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Bainbridge LJ, Teague R, Doherty AJ. Repriming DNA synthesis: an intrinsic restart pathway that maintains efficient genome replication. Nucleic Acids Res 2021; 49:4831-4847. [PMID: 33744934 PMCID: PMC8136793 DOI: 10.1093/nar/gkab176] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/01/2021] [Accepted: 03/05/2021] [Indexed: 12/25/2022] Open
Abstract
To bypass a diverse range of fork stalling impediments encountered during genome replication, cells possess a variety of DNA damage tolerance (DDT) mechanisms including translesion synthesis, template switching, and fork reversal. These pathways function to bypass obstacles and allow efficient DNA synthesis to be maintained. In addition, lagging strand obstacles can also be circumvented by downstream priming during Okazaki fragment generation, leaving gaps to be filled post-replication. Whether repriming occurs on the leading strand has been intensely debated over the past half-century. Early studies indicated that both DNA strands were synthesised discontinuously. Although later studies suggested that leading strand synthesis was continuous, leading to the preferred semi-discontinuous replication model. However, more recently it has been established that replicative primases can perform leading strand repriming in prokaryotes. An analogous fork restart mechanism has also been identified in most eukaryotes, which possess a specialist primase called PrimPol that conducts repriming downstream of stalling lesions and structures. PrimPol also plays a more general role in maintaining efficient fork progression. Here, we review and discuss the historical evidence and recent discoveries that substantiate repriming as an intrinsic replication restart pathway for maintaining efficient genome duplication across all domains of life.
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Affiliation(s)
- Lewis J Bainbridge
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, BN1 9RQ, UK
| | - Rebecca Teague
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, BN1 9RQ, UK
| | - Aidan J Doherty
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, BN1 9RQ, UK
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2
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Cronan GE, Kouzminova EA, Kuzminov A. Near-continuously synthesized leading strands in Escherichia coli are broken by ribonucleotide excision. Proc Natl Acad Sci U S A 2019; 116:1251-1260. [PMID: 30617079 PMCID: PMC6347710 DOI: 10.1073/pnas.1814512116] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
In vitro, purified replisomes drive model replication forks to synthesize continuous leading strands, even without ligase, supporting the semidiscontinuous model of DNA replication. However, nascent replication intermediates isolated from ligase-deficient Escherichia coli comprise only short (on average 1.2-kb) Okazaki fragments. It was long suspected that cells replicate their chromosomal DNA by the semidiscontinuous mode observed in vitro but that, in vivo, the nascent leading strand was artifactually fragmented postsynthesis by excision repair. Here, using high-resolution separation of pulse-labeled replication intermediates coupled with strand-specific hybridization, we show that excision-proficient E. coli generates leading-strand intermediates >10-fold longer than lagging-strand Okazaki fragments. Inactivation of DNA-repair activities, including ribonucleotide excision, further increased nascent leading-strand size to ∼80 kb, while lagging-strand Okazaki fragments remained unaffected. We conclude that in vivo, repriming occurs ∼70× less frequently on the leading versus lagging strands, and that DNA replication in E. coli is effectively semidiscontinuous.
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Affiliation(s)
- Glen E Cronan
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Elena A Kouzminova
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Andrei Kuzminov
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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3
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Bhardwaj A, Ghose D, Thakur KG, Dutta D. Escherichia coli β-clamp slows down DNA polymerase I dependent nick translation while accelerating ligation. PLoS One 2018; 13:e0199559. [PMID: 29924849 PMCID: PMC6010275 DOI: 10.1371/journal.pone.0199559] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 06/08/2018] [Indexed: 11/25/2022] Open
Abstract
The nick translation property of DNA polymerase I (Pol I) ensures the maturation of Okazaki fragments by removing primer RNAs and facilitating ligation. However, prolonged nick translation traversing downstream DNA is an energy wasting futile process, as Pol I simultaneously polymerizes and depolymerizes at the nick sites utilizing energy-rich dNTPs. Using an in vitro assay system, we demonstrate that the β-clamp of the Escherichia coli replisome strongly inhibits nick translation on the DNA substrate. To do so, β-clamp inhibits the strand displacement activity of Pol I by interfering with the interaction between the finger subdomain of Pol I and the downstream primer-template junction. Conversely, β-clamp stimulates the 5’ exonuclease property of Pol I to cleave single nucleotides or shorter oligonucleotide flaps. This single nucleotide flap removal at high frequency increases the probability of ligation between the upstream and downstream DNA strands at an early phase, terminating nick translation. Besides β-clamp-mediated ligation helps DNA ligase to seal the nick promptly during the maturation of Okazaki fragments.
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Affiliation(s)
- Amit Bhardwaj
- CSIR-Institute of Microbial Technology, Chandigarh, India
| | | | | | - Dipak Dutta
- CSIR-Institute of Microbial Technology, Chandigarh, India
- * E-mail:
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4
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Henrikus SS, Wood EA, McDonald JP, Cox MM, Woodgate R, Goodman MF, van Oijen AM, Robinson A. DNA polymerase IV primarily operates outside of DNA replication forks in Escherichia coli. PLoS Genet 2018; 14:e1007161. [PMID: 29351274 PMCID: PMC5792023 DOI: 10.1371/journal.pgen.1007161] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 01/31/2018] [Accepted: 12/19/2017] [Indexed: 11/18/2022] Open
Abstract
In Escherichia coli, damage to the chromosomal DNA induces the SOS response, setting in motion a series of different DNA repair and damage tolerance pathways. DNA polymerase IV (pol IV) is one of three specialised DNA polymerases called into action during the SOS response to help cells tolerate certain types of DNA damage. The canonical view in the field is that pol IV primarily acts at replisomes that have stalled on the damaged DNA template. However, the results of several studies indicate that pol IV also acts on other substrates, including single-stranded DNA gaps left behind replisomes that re-initiate replication downstream of a lesion, stalled transcription complexes and recombination intermediates. In this study, we use single-molecule time-lapse microscopy to directly visualize fluorescently labelled pol IV in live cells. We treat cells with the DNA-damaging antibiotic ciprofloxacin, Methylmethane sulfonate (MMS) or ultraviolet light and measure changes in pol IV concentrations and cellular locations through time. We observe that only 5–10% of foci induced by DNA damage form close to replisomes, suggesting that pol IV predominantly carries out non-replisomal functions. The minority of foci that do form close to replisomes exhibit a broad distribution of colocalisation distances, consistent with a significant proportion of pol IV molecules carrying out postreplicative TLS in gaps behind the replisome. Interestingly, the proportion of pol IV foci that form close to replisomes drops dramatically in the period 90–180 min after treatment, despite pol IV concentrations remaining relatively constant. In an SOS-constitutive mutant that expresses high levels of pol IV, few foci are observed in the absence of damage, indicating that within cells access of pol IV to DNA is dependent on the presence of damage, as opposed to concentration-driven competition for binding sites. Translesion DNA polymerases play a critical role in DNA damage tolerance in all cells. In Escherichia coli, the translesion polymerases include DNA polymerases II, IV, and V. At stalled replication forks, DNA polymerase IV is thought to compete with, and perhaps displace the polymerizing subunits of DNA polymerase III to facilitate translesion replication. The results of the current fluorescence microscopy study challenge that view. The results indicate that DNA polymerase IV acts predominantly at sites away from the replisome. These sites may include recombination intermediates, stalled transcription complexes, and single-stranded gaps left in the wake of DNA polymerase III replisomes that re-initiate replication downstream of a lesion.
