain. The binding isotherms of bisacridine with DNA in the presence of metal ions showed that the binding was mainly governed by the cation exchange reaction on the anionic DNA polymer chain, i.e., the exchange between metal ions and the cationic bisacridine. The bisacridine showed an increase DNA binding ability compared to quinacrine, the monoacridine counterpart, and caused an enhancement of DNA cleavage in the presence of Cu2+ ions. Additional experiments which included DNase 1 footprinting in the presence of bisacridine and the DNA cleavage by Cu2+/bisacridine using a 32P end-labelled DNA fragment, suggested that the Cu2(+)-assisted DNA cleavage sites in the presence of bisacridine were in reasonable overlap with the DNA binding sites of bisacridine.
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Affiliation(s)
- S Takenaka
- Department of Organic Synthesis, Faculty of Engineering, Kyushu University Higashi-ku, Fukuoka, Japan
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15
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Lewis PJ, Ralston GB, Christopherson RI, Wake RG. Identification of the replication terminator protein binding sites in the terminus region of the Bacillus subtilis chromosome and stoichiometry of the binding. J Mol Biol 1990; 214:73-84. [PMID: 2115089 DOI: 10.1016/0022-2836(90)90147-e] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
DNase I footprinting of the interaction between the replication terminator protein (RTP) of Bacillus subtilis and the inverted repeat region (IRR) at the chromosome terminus, to which it binds to block the clockwise replication fork, showed that two major regions of 41 base pairs (bp) were protected from cleavage. These regions corresponded approximately to the imperfect inverted repeats (IRI and IRII) identified previously. Band retardation analyses of the interaction between RTP and portions of the IRR established that each inverted repeat (IRI or IRII) contained two RTP binding sites. By sedimentation equilibrium in the ultracentrifuge, RTP was found to exist as a dimer of 29 kDa at neutral pH and concentrations above 0.2 g/l. Quantitative studies of the RTP-IRR interaction using [3H]RTP and [32P]IRR showed that the fully saturated complex contained eight RTP monomers per IRR. It is concluded that a dimer of RTP binds to each of the four sites in IRR. The apparent dissociation constant for the interaction was estimated (in the presence of 50% glycerol) to be 1.2 x 10(-11) M (dimer of RTP). Glycerol was found to have a marked effect on the affinity of RTP for the IRR and on the relative amounts of the interaction complexes formed; in the absence of glycerol the dissociation constant was approximately 50-fold higher and there was pronounced co-operative binding of RTP dimers to adjacent sites in each inverted repeat. Examination of the DNA sequence in IRI and IRII identified two 8 bp direct repeats in each. The regions protected from DNase I cleavage in each inverted repeat and the protection afforded by a core sequence spanning just one of the 8 bp direct repeats were consistent with each 8 bp repeat representing a recognition sequence for the RTP dimer. A model describing the binding of RTP to the IRR is presented.
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Affiliation(s)
- P J Lewis
- Department of Biochemistry, University of Sydney, N.S.W., Australia
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16
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Purification of a DNA Replication Terminus (ter) Site-binding Protein in Escherichia coli and Identification of the Structural Gene. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(19)30040-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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17
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Sista PR, Mukherjee S, Patel P, Khatri GS, Bastia D. A host-encoded DNA-binding protein promotes termination of plasmid replication at a sequence-specific replication terminus. Proc Natl Acad Sci U S A 1989; 86:3026-30. [PMID: 2654932 PMCID: PMC287057 DOI: 10.1073/pnas.86.9.3026] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
We have purified approximately 6600-fold an approximately 40-kDa protein (Ter protein) encoded by Escherichia coli that specifically binds to two sites at the 216-base-pair replication terminus (tau) of the plasmid R6K. Chemical footprinting experiments have shown that the Ter protein binds to two 14- to 16-base-pair sequences that exist as inverted repeats in the tau fragment. Site-directed mutagenesis of one of the terminus sequences (tau R) resulted in a mutant tau R that failed to bind to the Ter protein. The same mutant terminus also failed to terminate DNA replication in vivo. These experiments strongly suggest that the interaction of the Ter protein with tau sequences plays an essential role in the termination of DNA replication, specifically at tau.
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Affiliation(s)
- P R Sista
- Department of Microbiology and Immunology, Duke University Medical Center, Durham, NC 27710
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18
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Affiliation(s)
- M Masters
- Department of Molecular Biology, University of Edinburgh, UK
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19
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Pelletier AJ, Hill TM, Kuempel PL. Termination sites T1 and T2 from the Escherichia coli chromosome inhibit DNA replication in ColE1-derived plasmids. J Bacteriol 1989; 171:1739-41. [PMID: 2646296 PMCID: PMC209807 DOI: 10.1128/jb.171.3.1739-1741.1989] [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
Inhibition sites T1 and T2 from the Escherichia coli terminus functioned with the same characteristics in ColE1-derived plasmids and in the chromosome. These characteristics included polarity and dependence on tus, a trans-acting factor required for inhibition. Inhibition in the terminus region of the R6K plasmid was also tus dependent.
