1
|
Jameson KH, Rudolph CJ, Hawkins M. Termination of DNA replication at Tus-ter barriers results in under-replication of template DNA. J Biol Chem 2021; 297:101409. [PMID: 34780717 DOI: 10.1016/j.jbc.2021.101409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 11/02/2021] [Accepted: 11/10/2021] [Indexed: 02/05/2023] Open
Abstract
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 non-permissive 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 in vitro. We developed a termination mapping assay to measure leading strand replication fork progression and demonstrate that the DNA template is under-replicated by 15-24 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.
Collapse
Affiliation(s)
- Katie H Jameson
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Christian J Rudolph
- Division of Biosciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UB8 3PH, UK
| | - Michelle Hawkins
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK.
| |
Collapse
|
2
|
Hizume K, Araki H. Replication fork pausing at protein barriers on chromosomes. FEBS Lett 2019; 593:1449-1458. [PMID: 31199500 DOI: 10.1002/1873-3468.13481] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 06/07/2019] [Accepted: 06/10/2019] [Indexed: 12/16/2022]
Abstract
When a cell divides prior to completion of DNA replication, serious DNA damage may occur. Thus, in addition to accuracy, the processivity of the replication forks is important. DNA synthesis at replication forks should be completed in time, and forks overcome aberrant structures on the template DNA, including damaged sites, using trans-lesion synthesis, occasionally introducing mutations. By contrast, the protein barrier built on the DNA is known to block the progression of replication forks at specific chromosomal loci. Such protein barriers avert any collision of replication and transcription machineries, or control the recombination of specific loci. The components and the mechanisms of action of protein barriers have been revealed mainly using genetic and biochemical techniques. In addition to proteins involved in replication fork pausing, the interaction of the replicative helicase and DNA polymerase is also essential for replication fork pausing. Here, we provide an overview of replication fork pausing at protein barriers.
Collapse
Affiliation(s)
- Kohji Hizume
- Division of RI Laboratory, Biomedical Research Center, Saitama Medical University, Japan
| | - Hiroyuki Araki
- Microbial Genetics Laboratory, National Institute of Genetics, Mishima, Japan.,Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan
| |
Collapse
|
3
|
Hizume K, Endo S, Muramatsu S, Kobayashi T, Araki H. DNA polymerase ε-dependent modulation of the pausing property of the CMG helicase at the barrier. Genes Dev 2018; 32:1315-1320. [PMID: 30232092 PMCID: PMC6169835 DOI: 10.1101/gad.317073.118] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 07/31/2018] [Indexed: 11/25/2022]
Abstract
Here, Hizume et al. investigated the mechanisms underlying the proper pausing of replication forks at barriers on chromosomes, which is needed for genome integrity. Using reconstituted replication fork pausing from purified yeast replication proteins, the authors provide new insights into the mechanism of fork pausing and show that the processive properties of the fork against barriers are modulated by the association with regulatory factors. The proper pausing of replication forks at barriers on chromosomes is important for genome integrity. However, the detailed mechanism underlying this process has not been well elucidated. Here, we successfully reconstituted fork-pausing reactions from purified yeast proteins on templates that had binding sites for the LacI, LexA, and/or Fob1 proteins; the forks paused specifically at the protein-bound sites. Moreover, although the replicative helicase Cdc45–Mcm2–7–GINS (CMG) complex alone unwound the protein-bound templates, the unwinding of the LacI-bound site was impeded by the presence of a main leading strand DNA polymerase: polymerase ε (Polε). This suggests that Polε modulates CMG to pause at these sites.