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Affiliation(s)
- Sarah S. Henrikus
- School of Chemistry, University of Wollongong, Wollongong, Australia
| | - Elizabeth A. Wood
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - John P. McDonald
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Michael M. Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Myron F. Goodman
- Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, California, United States of America
| | | | - Andrew Robinson
- School of Chemistry, University of Wollongong, Wollongong, Australia
- * E-mail:
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5
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Beattie TR, Kapadia N, Nicolas E, Uphoff S, Wollman AJ, Leake MC, Reyes-Lamothe R. Frequent exchange of the DNA polymerase during bacterial chromosome replication. eLife 2017; 6. [PMID: 28362256 PMCID: PMC5403216 DOI: 10.7554/elife.21763] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 03/28/2017] [Indexed: 12/31/2022] Open
Abstract
The replisome is a multiprotein machine that carries out DNA replication. In Escherichia coli, a single pair of replisomes is responsible for duplicating the entire 4.6 Mbp circular chromosome. In vitro studies of reconstituted E. coli replisomes have attributed this remarkable processivity to the high stability of the replisome once assembled on DNA. By examining replisomes in live E. coli with fluorescence microscopy, we found that the Pol III* subassembly frequently disengages from the replisome during DNA synthesis and exchanges with free copies from solution. In contrast, the DnaB helicase associates stably with the replication fork, providing the molecular basis for how the E. coli replisome can maintain high processivity and yet possess the flexibility to bypass obstructions in template DNA. Our data challenges the widely-accepted semi-discontinuous model of chromosomal replication, instead supporting a fully discontinuous mechanism in which synthesis of both leading and lagging strands is frequently interrupted. DOI:http://dx.doi.org/10.7554/eLife.21763.001 New cells are created when an existing cell divides to produce two new ones. During this process the original cell must copy its DNA so each new cell inherits a full set of genetic material. DNA is made up of two strands that twist together to form a double helix. These strands need to be separated so they can be used as templates to make new DNA strands. An enzyme called DNA helicase is responsible for separating the two DNA strands and another enzyme makes the new DNA. These enzymes are part of a group of proteins collectively called the replisome that controls the whole DNA copying process. The replisome must be extremely reliable to avoid introducing mistakes into the cell’s genes. Previous research using replisomes extracted from cells indicated that replisomes are effective at copying DNA because the proteins they contain are strongly bound together and remain attached to the DNA for a long time. However, the behavior of replisomes in living cells has not been closely examined. Beattie, Kapadia et al. used microscopy to observe how the replisome copies DNA in a bacterium called Escherichia coli. The experiments revealed that most of the proteins within the replisome are constantly being replaced during DNA copying. The exception to this is DNA helicase, which stays in place at the front of the replisome, providing a landing platform for all the other parts of the machine to come and go. Future work will investigate why the parts of the replisome are replaced so frequently. This may allow us to alter the stability of the bacterial replisome, which may lead to new medical treatments and biotechnologies. DOI:http://dx.doi.org/10.7554/eLife.21763.002
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Affiliation(s)
| | - Nitin Kapadia
- Department of Biology, McGill University, Montreal, Canada
| | - Emilien Nicolas
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Stephan Uphoff
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Adam Jm Wollman
- Biological Physical Sciences Institute, Departments of Physics and Biology, University of York, Heslington, United Kingdom
| | - Mark C Leake
- Biological Physical Sciences Institute, Departments of Physics and Biology, University of York, Heslington, United Kingdom
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6
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Abstract
The bacteriophage λ Red homologous recombination system has been studied over the past 50 years as a model system to define the mechanistic details of how organisms exchange DNA segments that share extended regions of homology. The λ Red system proved useful as a system to study because recombinants could be easily generated by co-infection of genetically marked phages. What emerged from these studies was the recognition that replication of phage DNA was required for substantial Red-promoted recombination in vivo, and the critical role that double-stranded DNA ends play in allowing the Red proteins access to the phage DNA chromosomes. In the past 16 years, however, the λ Red recombination system has gained a new notoriety. When expressed independently of other λ functions, the Red system is able to promote recombination of linear DNA containing limited regions of homology (∼50 bp) with the Escherichia coli chromosome, a process known as recombineering. This review explains how the Red system works during a phage infection, and how it is utilized to make chromosomal modifications of E. coli with such efficiency that it changed the nature and number of genetic manipulations possible, leading to advances in bacterial genomics, metabolic engineering, and eukaryotic genetics.