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Affiliation(s)
- A J Pelletier
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder 80309-0347
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20
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Abstract
Replication of the approximately 200 tandem copies of yeast ribosomal RNA genes (rDNA) is known to be initiated within a subset of the repeats, with transcription continuing during the replication process. To examine replication fork movement in this gene cluster, we used a two-dimensional (2D) agarose gel electrophoresis procedure that distinguishes molecules with different branched structures. Replication forks move through most of the rDNA in the same direction in which RNA polymerase I transcribes the 35S rRNA precursor: the 3' end of this transcription unit acts as a barrier to replication forks moving in the direction opposite to RNA polymerase I. The replication fork barrier (RFB) is observed as the accumulation of branched intermediates of specific size. We propose that the act of transcription may influence the movement of replication forks, creating barriers at the 3' ends of actively transcribed genes.
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Affiliation(s)
- B J Brewer
- Department of Genetics, University of Washington, Seattle 98195
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21
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Hill TM, Pelletier AJ, Tecklenburg ML, Kuempel PL. Identification of the DNA sequence from the E. coli terminus region that halts replication forks. Cell 1988; 55:459-66. [PMID: 2846183 DOI: 10.1016/0092-8674(88)90032-3] [Citation(s) in RCA: 111] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The terminus region of the E. coli chromosome contains two loci, T1 and T2, that inhibit the progress of replication forks and require the trans-acting factor tus. We have identified a 23 bp terminator signal at T1 and T2 that is within 100 bp of the sites of replication arrest. When an oligodeoxyribonucleotide containing the terminator signal was inserted into a plasmid, replication was halted only in a tus+ strain and when the terminator signal was oriented properly. We also found this terminator sequence in the terminus region of the plasmid R6K and in the origin region of RepFIIA class plasmids. In addition, we found striking similarities between the E. coli terminator signal and the terminator sequence of B. subtilis.
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Affiliation(s)
- T M Hill
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder 80309
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22
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Hidaka M, Akiyama M, Horiuchi T. A consensus sequence of three DNA replication terminus sites on the E. coli chromosome is highly homologous to the terR sites of the R6K plasmid. Cell 1988; 55:467-75. [PMID: 3052852 DOI: 10.1016/0092-8674(88)90033-5] [Citation(s) in RCA: 89] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Using the "Ter assay" we developed, three separate replication terminus (terC1, terC2, and terC3) sites on the E. coli chromosome were identified. The locations are at 28.3, 35.6, and 33.9 min on the linkage map, respectively. The terC1 site can block the counter-clockwise replication fork only, while the terC2 and terC3 sites inhibit the clockwise fork traveling on the chromosome. DNA sequences of the terC sites required for termination of DNA replication are highly homologous to those of terminus (terR) sites of the R6K plasmid, and the 21 bp consensus DNA sequence of terC is 5'-(A or T) TTAGTTACAACAT (A or C) CT (A or T) (A or T) (A or T) T-3'. In addition, all Ter active pUC-terC plasmids had a low copy number and were unstable in the host cells.
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Affiliation(s)
- M Hidaka
- Department of Molecular Biology, Graduate School of Medical Science, Kyushu University, Fukuoka, Japan
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Horiuchi T, Hidaka M. Core sequence of two separable terminus sites of the R6K plasmid that exhibit polar inhibition of replication is a 20 bp inverted repeat. Cell 1988; 54:515-23. [PMID: 3042153 DOI: 10.1016/0092-8674(88)90073-6] [Citation(s) in RCA: 62] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The DNA replication terminus (terR) of the R6K plasmid located on a 216 bp Alul fragment (Alu216) can block progress of the DNA replication fork. We previously developed an electrophoresis assay that allows detection of terminus activity on any DNA fragment cloned in the pUC vector. For precise identification of terR, we tested Alu216, its subfragments, and synthetic oligonucleotides by this assay. We found terR to be composed of a pair of separable sites, terR1 and terR2, each of which can block the DNA replication fork traveling in a specific but not the opposite direction. Both terR sites were composed of 22 nucleotides containing the repeated 20 bp sequence 5'-TAGTTACAACAC(A or T) CAA(G or T) AGA-3', located 73 bp apart in the inverted position of Alu216. A DNA homology search suggested that the R6K plasmid and the E. coli chromosome share a common termination system.
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Affiliation(s)
- T Horiuchi
- Graduate School of Medical Science, Department of Molecular Biology, Kyushu University, Fukuoka, Japan
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