Collapse
Affiliation(s)
- Kohji Hizume
- Division of Microbial Genetics, National Institute of Genetics, Mishima 411-8540, Japan.,Department of Genetics, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan.,Division of RI Laboratory, Biomedical Research Center, Saitama Medical University, Moroyama-machi 350-0495, Japan
| | - Shizuko Endo
- Division of Microbial Genetics, National Institute of Genetics, Mishima 411-8540, Japan
| | - Sachiko Muramatsu
- Division of Microbial Genetics, National Institute of Genetics, Mishima 411-8540, Japan
| | - Takehiko Kobayashi
- Institute of Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Hiroyuki Araki
- Division of Microbial Genetics, National Institute of Genetics, Mishima 411-8540, Japan.,Department of Genetics, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
| |
Collapse
|
4
|
Berghuis BA, Raducanu VS, Elshenawy MM, Jergic S, Depken M, Dixon NE, Hamdan SM, Dekker NH. What is all this fuss about Tus? Comparison of recent findings from biophysical and biochemical experiments. Crit Rev Biochem Mol Biol 2017; 53:49-63. [DOI: 10.1080/10409238.2017.1394264] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Bojk A. Berghuis
- Department of Bionanoscience, Kavli institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Vlad-Stefan Raducanu
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Mohamed M. Elshenawy
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Slobodan Jergic
- Centre for Medical and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, Australia
| | - Martin Depken
- Department of Bionanoscience, Kavli institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Nicholas E. Dixon
- Centre for Medical and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, Australia
| | - Samir M. Hamdan
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Nynke H. Dekker
- Department of Bionanoscience, Kavli institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| |
Collapse
|
5
|
Jameson KH, Wilkinson AJ. Control of Initiation of DNA Replication in Bacillus subtilis and Escherichia coli. Genes (Basel) 2017; 8:E22. [PMID: 28075389 PMCID: PMC5295017 DOI: 10.3390/genes8010022] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Revised: 12/16/2016] [Accepted: 12/20/2016] [Indexed: 01/21/2023] Open
Abstract
Initiation of DNA Replication is tightly regulated in all cells since imbalances in chromosomal copy number are deleterious and often lethal. In bacteria such as Bacillus subtilis and Escherichia coli, at the point of cytokinesis, there must be two complete copies of the chromosome to partition into the daughter cells following division at mid-cell during vegetative growth. Under conditions of rapid growth, when the time taken to replicate the chromosome exceeds the doubling time of the cells, there will be multiple initiations per cell cycle and daughter cells will inherit chromosomes that are already undergoing replication. In contrast, cells entering the sporulation pathway in B. subtilis can do so only during a short interval in the cell cycle when there are two, and only two, chromosomes per cell, one destined for the spore and one for the mother cell. Here, we briefly describe the overall process of DNA replication in bacteria before reviewing initiation of DNA replication in detail. The review covers DnaA-directed assembly of the replisome at oriC and the multitude of mechanisms of regulation of initiation, with a focus on the similarities and differences between E. coli and B. subtilis.
Collapse
Affiliation(s)
- Katie H Jameson
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK.
| | - Anthony J Wilkinson
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK.
| |
Collapse
|
6
|
Moolman MC, Tiruvadi Krishnan S, Kerssemakers JWJ, de Leeuw R, Lorent V, Sherratt DJ, Dekker NH. The progression of replication forks at natural replication barriers in live bacteria. Nucleic Acids Res 2016; 44:6262-73. [PMID: 27166373 PMCID: PMC5291258 DOI: 10.1093/nar/gkw397] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 04/27/2016] [Accepted: 04/28/2016] [Indexed: 01/07/2023] Open
Abstract
Protein-DNA complexes are one of the principal barriers the replisome encounters during replication. One such barrier is the Tus-ter complex, which is a direction dependent barrier for replication fork progression. The details concerning the dynamics of the replisome when encountering these Tus-ter barriers in the cell are poorly understood. By performing quantitative fluorescence microscopy with microfuidics, we investigate the effect on the replisome when encountering these barriers in live Escherichia coli cells. We make use of an E. coli variant that includes only an ectopic origin of replication that is positioned such that one of the two replisomes encounters a Tus-ter barrier before the other replisome. This enables us to single out the effect of encountering a Tus-ter roadblock on an individual replisome. We demonstrate that the replisome remains stably bound after encountering a Tus-ter complex from the non-permissive direction. Furthermore, the replisome is only transiently blocked, and continues replication beyond the barrier. Additionally, we demonstrate that these barriers affect sister chromosome segregation by visualizing specific chromosomal loci in the presence and absence of the Tus protein. These observations demonstrate the resilience of the replication fork to natural barriers and the sensitivity of chromosome alignment to fork progression.
