Termination Structures in the Escherichia coli Chromosome Replication Fork Trap (2023)

Journal of Molecular Biology

Volume 387, Issue 3,

3 April 2009

, Pages 532-539

Author links open overlay panel,


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.

Section snippets

Termination in the TerCdif region

TerC, one of the innermost Ter sites, is located near dif, approximately 180° from oriC (Fig. 1). To determine whether replication termination occurs at TerC and/or near dif during normal E. coli chromosome replication, we analysed DNA replication intermediates in the TerCdif region using 2D agarose gel electrophoresis.19 Cells in mid-exponential-phase growth were suspended in agarose plugs and then lysed. The released DNA was then digested with appropriate restriction enzymes, the replication

Identification of chromosomal Ter sites

The rather broad distribution of Ter sequences in the terminal half of the chromosome (Fig. 1a) has been taken as evidence against their involvement in the termination of oriC-mediated chromosome replication; the Ter sites were proposed to act primarily in halting repair-associated or other non-oriC-initiated replication events on the chromosome.8 The fork trap model predicts that the innermost Ter sites would arrest a much greater proportion of forks compared with the outer Ter sites because

Replication fork pausing at chromosomal Ter sites in vivo

Chromosomal fragments containing the 14 sites were individually analysed by 2D gel analysis of DNA from MG1655 cells. Specific paused forks were evident in the fragments containing TerA, TerB and TerC (Fig. 2, Fig. 3), and much fainter pause spots were detected at TerD, TerG, TerH and TerI. In all cases, the position of the pause spots on the Y-arc was consistent with the position of the Ter site within each fragment. Furthermore, an enhanced level of paused fork was detected for most of the

Chromosomal replication fork pausing in the presence of overproduced Tus

To assess the effect of limited Tus occupancy at Ter sites, we overproduced Tus from the expression plasmid pTH311,23 to ensure essentially complete occupancy of the Ter sites, and we measured fork pausing at the 14 chromosomal Ter sites using 2D gels. Tus was overproduced to ∼5% of total cellular protein in MG1655.pTH311, providing a vast excess of Tus sufficient to saturate Ter sites in vivo,24 and the strain grew with a similar doubling time to MG1655 (Td of ∼50min). The results are shown

Measurement of the intrinsic activity of each Tus–Ter complex in vivo

To assess the influence of the natural efficiency of each Tus–Ter barrier, we carried out plasmid fork arrest assays for each Ter site. In this assay,24, 25 pausing at a cloned Ter site in vivo is measured under conditions of overproduced Tus to ensure occupancy of all Ter sites and allow comparisons with the chromosomal data (Fig. 3b). We cloned each of the Ter sites in Fig. 1b using pACYC184, which replicates using the endogenous polymerase III replisome.24, 26 Completion of unidirectional


This work was funded by the UK MRC, the UK BBSRC (grant BB/G00028X/1) and the EPA Trust. We thank D. J. Sherratt, H. Hendrickson and I. Grainge for scientific discussion and X. Wang for providing the Δtus strain WX184.

(Video) DNA Replication in Prokaryotes | Initiation

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  • Cited by (54)

    • chi sequences switch the RecBCD helicase–nuclease complex from degradative to replicative modes during the completion of DNA replication

      2023, Journal of Biological Chemistry

      Accurately completing DNA replication when two forks converge is essential to genomic stability. The RecBCD helicase–nuclease complex plays a central role in completion by promoting resection and joining of the excess DNA created when replisomes converge. chi sequences alter RecBCD activity and localize with crossover hotspots during sexual events in bacteria, yet their functional role during chromosome replication remains unknown. Here, we use two-dimensional agarose gel analysis to show that chi induces replication on substrates containing convergent forks. The induced replication is processive but uncoupled with respect to leading and lagging strand synthesis and can be suppressed by ter sites which limit replisome progression. Our observations demonstrate that convergent replisomes create a substrate that is processed by RecBCD and that chi, when encountered, switches RecBCD from a degradative to replicative function. We propose that chi serves to functionally differentiate DNA ends created during completion, which require degradation, from those created by chromosomal double-strand breaks, which require resynthesis.

    • Termination of DNA replication at Tus-ter barriers results in under-replication of template DNA

      2021, Journal of Biological Chemistry

      Citation Excerpt :

      Thus our results indicate that additional protein activities are necessary to complete DNA replication if one fork is paused at a Tus-ter complex and the second fork approaches from the permissive side. Indeed, the analysis of genetic data has led to the hypothesis that a fusion event between two freely moving forks will generate very different intermediates to the situation where one replisome blocked at the nonpermissive face of Tus-ter fuses with a freely moving replication fork complex that approaches from the opposite direction (23, 26) However, we previously observed that when DNA replication is forced to terminate at Tus-ter due to an additional ectopic replication origin, the majority of cells grow without much ill-effect (37, 38). Thus, cells are able to process this type of fusion event without much difficulty.