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Affiliation(s)
- Kenan C Murphy
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605
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Laureti L, Demol J, Fuchs RP, Pagès V. Bacterial Proliferation: Keep Dividing and Don't Mind the Gap. PLoS Genet 2015; 11:e1005757. [PMID: 26713761 PMCID: PMC4699847 DOI: 10.1371/journal.pgen.1005757] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 12/01/2015] [Indexed: 12/21/2022] Open
Abstract
DNA Damage Tolerance (DDT) mechanisms help dealing with unrepaired DNA lesions that block replication and challenge genome integrity. Previous in vitro studies showed that the bacterial replicase is able to re-prime downstream of a DNA lesion, leaving behind a single-stranded DNA gap. The question remains of what happens to this gap in vivo. Following the insertion of a single lesion in the chromosome of a living cell, we showed that this gap is mostly filled in by Homology Directed Gap Repair in a RecA dependent manner. When cells fail to repair this gap, or when homologous recombination is impaired, cells are still able to divide, leading to the loss of the damaged chromatid, suggesting that bacteria lack a stringent cell division checkpoint mechanism. Hence, at the expense of losing one chromatid, cell survival and proliferation are ensured. DNA Damage Tolerance (DDT) mechanisms help dealing with unrepaired DNA lesions that block replication, thus challenging genome integrity. Two DDT mechanisms have previously been described: error prone Translesion Synthesis operated by specialized DNA polymerases and error free bypass that uses the information of the sister chromatid to bypass the lesion. In this work, we set up a novel genetic system that allows to insert a single DNA blocking lesion in the chromosome of a living cell and to visualize the exchange of genetic information between the undamaged and the damaged strand. Using this system, we showed in vivo that the replication fork is able to re-prime downstream of the lesion, leaving a gap. This gap is mostly filled in by the error free pathway through the RecA homologous recombination mechanism. We show that when the gap is left unrepaired, cells are still able to divide by losing the damaged chromatid, which evidences the lack of a stringent cell division checkpoint system.
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Affiliation(s)
- Luisa Laureti
- Cancer Research Center of Marseille, Team DNA Damage Tolerance, CNRS, UMR7258; Inserm, U1068; Institut Paoli-Calmettes; Aix-Marseille University, Marseille, France
| | - Julien Demol
- Cancer Research Center of Marseille, Team DNA Damage Tolerance, CNRS, UMR7258; Inserm, U1068; Institut Paoli-Calmettes; Aix-Marseille University, Marseille, France
| | - Robert P. Fuchs
- Cancer Research Center of Marseille, Team DNA Damage Tolerance, CNRS, UMR7258; Inserm, U1068; Institut Paoli-Calmettes; Aix-Marseille University, Marseille, France
- * E-mail: (RPF); (VP)
| | - Vincent Pagès
- Cancer Research Center of Marseille, Team DNA Damage Tolerance, CNRS, UMR7258; Inserm, U1068; Institut Paoli-Calmettes; Aix-Marseille University, Marseille, France
- * E-mail: (RPF); (VP)
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8
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Abstract
This review describes the components of the Escherichia coli replisome and the dynamic process in which they function and interact under normal conditions. It also briefly describes the behavior of the replisome during situations in which normal replication fork movement is disturbed, such as when the replication fork collides with sites of DNA damage. E. coli DNA Pol III was isolated first from a polA mutant E. coli strain that lacked the relatively abundant DNA Pol I activity. Further biochemical studies, and the use of double mutant strains, revealed Pol III to be the replicative DNA polymerase essential to cell viability. In a replisome, DnaG primase must interact with DnaB for activity, and this constraint ensures that new RNA primers localize to the replication fork. The leading strand polymerase continually synthesizes DNA in the direction of the replication fork, whereas the lagging-strand polymerase synthesizes short, discontinuous Okazaki fragments in the opposite direction. Discontinuous lagging-strand synthesis requires that the polymerase rapidly dissociate from each new completed Okazaki fragment in order to begin the extension of a new RNA primer. Lesion bypass can be thought of as a two-step reaction that starts with the incorporation of a nucleotide opposite the lesion, followed by the extension of the resulting distorted primer terminus. A remarkable property of E. coli, and many other eubacterial organisms, is the speed at which it propagates. Rapid cell division requires the presence of an extremely efficient replication machinery for the rapid and faithful duplication of the genome.
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9
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Abstract
Reconstitution experiments using replication proteins from a number of different model organisms have firmly established that, in vitro, DNA replication is semi-discontinuous: continuous on the leading strand and discontinuous on the lagging strand. The mechanism by which DNA is replicated in vivo is less clear. In fact, there have been many observations of discontinuous replication in the absence of exogenous DNA-damaging agents. It has also been proposed that replication is discontinuous on the leading strand at least in part because of DNA lesion bypass. Several recent studies have revealed mechanistic details of pathways where replication of the leading strand introduces discontinuities. These mechanisms and their potential contributions to observations of discontinuous replication in vivo will be discussed.
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Amado L, Kuzminov A. Low-molecular-weight DNA replication intermediates in Escherichia coli: mechanism of formation and strand specificity. J Mol Biol 2013; 425:4177-91. [PMID: 23876705 DOI: 10.1016/j.jmb.2013.07.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 07/12/2013] [Accepted: 07/15/2013] [Indexed: 11/30/2022]
Abstract
Chromosomal DNA replication intermediates, revealed in ligase-deficient conditions in vivo, are of low molecular weight (LMW) independently of the organism, suggesting discontinuous replication of both the leading and the lagging DNA strands. Yet, in vitro experiments with purified enzymes replicating sigma-structured substrates show continuous synthesis of the leading DNA strand in complete absence of ligase, supporting the textbook model of semi-discontinuous DNA replication. The discrepancy between the in vivo and in vitro results is rationalized by proposing that various excision repair events nick continuously synthesized leading strands after synthesis, producing the observed LMW intermediates. Here, we show that, in an Escherichia coli ligase-deficient strain with all known excision repair pathways inactivated, new DNA is still synthesized discontinuously. Furthermore, hybridization to strand-specific targets demonstrates that the LMW replication intermediates come from both the lagging and the leading strands. These results support the model of discontinuous leading strand synthesis in E. coli.