Collapse
Affiliation(s)
- M Charl Moolman
- Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Sriram Tiruvadi Krishnan
- Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Jacob W J Kerssemakers
- Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Roy de Leeuw
- Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Vincent Lorent
- Université Paris 13, Sorbonne Paris Cité, Laboratoire de Physique des Lasers, CNRS, (UMR 7538), F-93430 Villetaneuse, France
| | - David J Sherratt
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| |
Collapse
|
7
|
Berghuis BA, Dulin D, Xu ZQ, van Laar T, Cross B, Janissen R, Jergic S, Dixon NE, Depken M, Dekker NH. Strand separation establishes a sustained lock at the Tus-Ter replication fork barrier. Nat Chem Biol 2015; 11:579-85. [PMID: 26147356 DOI: 10.1038/nchembio.1857] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 05/20/2015] [Indexed: 01/30/2023]
Abstract
The bidirectional replication of a circular chromosome by many bacteria necessitates proper termination to avoid the head-on collision of the opposing replisomes. In Escherichia coli, replisome progression beyond the termination site is prevented by Tus proteins bound to asymmetric Ter sites. Structural evidence indicates that strand separation on the blocking (nonpermissive) side of Tus-Ter triggers roadblock formation, but biochemical evidence also suggests roles for protein-protein interactions. Here DNA unzipping experiments demonstrate that nonpermissively oriented Tus-Ter forms a tight lock in the absence of replicative proteins, whereas permissively oriented Tus-Ter allows nearly unhindered strand separation. Quantifying the lock strength reveals the existence of several intermediate lock states that are impacted by mutations in the lock domain but not by mutations in the DNA-binding domain. Lock formation is highly specific and exceeds reported in vivo efficiencies. We postulate that protein-protein interactions may actually hinder, rather than promote, proper lock formation.
Collapse
Affiliation(s)
- Bojk A Berghuis
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - David Dulin
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Zhi-Qiang Xu
- Centre for Medical and Molecular Bioscience, University of Wollongong, Wollongong, Australia
| | - Theo van Laar
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Bronwen Cross
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Richard Janissen
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Slobodan Jergic
- Centre for Medical and Molecular Bioscience, University of Wollongong, Wollongong, Australia
| | - Nicholas E Dixon
- Centre for Medical and Molecular Bioscience, University of Wollongong, Wollongong, Australia
| | - Martin Depken
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| |
Collapse
|
8
|
Harmer CJ, Hall RM. The A to Z of A/C plasmids. Plasmid 2015; 80:63-82. [DOI: 10.1016/j.plasmid.2015.04.003] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Revised: 04/03/2015] [Accepted: 04/14/2015] [Indexed: 10/23/2022]
|
9
|
Bastia D, Zaman S. Mechanism and physiological significance of programmed replication termination. Semin Cell Dev Biol 2014; 30:165-73. [PMID: 24811316 DOI: 10.1016/j.semcdb.2014.04.030] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 04/25/2014] [Indexed: 11/26/2022]
Abstract
Replication forks in both prokaryotic and eukaryotic systems pause at random sites due to depletion of dNTP pools, DNA damage, tight binding nonhistone proteins or unusual DNA sequences and/or structures, in a mostly non-polar fashion. However, there is also physiologically programmed replication termination at sequence-specific authentic replication termini. Here, the structure and functions of programmed replication termini, their mechanism of action and their diverse physiological functions in prokaryotes and eukaryotes have been reviewed.
Collapse
Affiliation(s)
- Deepak Bastia
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, United States.
| | - Shamsu Zaman
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, United States
| |
Collapse
|
10
|
Pallejà A, Guzman E, Garcia-Vallvé S, Romeu A. In silico prediction of the origin of replication among bacteria: a case study of Bacteroides thetaiotaomicron. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2008; 12:201-10. [PMID: 18582175 DOI: 10.1089/omi.2008.0004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The initiation of chromosomal replication occurs only once during the prokaryote cell cycle. Some origins of replication have been experimentally determined and have led to the development of in silico approaches to find the origin of replication among other prokaryotes. DNA base composition asymmetry is the basis of numerous in silico methods used to detect the origin and terminus of replication in prokaryotes. However, the composition asymmetry does not allow us to locate precisely the positions of the origin and terminus. Since DNA replication is a key step in the cell cycle it is important to determine properly the origin and terminus regions. Therefore, we have reviewed here the methods, tools, and databases for predicting the origins and terminuses of replication, and we have proposed some complementary analyses to reinforce these predictions. These analyses include finding the dnaA gene and its binding sites; making BLAST analyses of the intergenic sequences compared to related species; studying the gene order around the origin sequence; and studying the distribution of the genes encoded in the leading versus the lagging strand.