      The complete and accurate duplication of genomic information is vital to maintain genome stability in all domains of life. In Escherichia coli, replication termination, the final stage of the duplication process, is confined to the “replication fork trap” region by multiple unidirectional fork barriers formed by the binding of Tus protein to genomic ter sites. Termination typically occurs away from Tus-ter complexes, but they become part of the fork fusion process when a delay to one replisome allows the second replisome to travel more than halfway around the chromosome. In this instance, replisome progression is blocked at the nonpermissive interface of the Tus-ter complex, termination then occurs when a converging replisome meets the permissive interface. To investigate the consequences of replication fork fusion at Tus-ter complexes, we established a plasmid-based replication system where we could mimic the termination process at Tus-ter complexes invitro. We developed a termination mapping assay to measure leading strand replication fork progression and demonstrate that the DNA template is under-replicated by 15 to 24 bases when replication forks fuse at Tus-ter complexes. This gap could not be closed by the addition of lagging strand processing enzymes or by the inclusion of several helicases that promote DNA replication. Our results indicate that accurate fork fusion at Tus-ter barriers requires further enzymatic processing, highlighting large gaps that still exist in our understanding of the final stages of chromosome duplication and the evolutionary advantage of having a replication fork trap.

    • Bacterial replisomes

      2018, Current Opinion in Structural Biology

      Bacterial replisomes are dynamic multiprotein DNA replication machines that are inherently difficult for structural studies. However, breakthroughs continue to come. The structures of Escherichia coli DNA polymerase III (core)–clamp–DNA subcomplexes solved by single-particle cryo-electron microscopy in both polymerization and proofreading modes and the discovery of the stochastic nature of the bacterial replisomes represent notable progress. The structures reveal an intricate interaction network in the polymerase–clamp subassembly, providing insights on how replisomes may work. Meantime, ensemble and single-molecule functional assays and fluorescence microscopy show that the bacterial replisomes can work in a decoupled and uncoordinated way, with polymerases quickly exchanging and both leading-strand and lagging-strand polymerases and the helicase working independently, contradictory to the elegant textbook view of a highly coordinated machine.

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    Copyright © 2009 Elsevier Ltd. All rights reserved.


    Termination Structures in the Escherichia coli Chromosome Replication Fork Trap? ›

    In Escherichia coli, termination takes place in a specialised termination area opposite the origin. A 'replication fork trap' is formed by unidirectional fork barriers via the binding of Tus protein to genomic ter sites.

    What is the termination of chromosome replication in E. coli? ›

    Termination of DNA replication occurs when the two forks meet and fuse, creating two separate double-stranded DNA molecules. In the well-studied bacteria Escherichia coli and Bacillus subtilis, this occurs in the terminus region, which is situated diametrically opposite the origin.

    What are the termination sites in E. coli? ›

    In Escherichia coli, replication termination, the final stage of the duplication process, is confined to the “replication fork trap” region by multiple unidirectional fork barriers formed by the binding of Tus protein to genomic ter sites.

    What is the termination of replication fork? ›

    Termination of DNA replication occurs when two replication forks meet on the same stretch of DNA, during which the following events occur, though not necessarily in this order: forks converge until all intervening DNA is unwound; any remaining gaps are filled in and ligated; catenanes are removed; replication proteins ...

    What are the components of the replication fork in E. coli? ›

    • DNA, Bacterial.
    • DNA Primase.
    • DNA Polymerase III.
    May 13, 2016

    What are the two types of termination in E. coli? ›

    In bacteria, two mechanisms are responsible for proper transcript termination: intrinsic termination and Rho-dependent termination.

    What DNA sequence is required for termination of replication in E. coli? ›

    tus, the trans-acting gene required for termination of DNA replication in Escherichia coli, encodes a DNA-binding protein.

    Which of the following are the two mechanisms of transcription termination in E. coli? ›

    In bacteria, two mechanisms are responsible for terminating transcription: intrinsic (Rho-independent) termination and Rho-dependent termination. Growing examples suggest that neither type of transcription termination is static, but instead are highly dynamic and regulated.

    What is the termination site? ›

    Termination in bacteria

    Rho-dependent termination. The terminator is a region of DNA that includes the sequence that codes for the Rho binding site in the mRNA, as well as the actual transcription stop point (which is a sequence that causes the RNA polymerase to pause so that Rho can catch up to it).