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Affiliation(s)
- Luciana Amado
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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11
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Yanga W, Lib X. Next-generation sequencing of Okazaki fragments extracted from Saccharomyces cerevisiae. FEBS Lett 2013; 587:2441-7. [PMID: 23792162 DOI: 10.1016/j.febslet.2013.06.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 06/11/2013] [Indexed: 11/19/2022]
Abstract
Genome-wide Okazaki fragment distribution can differentiate the discontinuous from the semi-discontinuous DNA replication model. Here, we investigated the genome-wide Okazaki fragment distribution in Saccharomyces cerevisiae S288C. We improved the method based upon lambda exonuclease digestion to purify Okazaki fragments from S288C yeast cells, followed by Illumina sequencing. The distribution of Okazaki fragments around confirmed replication origins, including two highly efficient replication origins, supported the discontinuous DNA replication model. In S. cerevisiae mitochondria, Okazaki fragments were overrepresented in the transcribed regions, indicating the interplay between transcription and DNA replication.
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Affiliation(s)
- Wenchao Yanga
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China.
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12
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Li XT, Thomason LC, Sawitzke JA, Costantino N, Court DL. Bacterial DNA polymerases participate in oligonucleotide recombination. Mol Microbiol 2013; 88:906-20. [PMID: 23634873 PMCID: PMC7523544 DOI: 10.1111/mmi.12231] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2013] [Indexed: 02/01/2023]
Abstract
Synthetic single-strand oligonucleotides (oligos) with homology to genomic DNA have proved to be highly effective for constructing designed mutations in targeted genomes, a process referred to as recombineering. The cellular functions important for this type of homologous recombination have yet to be determined. Towards this end, we have identified Escherichia coli functions that process the recombining oligo and affect bacteriophage λ Red-mediated oligo recombination. To determine the nature of oligo processing during recombination, each oligo contained multiple nucleotide changes: a single base change allowing recombinant selection, and silent changes serving as genetic markers to determine the extent of oligo processing during the recombination. Such oligos were often not incorporated into the host chromosome intact; many were partially degraded in the process of recombination. The position and number of these silent nucleotide changes within the oligo strongly affect both oligo processing and recombination frequency. Exonucleases, especially those associated with DNA Polymerases I and III, affect inheritance of the silent nucleotide changes in the oligos. We demonstrate for the first time that the major DNA polymerases (Pol I and Pol III) and DNA ligase are directly involved with oligo recombination.
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Affiliation(s)
- Xin-tian Li
- Molecular Control and Genetics Section, Gene Regulation and Chromosome Biology, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Lynn C. Thomason
- Molecular Control and Genetics Section, Gene Regulation and Chromosome Biology, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
- Basic Science Program, SAIC-Frederick, Inc., Frederick, MD 21702, USA
| | - James A. Sawitzke
- Molecular Control and Genetics Section, Gene Regulation and Chromosome Biology, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Nina Costantino
- Molecular Control and Genetics Section, Gene Regulation and Chromosome Biology, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Donald L. Court
- Molecular Control and Genetics Section, Gene Regulation and Chromosome Biology, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
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13
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Indiani C, O'Donnell M. A proposal: Source of single strand DNA that elicits the SOS response. Front Biosci (Landmark Ed) 2013; 18:312-23. [PMID: 23276924 DOI: 10.2741/4102] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Chromosome replication is performed by numerous proteins that function together as a "replisome". The replisome machinery duplicates both strands of the parental DNA simultaneously. Upon DNA damage to the cell, replisome action produces single-strand DNA to which RecA binds, enabling its activity in cleaving the LexA repressor and thus inducing the SOS response. How single-strand DNA is produced by a replisome acting on damaged DNA is not clear. For many years it has been assumed the single-strand DNA is generated by the replicative helicase, which continues unwinding DNA even after DNA polymerase stalls at a template lesion. Recent studies indicate another source of the single-strand DNA, resulting from an inherently dynamic replisome that may hop over template lesions on both leading and lagging strands, thereby leaving single-strand gaps in the wake of the replication fork. These single-strand gaps are proposed to be the origin of the single-strand DNA that triggers the SOS response after DNA damage.
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Affiliation(s)
- Chiara Indiani
- Manhattan College 4513 Manhattan College Pkwy, Riverdale, NY 10471, USA.
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14
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Abstract
Homologous recombination is an ubiquitous process that shapes genomes and repairs DNA damage. The reaction is classically divided into three phases: presynaptic, synaptic, and postsynaptic. In Escherichia coli, the presynaptic phase involves either RecBCD or RecFOR proteins, which act on DNA double-stranded ends and DNA single-stranded gaps, respectively; the central synaptic steps are catalyzed by the ubiquitous DNA-binding protein RecA; and the postsynaptic phase involves either RuvABC or RecG proteins, which catalyze branch-migration and, in the case of RuvABC, the cleavage of Holliday junctions. Here, we review the biochemical properties of these molecular machines and analyze how, in light of these properties, the phenotypes of null mutants allow us to define their biological function(s). The consequences of point mutations on the biochemical properties of recombination enzymes and on cell phenotypes help refine the molecular mechanisms of action and the biological roles of recombination proteins. Given the high level of conservation of key proteins like RecA and the conservation of the principles of action of all recombination proteins, the deep knowledge acquired during decades of studies of homologous recombination in bacteria is the foundation of our present understanding of the processes that govern genome stability and evolution in all living organisms.
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15
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Rodriguez GP, Song JB, Crouse GF. Transformation with oligonucleotides creating clustered changes in the yeast genome. PLoS One 2012; 7:e42905. [PMID: 22916177 PMCID: PMC3422593 DOI: 10.1371/journal.pone.0042905] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 07/12/2012] [Indexed: 12/17/2022] Open
Abstract
We have studied single-strand oligonucleotide (oligo) transformation of yeast by using 40-nt long oligos that create multiple base changes to the yeast genome spread throughout the length of the oligos, making it possible to measure the portions of an oligo that are incorporated during transformation. Although the transformation process is greatly inhibited by DNA mismatch repair (MMR), the pattern of incorporation is essentially the same in the presence or absence of MMR, whether the oligo anneals to the leading or lagging strand of DNA replication, or whether phosphorothioate linkages are used at either end. A central core of approximately 15 nt is incorporated with a frequency of >90%; the ends are incorporated with a lower frequency, and loss of the two ends appears to be by different mechanisms. Bases that are 5–10 nt from the 5′ end are generally lost with a frequency of >95%, likely through a process involving flap excision. On the 3′ end, bases 5–10 nt from the 3′ end are lost about 1/3 of the time. These results indicate that oligos can be used to create multiple simultaneous changes to the yeast genome, even in the presence of MMR.