Collapse
Affiliation(s)
- Albert Pallejà
- Department of Biochemistry and Biotechnology, Evolutionary Genomics Group, Rovira i Virgili University, Tarragona, Catalunya, Spain.
| | | | | | | |
Collapse
|
11
|
Hendrickson H, Lawrence JG. Mutational bias suggests that replication termination occurs near the dif site, not at Ter sites. Mol Microbiol 2007; 64:42-56. [PMID: 17376071 DOI: 10.1111/j.1365-2958.2007.05596.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
In bacteria, Ter sites bound to Tus/Rtp proteins halt replication forks moving only in one direction, providing a convenient mechanism to terminate them once the chromosome had been replicated. Considering the importance of replication termination and its position as a checkpoint in cell division, the accumulated knowledge on these systems has not dispelled fundamental questions regarding its role in cell biology: why are there so many copies of Ter, why are they distributed over such a large portion of the chromosome, why is the tus gene not conserved among bacteria, and why do tus mutants lack measurable phenotypes? Here we examine bacterial genomes using bioinformatics techniques to identify the region(s) where DNA polymerase III-mediated replication has historically been terminated. We find that in both Escherichia coli and Bacillus subtilis, changes in mutational bias patterns indicate that replication termination most likely occurs at or near the dif site. More importantly, there is no evidence from mutational bias signatures that replication forks originating at oriC have terminated at Ter sites. We propose that Ter sites participate in halting replication forks originating from DNA repair events, and not those originating at the chromosomal origin of replication.
Collapse
Affiliation(s)
- Heather Hendrickson
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | | |
Collapse
|
12
|
Abstract
The Tus-Ter protein-DNA complex of Escherichia coli blocks progression of DNA replication from only one direction at the replication terminus. As the replication fork helicase unwinds one side of Ter, a conserved cytosine flips out of the duplex and binds to Tus, thereby creating a locked complex that blocks the advancing helicase.
Collapse
Affiliation(s)
- Daniel L Kaplan
- Vanderbilt University, Department of Biological Sciences, VU Station B, Box 35-1634, Nashville, Tennessee 37235, USA.
| |
Collapse
|
13
|
Mulcair MD, Schaeffer PM, Oakley AJ, Cross HF, Neylon C, Hill TM, Dixon NE. A molecular mousetrap determines polarity of termination of DNA replication in E. coli. Cell 2006; 125:1309-19. [PMID: 16814717 DOI: 10.1016/j.cell.2006.04.040] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2005] [Revised: 03/16/2006] [Accepted: 04/26/2006] [Indexed: 11/24/2022]
Abstract
During chromosome synthesis in Escherichia coli, replication forks are blocked by Tus bound Ter sites on approach from one direction but not the other. To study the basis of this polarity, we measured the rates of dissociation of Tus from forked TerB oligonucleotides, such as would be produced by the replicative DnaB helicase at both the fork-blocking (nonpermissive) and permissive ends of the Ter site. Strand separation of a few nucleotides at the permissive end was sufficient to force rapid dissociation of Tus to allow fork progression. In contrast, strand separation extending to and including the strictly conserved G-C(6) base pair at the nonpermissive end led to formation of a stable locked complex. Lock formation specifically requires the cytosine residue, C(6). The crystal structure of the locked complex showed that C(6) moves 14 A from its normal position to bind in a cytosine-specific pocket on the surface of Tus.
Collapse
Affiliation(s)
- Mark D Mulcair
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | | | | | | | | | | | | |
Collapse
|
14
|
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.