    What are the sites for termination of transcription? ›

    Transcription termination occurs in a reaction coupled to RNA 3′-end processing. Most eukaryotic mRNA precursors are cleaved in a site-specific manner in the 3′-untranslated region, followed by polyadenylation of the upstream cleavage product. A large number of proteins are involved in these reactions.

    What is termination signal in DNA replication? ›

    Termination signals are found at the end of the part of the chromosome being transcribed during transcription of mRNA. Termination signals bring a stop to transcription, ensuring that only gene-encoding parts of the chromosome are transcribed.

    What is the structure of the replication fork? ›

    The replication fork is a structure that forms within the long helical DNA during DNA replication. It is created by helicases, which break the hydrogen bonds holding the two DNA strands together in the helix. The resulting structure has two branching "prongs", each one made up of a single strand of DNA.

    What is the termination process of DNA replication in prokaryotes? ›

    Termination. Termination of DNA replication in E. coli is completed through the use of termination sequences and the Tus protein. These sequences allow the two replication forks to pass through in only one direction, but not the other.

    What DNA sequence is required for termination of replication in E. coli quizlet? ›

    DNA polymerase operates in 5'-3' direction on both strands. The leading strand moves in direction of unwinding DNA. Lagging strand must move forward and then go backwards. ter is the sequence for terminating replication.

    What is the mechanism of DNA replication in Escherichia coli? ›

    The correct answer is D. DNA replication is semi-conservative and bidirectional in E. coli.

    How many replication forks does E. coli chromosome have? ›

    (A) Schematic representation of the circular E. coli chromosome. Two replication forks are assembled at the origin (oriC) and move in opposite directions along the DNA (grey arrows) until they eventually approach one other and fuse within the terminus region diametrically opposite to oriC.

    What are the two main types of termination? ›

    The two types of termination of employment are involuntary and voluntary termination. The main difference between voluntary vs. involuntary termination is that voluntary termination occurs when the employee decides to leave the workforce. In involuntary termination, the decision is made by the employer.

    What are the two types of termination? ›

    There are two types of employment termination first is termination by employer and the second is voluntary resignation or termination by employee.

    What are the three stages of chromosome replication in Escherichia coli? ›

    In bacteria, the DNA replication cycle (or C-period) is divided into three stages: initiation, elongation, and termination [5]. Both E.

    Which two proteins are involved in replication termination in E. coli? ›

    Mechanism of termination of DNA replication of Escherichia coli involves helicase–contrahelicase interaction - PMC. The . gov means it's official. Federal government websites often end in .

    Which protein is required to terminate DNA replication in bacteria? ›

    Abstract. The replication terminator protein (RTP) of Bacillus subtilis is a dimer with a monomeric molecular mass of 14.5 kDa. The protein terminates DNA replication at a specific binding site.

    What is intrinsic termination of transcription in Escherichia coli in molecular detail? ›

    Intrinsic termination of transcription in Escherichia coli involves the formation of an RNA hairpin in the nascent RNA. This hairpin plays a central role in the release of the transcript and polymerase at intrinsic termination sites on the DNA template.

    What is the termination process of transcription in bacteria? ›

    Bacterial transcription termination, described mostly for Escherichia coli, occurs in three recognized ways: intrinsic termination, an activity only of the core RNAP enzyme and transcript sequences that encode an RNA hairpin and terminal uridine-rich segment; termination by the enzyme Rho, an ATP-dependent RNA ...

    What are the processes of termination? ›

    Process termination occurs when the last enclave in the process terminates. Process termination deletes the structure that kept track of the enclaves within the process, releases the process control block (PCB) and associated resources, and returns control to the creator of the process.

    Which of the following factor is responsible for termination of transcription? ›

    Rho-factor: Transcription termination factor Rho is a bacterial ATP-dependent RNA/DNA helicase. b.

    How many types of termination are there in transcription? ›

    Two types of transcription termination mechanisms have been documented in prokaryotic organisms in vitro: (i) Rho-dependent termination (RDT) facilitated by binding of Rho protein to a cytidine-rich (C-rich) segment in the nascent RNA followed by dissociation of the RNA; and (ii) intrinsic or Rho-independent ...

    Is the site of termination where DNA replication ends? ›

    DNA replication ends when converging replication forks meet. During this process, which is known as replication termination, DNA synthesis is completed, the replication machinery is disassembled and daughter molecules are resolved.

    Where does transcription start and terminate? ›

    Termination is the ending of transcription, and occurs when RNA polymerase crosses a stop (termination) sequence in the gene. The mRNA strand is complete, and it detaches from DNA.

    What is the termination of replication proteins? ›

    The replication termination protein or replication terminator protein (RTP) is one of only two well-defined proteins known to be involved in arresting DNA replication forks, the other being a protein known as Tus (termination utilisation substance or DNA replication terminus site-binding protein or ter-binding protein) ...