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Affiliation(s)
- Gina P. Rodriguez
- Department of Biology, Emory University, Atlanta, Georgia, United States of America
| | - Joseph B. Song
- Department of Biology, Emory University, Atlanta, Georgia, United States of America
| | - Gray F. Crouse
- Department of Biology, Emory University, Atlanta, Georgia, United States of America
- Winship Cancer Institute, Emory University, Atlanta, Georgia, United States of America
- * E-mail:
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16
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Pomerantz RT, O'Donnell M. What happens when replication and transcription complexes collide? Cell Cycle 2011; 9:2537-43. [PMID: 20581460 DOI: 10.4161/cc.9.13.12122] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The arrest of replication forks due to collisions with transcription complexes leads to genomic instability and cell death. Mechanisms that promote the progression of replication forks past transcription complexes are therefore essential for propagation and preservation of the genome. Recent studies of E. coli directly investigate the consequences of collisions of the replisome with RNAP polymerase (RNAP) in vitro and provide novel mechanisms by which these encounters may be resolved. Additionally, recent in vivo and in vitro studies support the longstanding hypothesis that auxiliary DNA helicases promote replication through roadblocks such as transcription complexes. Here we review past and recent advances that formulate our current understanding of how the bacterial replisome deals with transcription complexes along the path of chromosome duplication.
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Affiliation(s)
- Richard T Pomerantz
- The Rockefeller University, Howard Hughes Medical Institute, New York, NY, USA
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17
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Allen JM, Simcha DM, Ericson NG, Alexander DL, Marquette JT, Van Biber BP, Troll CJ, Karchin R, Bielas JH, Loeb LA, Camps M. Roles of DNA polymerase I in leading and lagging-strand replication defined by a high-resolution mutation footprint of ColE1 plasmid replication. Nucleic Acids Res 2011; 39:7020-33. [PMID: 21622658 PMCID: PMC3167613 DOI: 10.1093/nar/gkr157] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
DNA polymerase I (pol I) processes RNA primers during lagging-strand synthesis and fills small gaps during DNA repair reactions. However, it is unclear how pol I and pol III work together during replication and repair or how extensive pol I processing of Okazaki fragments is in vivo. Here, we address these questions by analyzing pol I mutations generated through error-prone replication of ColE1 plasmids. The data were obtained by direct sequencing, allowing an accurate determination of the mutation spectrum and distribution. Pol I’s mutational footprint suggests: (i) during leading-strand replication pol I is gradually replaced by pol III over at least 1.3 kb; (ii) pol I processing of Okazaki fragments is limited to ∼20 nt and (iii) the size of Okazaki fragments is short (∼250 nt). While based on ColE1 plasmid replication, our findings are likely relevant to other pol I replicative processes such as chromosomal replication and DNA repair, which differ from ColE1 replication mostly at the recruitment steps. This mutation footprinting approach should help establish the role of other prokaryotic or eukaryotic polymerases in vivo, and provides a tool to investigate how sequence topology, DNA damage, or interactions with protein partners may affect the function of individual DNA polymerases.
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Affiliation(s)
- Jennifer M Allen
- Department of Microbiology and Environmental Toxicology, University of California Santa Cruz, 1156 High Street Santa Cruz, CA 95060, USA
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18
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Simultaneous single-molecule measurements of phage T7 replisome composition and function reveal the mechanism of polymerase exchange. Proc Natl Acad Sci U S A 2011; 108:3584-9. [PMID: 21245349 DOI: 10.1073/pnas.1018824108] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A complete understanding of the molecular mechanisms underlying the functioning of large, multiprotein complexes requires experimental tools capable of simultaneously visualizing molecular architecture and enzymatic activity in real time. We developed a novel single-molecule assay that combines the flow-stretching of individual DNA molecules to measure the activity of the DNA-replication machinery with the visualization of fluorescently labeled DNA polymerases at the replication fork. By correlating polymerase stoichiometry with DNA synthesis of T7 bacteriophage replisomes, we are able to quantitatively describe the mechanism of polymerase exchange. We find that even at relatively modest polymerase concentration (∼2 nM), soluble polymerases are recruited to an actively synthesizing replisome, dramatically increasing local polymerase concentration. These excess polymerases remain passively associated with the replisome through electrostatic interactions with the T7 helicase for ∼50 s until a stochastic and transient dissociation of the synthesizing polymerase from the primer-template allows for a polymerase exchange event to occur.
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19
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Chen YY, Huang H, Wang TCV. PriA participates in nascent DNA synthesis in Escherichia coli. Mol Biol Rep 2010; 37:3165-70. [DOI: 10.1007/s11033-009-9896-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2009] [Accepted: 10/02/2009] [Indexed: 10/20/2022]
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20
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Murphy KC, Marinus MG. RecA-independent single-stranded DNA oligonucleotide-mediated mutagenesis. F1000 BIOLOGY REPORTS 2010; 2:56. [PMID: 20711416 PMCID: PMC2920528 DOI: 10.3410/b2-56] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The expression of Beta, the single-stranded annealing protein (SSAP) of bacteriophage λ in Escherichia coli promotes high levels of oligonucleotide (oligo)-mediated mutagenesis and offers a quick way to create single or multiple base pair insertions, deletions, or substitutions in the bacterial chromosome. High rates of mutagenesis can be obtained by the use of mismatch repair (MMR)-resistant mismatches or MMR-deficient hosts, which allow for the isolation of unselected mutations. It has recently become clear that many bacteria can be mutagenized with oligos in the absence of any SSAP expression, albeit at a much lower frequency. Studies have shown that inactivation or inhibition of single-stranded DNA (ssDNA) exonucleases in vivo increases the rate of SSAP-independent oligo-mediated mutagenesis. These results suggest that λ Beta, in addition to its role in annealing the oligo to ssDNA regions of the replication fork, promotes high rates of oligo-mediated mutagenesis by protecting the oligo from destruction by host ssDNA exonucleases.