Collapse
Affiliation(s)
- Cameron Neylon
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom.
| | | | | | | |
Collapse
|
15
|
Kobayashi T. The replication fork barrier site forms a unique structure with Fob1p and inhibits the replication fork. Mol Cell Biol 2004; 23:9178-88. [PMID: 14645529 PMCID: PMC309713 DOI: 10.1128/mcb.23.24.9178-9188.2003] [Citation(s) in RCA: 126] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The replication fork barrier site (RFB) is an approximately 100-bp DNA sequence located near the 3' end of the rRNA genes in the yeast Saccharomyces cerevisiae. The gene FOB1 is required for this RFB activity. FOB1 is also necessary for recombination in the ribosomal DNA (rDNA), including increase and decrease of rDNA repeat copy number, production of extrachromosomal rDNA circles, and possibly homogenization of the repeats. Despite the central role that Foblp plays in both replication fork blocking and rDNA recombination, the molecular mechanism by which Fob1p mediates these activities has not been determined. Here, I show by using chromatin immunoprecipitation, gel shift, footprinting, and atomic force microscopy assays that Fob1p directly binds to the RFB. Fob1p binds to two separated sequences in the RFB. A predicted zinc finger motif in Fob1p was shown to be essential for the RFB binding, replication fork blocking, and rDNA recombination activities. The RFB seems to wrap around Fob1p, and this wrapping structure may be important for function in the rDNA repeats.
Collapse
Affiliation(s)
- Takehiko Kobayashi
- National Institute for Basic Biology, 38 Nishigonaka, Myodaijicho, Okazaki 444-8585, Japan.
| |
Collapse
|
16
|
Neylon C, Brown SE, Kralicek AV, Miles CS, Love CA, Dixon NE. Interaction of the Escherichia coli replication terminator protein (Tus) with DNA: a model derived from DNA-binding studies of mutant proteins by surface plasmon resonance. Biochemistry 2000; 39:11989-99. [PMID: 11009613 DOI: 10.1021/bi001174w] [Citation(s) in RCA: 132] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Escherichia coli replication terminator protein (Tus) binds tightly and specifically to termination sites such as TerB in order to halt DNA replication. To better understand the process of Tus-TerB interaction, an assay based on surface plasmon resonance was developed to allow the determination of the equilibrium dissociation constant of the complex (K(D)) and association and dissocation rate constants for the interaction between Tus and various DNA sequences, including TerB, single-stranded DNA, and two nonspecific sequences that had no relationship to TerB. The effects of factors such as the KCl concentration, the orientation and length of the DNA, and the presence of a single-stranded tail on the binding were also examined. The K(D) measured for the binding of wild type and His(6)-Tus to TerB was 0.5 nM in 250 mM KCl. Four variants of Tus containing single-residue mutations were assayed for binding to TerB and the nonspecific sequences. Three of these substitutions (K89A, R198A, and Q250A) increased K(D) by 200-300-fold, whereas the A173T substitution increased K(D) by 4000-fold. Only the R198A substitution had a significant effect on binding to the nonspecific sequences. The kinetic and thermodynamic data suggest a model for Tus binding to TerB which involves an ordered series of events that include structural changes in the protein.
Collapse
Affiliation(s)
- C Neylon
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | | | | | | | | | | |
Collapse
|
17
|
Abstract
This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715-1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included.
Collapse
Affiliation(s)
- M K Berlyn
- Department of Biology and School of Forestry and Environmental Studies, Yale University, New Haven, Connecticut 06520-8104, USA.
| |
Collapse
|
18
|
Bastia D, Manna AC, Sahoo T. Termination of DNA replication in prokaryotic chromosomes. GENETIC ENGINEERING 1997; 19:101-19. [PMID: 9193105 DOI: 10.1007/978-1-4615-5925-2_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- D Bastia
- Department of Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | | | | |
Collapse
|
19
|
Howell RM, Woodford KJ, Weitzmann MN, Usdin K. The chicken beta-globin gene promoter forms a novel "cinched" tetrahelical structure. J Biol Chem 1996; 271:5208-14. [PMID: 8617804 DOI: 10.1074/jbc.271.9.5208] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
We have previously shown that the G-rich sequence G16CG(GGT)2GG in the promoter region of the chicken beta-globin gene poses a formidable barrier to DNA synthesis in vitro (Woodford et al., 1994, J. Biol. Chem. 269, 27029-27035). The K+ requirement, template-strand specificity, template concentration independence, and involvement of Hoogsteen bonding suggested that the underlying basis of this new type of DNA synthesis arrest site might be an intrastrand tetrahelical structure. However, the arrest site lacks the four G-rich repeats that are a hallmark of previously described intramolecular tetraplexes and contains a number of noncanonical bases that would be expected to greatly destabilize such a structure. Here we report evidence for an unusual K+-dependent intrastrand "cinched" tetraplex. This structure has several unique features including the incorporation of bases other than guanine into the stem of the tetraplex, interaction between loop bases and bases in the flanking region, and base pairing between bases 3 and 5 of the tetrahelix-forming region to form a molecular "cinch." This finding extends the range of sequences capable of tetraplex formation as well as our appreciation of the conformational complexity of the chicken beta-globin promoter.