    What are the three steps of DNA replication initiation and termination? ›

    It occurs in three main stages: initiation, elongation, and termination. DNA replication in eukaryotes occurs in three stages: initiation, elongation, and termination, which are aided by several enzymes.

    Why is termination in DNA replication important? ›

    However, very little is known as to how this process terminates. Resolution of structures created during termination of DNA replication is essential for accurate duplication of eukaryotic genomes since, if not resolved efficiently, terminating replication forks can result in genomic instability.

    What are the components of the replication fork in DNA replication? ›

    At the eukaryotic replication fork, three distinct replicative polymerase complexes contribute to canonical DNA replication: α, δ, and ε. These three polymerases are essential for viability of the cell [10,11,12,13].

    What happens at a DNA replication fork during replication quizlet? ›

    Describe what happens at a DNA replication fork during replication. The DNA strands separate, and complementary nucleotides are added to each strand. Describe the role of helicases and DNA polymerases during DNA replication. DNA helicases catalyze the break up of the hydrogen bonds between strands.

    What is the replication fork quizlet? ›

    Replication fork. A Y-shaped region on a replicating DNA molecule where new strands are growing.

    What is the termination step of DNA transcription? ›

    Transcription termination occurs when a transcribing RNA polymerase releases the DNA template and the nascent RNA. Termination is required for preventing the inappropriate transcription of downstream genes, and for recycling of the polymerase.

    How is the termination of DNA replication different in prokaryotes vs eukaryotes? ›

    In prokaryotes, a single termination site is present midway between the circular chromosome. The two replication forks meet at this site, thus, halting the replication process. In eukaryotes, the linear DNA molecules have several termination sites along the chromosome, corresponding to each origin of replication.

    What is the termination process of translation in prokaryotes? ›

    In prokaryotic and eukaryotic organisms termination of translation differs in many aspects. In the first step of termination the release factors recognize stop codons in A site of the ribosome. These factors are responsible for hydrolysis of peptide-tRNA bond and release of newly synthesized peptide.

    Which of the following statement about DNA replication in E. coli is correct? ›

    So, the correct answer is 'DNA synthesis takes place mainly by DNA–polymerase I in E. coli'.

    What is the nature of replication of the chromosome in E. coli? ›

    Escherichia coli, like many other bacteria, possesses one circular chromosome. DNA replication is initiated from a single origin of replication (oriC) and carried out bidirectionally, terminating in the opposite replication terminus region (terC)1,2,15,16.

    How does E. coli package its DNA? ›

    coli are encoded on a single circular chromosome packaged within the cell nucleoid (Mason & Powelson, 1956; Cairns, 1963). Prokaryotic cells do not contain nuclei or other membrane-bound organelles.

    What are the key E. coli DNA sequences that control the start of DNA replication and how do they work? ›

    Replication in E. coli begins at a specific sequence called oriC. This is the single origin of replication on this chromosome, and DNA synthesis proceeds in both directions from it (Figure 6.7). The sequence oriC was identified by its ability to confer the capacity for autonomous replication on a DNA molecule.

    What are replication fork traps? ›

    The fork trap is an arrangement of replication pause sites that ensures that the two replication forks fuse within the terminus region of the chromosome, approximately opposite the origin on the circular map.

    What is the mode of replication of the Escherichia coli chromosome? ›

    The circular Escherichia coli chromosome is replicated from a single origin (oriC), and a single fork fusion takes place in a specialised termination area opposite oriC that establishes a fork trap mediated by Tus protein bound at ter sequences that allows forks to enter but not leave.

    What is the structure of the chromosome in E. coli? ›

    The Escherichia coli chromosome or nucleoid is composed of the genomic DNA, RNA, and protein. The nucleoid forms by condensation and functional arrangement of a single chromosomal DNA with the help of chromosomal architectural proteins and RNA molecules as well as DNA supercoiling.

    What are the three main parts of a replicated chromosome? ›

    It turns out that chromosome can be divided into three different parts: the centromere, the arm and the telomere.

    What are the steps of cell division in E. coli? ›

    This process can be divided into three major steps. The first step involves the replication of the DNA, followed by an elongation step in which the cells become twice as long. In the last step the elongated cell constricts in the middle and the two daughter cells are separated.

    What is the process of chromosome replication? ›

    During every cell division, a cell must duplicate its chromosomal DNA through a process called DNA replication. The duplicated DNA is then segregated into two "daughter" cells that inherit the same genetic information. This process is called chromosome segregation.

    How many DNA replication origins are there in the E. coli chromosome? ›

    E. coli has a single circular chromosome that is ~4.6 megabases in length, containing a single origin of replication (oriC).


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