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Affiliation(s)
- Kenan C Murphy
- Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, 55 Lake Ave North, Worcester, MA 01655, USA
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21
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Loot C, Bikard D, Rachlin A, Mazel D. Cellular pathways controlling integron cassette site folding. EMBO J 2010; 29:2623-34. [PMID: 20628355 DOI: 10.1038/emboj.2010.151] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2009] [Accepted: 06/11/2010] [Indexed: 11/09/2022] Open
Abstract
By mobilizing small DNA units, integrons have a major function in the dissemination of antibiotic resistance among bacteria. The acquisition of gene cassettes occurs by recombination between the attI and attC sites catalysed by the IntI1 integron integrase. These recombination reactions use an unconventional mechanism involving a folded single-stranded attC site. We show that cellular bacterial processes delivering ssDNA, such as conjugation and replication, favour proper folding of the attC site. By developing a very sensitive in vivo assay, we also provide evidence that attC sites can recombine as cruciform structures by extrusion from double-stranded DNA. Moreover, we show an influence of DNA superhelicity on attC site extrusion in vitro and in vivo. We show that the proper folding of the attC site depends on both the propensity to form non-recombinogenic structures and the length of their variable terminal structures. These results draw the network of cell processes that regulate integron recombination.
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Affiliation(s)
- Céline Loot
- Institut Pasteur, Unité Plasticité du Génome Bactérien, Paris, France
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22
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Gari K, Constantinou A. The role of the Fanconi anemia network in the response to DNA replication stress. Crit Rev Biochem Mol Biol 2009; 44:292-325. [PMID: 19728769 DOI: 10.1080/10409230903154150] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Fanconi anemia is a genetically heterogeneous disorder associated with chromosome instability and a highly elevated risk for developing cancer. The mutated genes encode proteins involved in the cellular response to DNA replication stress. Fanconi anemia proteins are extensively connected with DNA caretaker proteins, and appear to function as a hub for the coordination of DNA repair with DNA replication and cell cycle progression. At a molecular level, however, the raison d'être of Fanconi anemia proteins still remains largely elusive. The thirteen Fanconi anemia proteins identified to date have not been embraced into a single and defined biological process. To help put the Fanconi anemia puzzle into perspective, we begin this review with a summary of the strategies employed by prokaryotes and eukaryotes to tolerate obstacles to the progression of replication forks. We then summarize what we know about Fanconi anemia with an emphasis on biochemical aspects, and discuss how the Fanconi anemia network, a late acquisition in evolution, may function to permit the faithful and complete duplication of our very large vertebrate chromosomes.
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Affiliation(s)
- Kerstin Gari
- DNA Damage Response Laboratory, Cancer Research UK, London Research Institute, Clare Hall Laboratories, South Mimms, UK
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23
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Langston LD, Indiani C, O'Donnell M. Whither the replisome: emerging perspectives on the dynamic nature of the DNA replication machinery. Cell Cycle 2009; 8:2686-91. [PMID: 19652539 DOI: 10.4161/cc.8.17.9390] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Replisomes were originally thought to be multi-protein machines with a stabile and defined structure during replication. Discovery that replisomes repeatedly discard sliding clamps and assemble a new clamp to start each Okazaki fragment provided the first hint that the replisome structure changes during replication. Recent studies reveal that the replisome is more dynamic than ever thought possible. Replisomes can utilize many different polymerases; the helicase is regulated to travel at widely different speeds; leading and lagging strands need not always act in a coupled fashion with DNA loops; and the replication fork does not always exhibit semi-discontinuous replication. We review some of these findings here and discuss their implications for cell physiology as well as enzyme mechanism.
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24
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Pavlov YI, Shcherbakova PV. DNA polymerases at the eukaryotic fork-20 years later. Mutat Res 2009; 685:45-53. [PMID: 19682465 DOI: 10.1016/j.mrfmmm.2009.08.002] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Accepted: 08/05/2009] [Indexed: 10/20/2022]
Abstract
Function of the eukaryotic genome depends on efficient and accurate replication of anti-parallel DNA strands. Eukaryotic DNA polymerases have different properties adapted to perform a wide spectrum of DNA transactions. Here we focus on major players in the bulk replication, DNA polymerases of the B-family. We review the organization of the replication fork in eukaryotes in a historical perspective, analyze contemporary models and propose a new integrative model of the fork.
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Affiliation(s)
- Youri I Pavlov
- Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, NE 68198-6805, USA.
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25
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Yao NY, O'Donnell M. Replisome structure and conformational dynamics underlie fork progression past obstacles. Curr Opin Cell Biol 2009; 21:336-43. [PMID: 19375905 PMCID: PMC3732650 DOI: 10.1016/j.ceb.2009.02.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2009] [Accepted: 02/24/2009] [Indexed: 11/29/2022]
Abstract
Replisomes are multiprotein complexes that unzip the parental helix and duplicate the separated strands during genome replication. The antiparallel structure of DNA poses unique geometric constraints to the process, and the replisome has evolved unique dynamic features that solve this problem. Interestingly, the solution to duplex DNA replication has been co-opted to solve many other important problems that replisomes must contend with during the duplication of long chromosomes. For example, along its path the replisome will encounter lesions and DNA-bound proteins. Recent studies show that the replisome can circumvent lesions on either strand, using the strategy normally applied to the lagging strand synthesis. Circumventing lesions can also be assisted by other proteins that transiently become a part of the replisome. The replisome must also contend with DNA-binding proteins and recent studies reveal a fascinating process that enables it to bypass RNA polymerase without stopping.