Collapse
Affiliation(s)
- R M Howell
- Section on Genomic Structure and Function, Laboratory of Biochemical Pharmacology, NIDDK, National Institutes of Health, Bethesda, Maryland 20892-0830, USA
| | | | | | | |
Collapse
|
20
|
Kamada K, Ohsumi K, Horiuchi T, Shimamoto N, Morikawa K. Crystallization and preliminary X-ray analysis of the Escherichia coli replication terminator protein complexed with DNA. Proteins 1996; 24:402-3. [PMID: 8778788 DOI: 10.1002/(sici)1097-0134(199603)24:3<402::aid-prot14>3.0.co;2-q] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Crystals of the Escherichia coli replication terminator protein (Tus) complexed with its binding site DNA were obtained by a microdialysis method using PEG 4000. They belong to the tetragonal space group P4(1)2(1)2 or P4(3)2(1)2 with the unit cell parameter: a = 68.1 A, c = 230.7 A and contain one protein-DNA complex in an asymmetric unit. The native data set has been collected to 2.7 A resolution.
Collapse
Affiliation(s)
- K Kamada
- Department of Genetics, Graduate University for Advanced Studies, Shizuoka, Japan
| | | | | | | | | |
Collapse
|
21
|
Horiuchi T, Fujimura Y. Recombinational rescue of the stalled DNA replication fork: a model based on analysis of an Escherichia coli strain with a chromosome region difficult to replicate. J Bacteriol 1995; 177:783-91. [PMID: 7836313 PMCID: PMC176657 DOI: 10.1128/jb.177.3.783-791.1995] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
To examine the physiological effects of DNA replication arrest at the terminus (Ter), we constructed a replication-blocked Escherichia coli strain so that both bidirectional replication forks would be impeded at two flanking Ter sites, one artificial and the other natural. While the blocked strain grew slightly more slowly than a control strain, it had abnormal phenotypes similar to those of E. coli dam mutants, i.e., hyper-Rec phenotype, recA(+)- and recB+ (C+)-dependent growth, and constitutive SOS induction. The observation that these two apparently unrelated mutants cause similar phenotypes led us to design a model. We propose that the following sequential events may occur in both strains. A double-strand (ds) break occurs at the blocked replication fork in the blocked strain and at the ongoing fork in the dam mutant, through which RecBCD enzyme enters and degrades the ds DNA molecule, and the degradation product serves as the signal molecule for SOS induction. When RecBCD enzyme meets an appropriately oriented Chi sequence, its DNase activity is converted to recombinase enzyme, which is able to repair the ds end, recombinationally. this model (i) explains the puzzling phenotype of recA and recB (C) mutants and the SOS-inducing phenotype of polA, lig, and dna mutants under restrictive conditions, (ii) provides an interpretation for the role of the Chi sequence, and (iii) suggests a possible key role for homologous recombination with regard to cell survival following the arrest of DNA replication.