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Affiliation(s)
- Nina Y Yao
- Rockefeller University, Howard Hughes Medical Institute, 1230 York Avenue, New York, NY 10065, United States
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26
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Pomerantz RT, O'Donnell M. The replisome uses mRNA as a primer after colliding with RNA polymerase. Nature 2008; 456:762-6. [PMID: 19020502 PMCID: PMC2605185 DOI: 10.1038/nature07527] [Citation(s) in RCA: 150] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2008] [Accepted: 10/06/2008] [Indexed: 11/09/2022]
Abstract
Replication forks are impeded by DNA damage and protein-nucleic acid complexes such as transcribing RNA polymerase. For example, head-on collision of the replisome with RNA polymerase results in replication fork arrest. However, co-directional collision of the replisome with RNA polymerase has little or no effect on fork progression. Here we examine co-directional collisions between a replisome and RNA polymerase in vitro. We show that the Escherichia coli replisome uses the RNA transcript as a primer to continue leading-strand synthesis after the collision with RNA polymerase that is displaced from the DNA. This action results in a discontinuity in the leading strand, yet the replisome remains intact and bound to DNA during the entire process. These findings underscore the notable plasticity by which the replisome operates to circumvent obstacles in its path and may explain why the leading strand is synthesized discontinuously in vivo.
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Affiliation(s)
- Richard T Pomerantz
- The Rockefeller University, Howard Hughes Medical Institute, 1230 York Avenue, New York, New York 10021, USA
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27
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Yao NY, O'Donnell M. Replisome dynamics and use of DNA trombone loops to bypass replication blocks. MOLECULAR BIOSYSTEMS 2008; 4:1075-84. [PMID: 18931783 DOI: 10.1039/b811097b] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Replisomes are dynamic multiprotein machines capable of simultaneously replicating both strands of the DNA duplex. This review focuses on the structure and function of the E. coli replisome, many features of which generalize to other bacteria and eukaryotic cells. For example, the bacterial replisome utilizes clamps and clamp loaders to coordinate the actions required of the trombone model of lagging strand synthesis made famous by Bruce Alberts. All cells contain clamps and clamp loaders and this review summarizes their structure and function. Clamp loaders are pentameric spirals that bind DNA in a structure specific fashion and thread it through the ring shaped clamp. The recent structure of the E. coli beta clamp in complex with primed DNA has implications for how multiple polymerases function on sliding clamps and how the primed DNA template is exchanged between them. Recent studies reveal a remarkable fluidity in replisome function that enables it to bypass template lesions on either DNA strand. During these processes the polymerases within the replisome functionally uncouple from one another. Mechanistic processes that underlie these actions may involve DNA looping, similar to the trombone loops that mediate the lagging strand Okazaki fragment synthesis cycle.
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Affiliation(s)
- Nina Y Yao
- The Rockefeller University and Howard Hughes Medical Institute, 1230 York Avenue, New York, NY 10065-6399, USA
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28
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Genetics of recombination in the model bacterium Escherichia coli. MOLECULAR GENETICS OF RECOMBINATION 2007. [DOI: 10.1007/978-3-540-71021-9_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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29
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Lehmann AR, Fuchs RP. Gaps and forks in DNA replication: Rediscovering old models. DNA Repair (Amst) 2006; 5:1495-8. [PMID: 16956796 DOI: 10.1016/j.dnarep.2006.07.002] [Citation(s) in RCA: 136] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2006] [Accepted: 07/11/2006] [Indexed: 11/26/2022]
Abstract
Most current models for replication past damaged lesions envisage that translesion synthesis occurs at the replication fork. However older models suggested that gaps were left opposite lesions to allow the replication fork to proceed, and these gaps were subsequently sealed behind the replication fork. Two recent articles lend support to the idea that bypass of the damage occurs behind the fork. In the first paper, electron micrographs of DNA replicated in UV-irradiated yeast cells show regions of single-stranded DNA both at the replication forks and behind the fork, the latter being consistent with the presence of gaps in the daughter-strands opposite lesions. The second paper describes an in vitro DNA replication system reconstituted from purified bacterial proteins. Repriming of synthesis downstream from a blocked fork occurred not only on the lagging strand as expected, but also on the leading strand, demonstrating that contrary to widely accepted beliefs, leading strand synthesis does not need to be continuous.
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Affiliation(s)
- Alan R Lehmann
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, UK.
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30
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Heller RC, Marians KJ. Replisome assembly and the direct restart of stalled replication forks. Nat Rev Mol Cell Biol 2006; 7:932-43. [PMID: 17139333 DOI: 10.1038/nrm2058] [Citation(s) in RCA: 238] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Failure to reactivate either stalled or collapsed replication forks is a source of genomic instability in both prokaryotes and eukaryotes. In prokaryotes, dedicated fork repair systems that involve both recombination and replication proteins have been identified genetically and characterized biochemically. Replication conflicts are solved through several pathways, some of which require recombination and some of which operate directly at the stalled fork. Some recent biochemical observations support models of direct fork repair in which the removal of the blocking template lesion is not always required for replication restart.
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Affiliation(s)
- Ryan C Heller
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA
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31
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Langston LD, O'Donnell M. DNA replication: keep moving and don't mind the gap. Mol Cell 2006; 23:155-60. [PMID: 16857582 DOI: 10.1016/j.molcel.2006.05.034] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2006] [Revised: 05/10/2006] [Accepted: 05/12/2006] [Indexed: 10/24/2022]
Abstract
As the replication fork progresses, synthesis of the discontinuous lagging strand requires frequent priming and cycling of the lagging strand polymerase to the new primers. It appears that this mechanism also permits bypass of template lesions on both strands, leaving the damage behind in a single-strand gap and precluding fork stalling or collapse.
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Affiliation(s)
- Lance D Langston
- Howard Hughes Medical Institute, The Rockefeller University, New York City, New York 10021, USA
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32
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Amado L, Kuzminov A. The replication intermediates in Escherichia coli are not the product of DNA processing or uracil excision. J Biol Chem 2006; 281:22635-46. [PMID: 16772291 DOI: 10.1074/jbc.m602320200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The current model of DNA replication in Escherichia coli postulates continuous synthesis of the leading strand, based on in vitro experiments with purified enzymes. In contrast, in vivo experiments in E. coli and its bacteriophages, in which maturation of replication intermediates was blocked, report discontinuous DNA synthesis of both the lagging and the leading strands. To address this discrepancy, we analyzed nascent DNA species from ThyA+ E. coli cells replicating their DNA in ligase-deficient conditions to block maturation of replication intermediates. We report here that the bulk of the newly synthesized DNA isolated from ligase-deficient cells have a length between 0.3 and 3 kb, with a minor fraction being longer that 11 kb but shorter than the chromosome. The low molecular weight of the replication intermediates is unchanged by blocking linear DNA processing with a recBCD mutation or by blocking uracil excision with an ung mutation. These results are consistent with the previously proposed discontinuous replication of the leading strand in E. coli.