Collapse
Affiliation(s)
- T Horiuchi
- National Institute for Basic Biology, Okazaki, Japan
| | | |
Collapse
|
22
|
Horiuchi T, Nishitani H, Kobayashi T. A new type of E. coli recombinational hotspot which requires for activity both DNA replication termination events and the Chi sequence. ADVANCES IN BIOPHYSICS 1995; 31:133-47. [PMID: 7625270 DOI: 10.1016/0065-227x(95)99388-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
In E. coli rnh- mutants we identified chromosome-derived, specific DNA fragments termed Hot DNA. When the DNA in the ccc form is integrated into the E. coli genome by homologous recombination to form a directly repeated structure, a striking enhancement of excisional recombination between the repeats occurs. We obtained 8 groups of such Hot DNA, 7 of which were clustered in a narrow region called the replication terminus region (about 280 kb) on the circular E. coli genome. A Ter site can impede the replication fork in a polar fashion. The six Ter sites are approximately symmetrical in the terminus and surrounding region. To block the fork at the Ter site, a protein factor, Ter binding protein encoded in the tau (or tus) gene, is required. In tau- cells, Hot activity of HotA, B, and C DNAs disappears, thereby indicating that the Hot activity is fork arrest-dependent. Other Hot activities were tau-independent. In addition, for at least HotA activity, the presence of Chi, and E. coli recombinational hotspot sequence, is required; the Chi dependent HotA activity was detected in a wild type strain but to a lesser extent than that in the rnh- mutant. To explain the HotA phenomenon at the molecular level, we propose a model in which a ds-break occurs at the replication fork arrested at the Ter site. Our recent data that HOT1, a yeast recombinational hotspot, may also depend on the fork blocking event for activity, suggests that a similar ds-break occurs in both eucaryotes and procaryotes.
Collapse
Affiliation(s)
- T Horiuchi
- Laboratory of Gene Expression and Regulation, National Institute for Basic Biology, Aichi, Japan
| | | | | |
Collapse
|
23
|
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
|
24
|
Horiuchi T, Fujimura Y, Nishitani H, Kobayashi T, Hidaka M. The DNA replication fork blocked at the Ter site may be an entrance for the RecBCD enzyme into duplex DNA. J Bacteriol 1994; 176:4656-63. [PMID: 8045897 PMCID: PMC196287 DOI: 10.1128/jb.176.15.4656-4663.1994] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
In Escherichia coli, eight kinds of chromosome-derived DNA fragments (named Hot DNA) were found to exhibit homologous recombinational hotspot activity, with the following properties. (i) The Hot activities of all Hot DNAs were enhanced extensively under RNase H-defective (rnh) conditions. (ii) Seven Hot DNAs were clustered at the DNA replication terminus region on the E. coli chromosome and had Chi activities (H. Nishitani, M. Hidaka, and T. Horiuchi, Mol. Gen. Genet. 240:307-314, 1993). Hot activities of HotA, -B, and -C, the locations of which were close to three DNA replication terminus sites, the TerB, -A, and -C sites, respectively, disappeared when terminus-binding (Tau or Tus) protein was defective, thereby suggesting that their Hot activities are termination event dependent. Other Hot groups showed termination-independent Hot activities. In addition, at least HotA activity proved to be dependent on a Chi sequence, because mutational destruction of the Chi sequence on the HotA DNA fragment resulted in disappearance of the HotA activity. The HotA activity which had disappeared was reactivated by insertion of a new, properly oriented Chi sequence at the position between the HotA DNA and the TerB site. On the basis of these observations and positional and orientational relationships between the Chi and the Ter sequences, we propose a model in which the DNA replication fork blocked at the Ter site provides an entrance for the RecBCD enzyme into duplex DNA.
Collapse
Affiliation(s)
- T Horiuchi
- National Institute for Basic Biology, Kyushu University, Fukuoka, Japan
| | | | | | | | | |
Collapse
|
25
|
Coskun-Ari F, Skokotas A, Moe G, Hill T. Biophysical characteristics of Tus, the replication arrest protein of Escherichia coli. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)41737-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
|
26
|
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.
Collapse
Affiliation(s)
- B Sharma
- Department of Bioscience and Biotechnology, Drexel University, Philadelphia, Pennsylvania 19104
| | | |
Collapse
|
27
|
Zyskind JW, Svitil AL, Stine WB, Biery MC, Smith DW. RecA protein of Escherichia coli and chromosome partitioning. Mol Microbiol 1992; 6:2525-37. [PMID: 1406288 DOI: 10.1111/j.1365-2958.1992.tb01429.x] [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
Escherichia coli cells deficient in RecA protein frequently contain an abnormal number of chromosomes after completion of ongoing rounds of DNA replication. This suggests that RecA protein may be required for correct timing of initiation of DNA replication; however, we show here that initiation of DNA replication is properly timed in recA mutants. We also find that more than 10% of recA mutant cells contain no DNA. These anucleate cells appear to arise from partitioning of all the DNA into one daughter cell and no DNA into the other daughter cell. Based on these and previously published results, we propose that RecA protein is required for equal partitioning of chromosomes into the two daughter cells.
Collapse
Affiliation(s)
- J W Zyskind
- Department of Biology, San Diego State University, California 92182
| | | | | | | | | |
Collapse
|
28
|
Kobayashi T, Hidaka M, Nishizawa M, Horiuchi T. Identification of a site required for DNA replication fork blocking activity in the rRNA gene cluster in Saccharomyces cerevisiae. MOLECULAR & GENERAL GENETICS : MGG 1992; 233:355-62. [PMID: 1620093 DOI: 10.1007/bf00265431] [Citation(s) in RCA: 88] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The yeast genome has DNA replication fork blocking sites, that we have named sog sites, in the ribosomal RNA gene (rDNA) cluster. These are located at the 3' end of the 35S rRNA transcription unit and they block replication fork movement in a direction opposite to that of RNA polymerase I. We cloned this replication blocking site into a YEp-type plasmid and analyzed DNA replication intermediates, using two-dimensional (2D) agarose gel electrophoresis. The blocking activity remained even on a plasmid not involved in 35S rRNA transcription and inhibited fork movement in the same polar fashion as on the yeast chromosome. To define the site further, smaller fragments were subcloned into the YEp-type plasmid. A small 109 bp region exhibited sog activity and was located near the enhancer region for 35S rRNA transcription. It overlaps an essential element of the recombinational hot spot HOT1.
Collapse
Affiliation(s)
- T Kobayashi
- Department of Molecular Biology, Graduate School of Medical Science, Kyushu University, Fukuoka, Japan
| | | | | | | |
Collapse
|
29
|
Abstract
The tus gene encodes a DNA-binding protein (Tus) that inhibits replication forks at specific block-sites within the terminus region of the Escherichia coli chromosome. One of these block-sites, TerB, is adjacent to the tus gene. Using primer extension and a promoter fusion to characterize in vivo expression, we have demonstrated that the tus transcription start site is within TerB, and that Tus protein autoregulates expression at this weak promoter. We have also demonstrated that a minority of tus transcripts are initiated from an upstream region that contains two additional open reading frames. This readthrough transcription into tus is reduced in the presence of Tus protein.
Collapse
Affiliation(s)
- B A Roecklein
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder 80309
| | | |
Collapse
|
30
|
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
|
31
|
Gottlieb P, Wu S, Zhang X, Tecklenburg M, Kuempel P, Hill T. Equilibrium, kinetic, and footprinting studies of the Tus-Ter protein-DNA interaction. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(18)42536-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|
32
|
Hidaka M, Kobayashi T, Ishimi Y, Seki M, Enomoto T, Abdel-Monem M, Horiuchi T. Termination complex in Escherichia coli inhibits SV40 DNA replication in vitro by impeding the action of T antigen helicase. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(18)42774-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|
33
|
Hidaka M, Kobayashi T, Horiuchi T. A newly identified DNA replication terminus site, TerE, on the Escherichia coli chromosome. J Bacteriol 1991; 173:391-3. [PMID: 1824765 PMCID: PMC207198 DOI: 10.1128/jb.173.1.391-393.1991] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
To search for heretofore unidentified DNA replication termination (Ter) sites on the Escherichia coli chromosome, we screened the entire Kohara lambda bacteriophage library using as probes the four known 22-bp Ter sequences. We found a Ter site, which we named TerE, located at 23.2 min on the linkage map. TerE inhibits only counterclockwise DNA replication. Macroscopically, five Ter sites are located in a periodic arrangement on the genome.
Collapse
Affiliation(s)
- M Hidaka
- Department of Molecular Biology, Graduate School of Medical Science, Kyushu University, Fukuoka, Japan
| | | | | |
Collapse
|