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Affiliation(s)
- Luciana Amado
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3709, USA
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33
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Lopes M, Foiani M, Sogo JM. Multiple mechanisms control chromosome integrity after replication fork uncoupling and restart at irreparable UV lesions. Mol Cell 2006; 21:15-27. [PMID: 16387650 DOI: 10.1016/j.molcel.2005.11.015] [Citation(s) in RCA: 421] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2005] [Revised: 09/26/2005] [Accepted: 11/15/2005] [Indexed: 10/25/2022]
Abstract
DNA replication forks pause in front of lesions on the template, eventually leading to cytotoxic chromosomal rearrangements. The in vivo structure of damaged eukaryotic replication intermediates has been so far elusive. Combining electron microscopy (EM) and two-dimensional (2D) gel electrophoresis, we found that UV-irradiated S. cerevisiae cells uncouple leading and lagging strand replication at irreparable UV lesions, thus generating long ssDNA regions on one side of the fork. Furthermore, small ssDNA gaps accumulate along replicated duplexes, likely resulting from repriming events downstream of the lesions on both leading and lagging strands. Translesion synthesis and homologous recombination counteract gap accumulation, without affecting fork progression. The DNA damage checkpoint contributes to gap repair and maintains a replication-competent fork structure. We propose that the coordinated action of checkpoint, recombination, and translesion synthesis-mediated processes at the fork and behind the fork preserves the integrity of replicating chromosomes by allowing efficient replication restart and filling the resulting ssDNA gaps.
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Affiliation(s)
- Massimo Lopes
- Department of Biology, Institute of Cell Biology, ETH Hönggerberg, CH-8093 Zürich, Switzerland.
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34
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Baharoglu Z, Petranovic M, Flores MJ, Michel B. RuvAB is essential for replication forks reversal in certain replication mutants. EMBO J 2006; 25:596-604. [PMID: 16424908 PMCID: PMC1383526 DOI: 10.1038/sj.emboj.7600941] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2005] [Accepted: 12/14/2005] [Indexed: 12/28/2022] Open
Abstract
Inactivated replication forks may be reversed by the annealing of leading- and lagging-strand ends, resulting in the formation of a Holliday junction (HJ) adjacent to a DNA double-strand end. In Escherichia coli mutants deficient for double-strand end processing, resolution of the HJ by RuvABC leads to fork breakage, a reaction that we can directly quantify. Here we used the HJ-specific resolvase RusA to test a putative role of the RuvAB helicase in replication fork reversal (RFR). We show that the RuvAB complex is required for the formation of a RusA substrate in the polymerase III mutants dnaEts and holD, affected for the Pol III catalytic subunit and clamp loader, and in the helicase mutant rep. This finding reveals that the recombination enzyme RuvAB targets forks in vivo and we propose that it directly converts forks into HJs. In contrast, RFR occurs in the absence of RuvAB in the dnaNts mutant, affected for the processivity clamp of Pol III, and in the priA mutant, defective for replication restart. This suggests alternative pathways of RFR.
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Affiliation(s)
- Zeynep Baharoglu
- Laboratoire de Génétique Microbienne, Institut National de la Recherche Agronomique, Jouy en Josas Cedex, France
- Present address: Centre de génétique Moléculaire, CNRS Bâtiment 26, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France
| | - Mirjana Petranovic
- Laboratoire de Génétique Microbienne, Institut National de la Recherche Agronomique, Jouy en Josas Cedex, France
| | - Maria-Jose Flores
- Laboratoire de Génétique Microbienne, Institut National de la Recherche Agronomique, Jouy en Josas Cedex, France
| | - Bénédicte Michel
- Laboratoire de Génétique Microbienne, Institut National de la Recherche Agronomique, Jouy en Josas Cedex, France
- Present address: Centre de génétique Moléculaire, CNRS Bâtiment 26, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France
- Centre de génétique Moléculaire, CNRS Bâtiment 26, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France. Tel.: +33 1 69 82 32 29; Fax: +33 1 69 82 31 40; E-mail:
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35
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Abdulovic A, Kim N, Jinks-Robertson S. Mutagenesis and the three R's in yeast. DNA Repair (Amst) 2006; 5:409-21. [PMID: 16412705 DOI: 10.1016/j.dnarep.2005.11.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2005] [Revised: 11/17/2005] [Accepted: 11/17/2005] [Indexed: 11/19/2022]
Abstract
Mutagenesis is a prerequisite for evolution and also is an important contributor to human diseases. Most mutations in actively dividing cells originate during DNA replication as errors introduced when copying an undamaged DNA template or during the bypass of DNA lesions. In addition, mutations can be introduced during the repair of DNA double-strand breaks by either homologous recombination or non-homologous end-joining pathways. Finally, although generally considered to be a very high-fidelity process, the excision repair of DNA damage may be an important contributor to mutagenesis in non-dividing cells. In this review, we will discuss the well-known contributions of DNA replication to mutagenesis in Saccharomyces cerevisiae, as well as the less-appreciated contributions of recombination and repair to mutagenesis in this organism.
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Affiliation(s)
- Amy Abdulovic
- Biochemistry, Cell and Developmental Biology Program of the Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA 30322, USA
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36
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Abstract
When cells that are actively replicating DNA encounter sites of base damage or strand breaks, replication might stall or arrest. In this situation, cells rely on DNA-damage-tolerance mechanisms to bypass the damage effectively. One of these mechanisms, known as translesion DNA synthesis, is supported by specialized DNA polymerases that are able to catalyse nucleotide incorporation opposite lesions that cannot be negotiated by high-fidelity replicative polymerases. A second category of tolerance mechanism involves alternative replication strategies that obviate the need to replicate directly across sites of template-strand damage.
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Affiliation(s)
- Errol C Friedberg
- Laboratory of Molecular Pathology, Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9072, USA.
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