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Pedersen IB, Helgesen E, Flåtten I, Fossum-Raunehaug S, Skarstad K. SeqA structures behind Escherichia coli replication forks affect replication elongation and restart mechanisms. Nucleic Acids Res 2017; 45:6471-6485. [PMID: 28407100 PMCID: PMC5499823 DOI: 10.1093/nar/gkx263] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 04/07/2017] [Indexed: 12/13/2022] Open
Abstract
The SeqA protein binds hemi-methylated GATC sites and forms structures that sequester newly replicated origins and trail the replication forks. Cells that lack SeqA display signs of replication fork disintegration. The broken forks could arise because of over-initiation (the launching of too many forks) or lack of dynamic SeqA structures trailing the forks. To confirm one or both of these possible mechanisms, we compared two seqA mutants with the oriCm3 mutant. The oriCm3 mutant over-initiates because of a lack of origin sequestration but has wild-type SeqA protein. Cells with nonfunctional SeqA, but not oriCm3 mutant cells, had problems with replication elongation, were highly dependent on homologous recombination, and exhibited extensive chromosome fragmentation. The results indicate that replication forks frequently break in the absence of SeqA function and that the broken forks are rescued by homologous recombination. We suggest that SeqA may act in two ways to stabilize replication forks: (i) by enabling vital replication fork repair and restarting reactions and (ii) by preventing replication fork rear-end collisions.
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Affiliation(s)
- Ida Benedikte Pedersen
- Department of Molecular Cell Biology and Department of Microbiology, Oslo University Hospital, P.O. Box 4950, 0424 Oslo, Norway
| | - Emily Helgesen
- Department of Molecular Cell Biology and Department of Microbiology, Oslo University Hospital, P.O. Box 4950, 0424 Oslo, Norway
| | - Ingvild Flåtten
- Department of Molecular Cell Biology and Department of Microbiology, Oslo University Hospital, P.O. Box 4950, 0424 Oslo, Norway
| | - Solveig Fossum-Raunehaug
- Department of Molecular Cell Biology and Department of Microbiology, Oslo University Hospital, P.O. Box 4950, 0424 Oslo, Norway.,School of Pharmacy, Faculty of Mathematics and Natural Sciences, University of Oslo, P.O. Box 4950, 0424 Oslo, Norway
| | - Kirsten Skarstad
- Department of Molecular Cell Biology and Department of Microbiology, Oslo University Hospital, P.O. Box 4950, 0424 Oslo, Norway.,School of Pharmacy, Faculty of Mathematics and Natural Sciences, University of Oslo, P.O. Box 4950, 0424 Oslo, Norway
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2
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Lack of the H-NS Protein Results in Extended and Aberrantly Positioned DNA during Chromosome Replication and Segregation in Escherichia coli. J Bacteriol 2016; 198:1305-16. [PMID: 26858102 DOI: 10.1128/jb.00919-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 02/02/2016] [Indexed: 01/08/2023] Open
Abstract
UNLABELLED The architectural protein H-NS binds nonspecifically to hundreds of sites throughout the chromosome and can multimerize to stiffen segments of DNA as well as to form DNA-protein-DNA bridges. H-NS has been suggested to contribute to the orderly folding of the Escherichia coli chromosome in the highly compacted nucleoid. In this study, we investigated the positioning and dynamics of the origins, the replisomes, and the SeqA structures trailing the replication forks in cells lacking the H-NS protein. In H-NS mutant cells, foci of SeqA, replisomes, and origins were irregularly positioned in the cell. Further analysis showed that the average distance between the SeqA structures and the replisome was increased by ∼100 nm compared to that in wild-type cells, whereas the colocalization of SeqA-bound sister DNA behind replication forks was not affected. This result may suggest that H-NS contributes to the folding of DNA along adjacent segments. H-NS mutant cells were found to be incapable of adopting the distinct and condensed nucleoid structures characteristic of E. coli cells growing rapidly in rich medium. It appears as if H-NS mutant cells adopt a “slow-growth” type of chromosome organization under nutrient-rich conditions, which leads to a decreased cellular DNA content. IMPORTANCE It is not fully understood how and to what extent nucleoid-associated proteins contribute to chromosome folding and organization during replication and segregation in Escherichia coli. In this work, we find in vivo indications that cells lacking the nucleoid-associated protein H-NS have a lower degree of DNA condensation than wild-type cells. Our work suggests that H-NS is involved in condensing the DNA along adjacent segments on the chromosome and is not likely to tether newly replicated strands of sister DNA. We also find indications that H-NS is required for rapid growth with high DNA content and for the formation of a highly condensed nucleoid structure under such conditions.
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3
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Adiciptaningrum A, Osella M, Moolman MC, Cosentino Lagomarsino M, Tans SJ. Stochasticity and homeostasis in the E. coli replication and division cycle. Sci Rep 2015; 5:18261. [PMID: 26671779 PMCID: PMC4680914 DOI: 10.1038/srep18261] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 11/11/2015] [Indexed: 11/09/2022] Open
Abstract
How cells correct for stochasticity to coordinate the chromosome replication and cellular division cycle is poorly understood. We used time-lapse microscopy and fluorescently labelled SeqA to determine the timing of birth, initiation, termination, and division, as well as cell size throughout the cell cycle. We found that the time between birth and initiation (B-period) compensates for stochastic variability in birth size and growth rate. The time between termination and division (D-period) also compensates for size and growth variability, invalidating the notion that replication initiation is the principal trigger for cell division. In contrast, the time between initiation and termination (C-period) did not display such compensations. Interestingly, the C-period did show small but systematic decreases for cells that spontaneously grew faster, which suggests a coupling between metabolic fluctuations and replication. An auto-regressive theoretical framework was employed to compare different possible models of sub-period control.
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Affiliation(s)
| | - Matteo Osella
- Dipartimento di Fisica and INFN, University of Torino, V. Pietro Giuria 1, Torino, I-10125, Italy
| | - M Charl Moolman
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Marco Cosentino Lagomarsino
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7238, Computational and Quantitative Biology, 15 rue de l'École de Médecine, Paris, France.,CNRS, UMR 7238 Paris, France
| | - Sander J Tans
- FOM Institute AMOLF, 1098 XG Amsterdam, the Netherlands
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4
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Cagliero C, Zhou YN, Jin DJ. Spatial organization of transcription machinery and its segregation from the replisome in fast-growing bacterial cells. Nucleic Acids Res 2015; 42:13696-705. [PMID: 25416798 PMCID: PMC4267616 DOI: 10.1093/nar/gku1103] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
In a fast-growing Escherichia coli cell, most RNA polymerase (RNAP) is allocated to rRNA synthesis forming transcription foci at clusters of rrn operons or bacterial nucleolus, and each of the several nascent nucleoids contains multiple pairs of replication forks. The composition of transcription foci has not been determined. In addition, how the transcription machinery is three-dimensionally organized to promote cell growth in concord with replication machinery in the nucleoid remains essentially unknown. Here, we determine the spatial and functional landscapes of transcription and replication machineries in fast-growing E. coli cells using super-resolution-structured illumination microscopy. Co-images of RNAP and DNA reveal spatial compartmentation and duplication of the transcription foci at the surface of the bacterial chromosome, encompassing multiple nascent nucleoids. Transcription foci cluster with NusA and NusB, which are the rrn anti-termination system and are associated with nascent rRNAs. However, transcription foci tend to separate from SeqA and SSB foci, which track DNA replication forks and/or the replisomes, demonstrating that transcription machinery and replisome are mostly located in different chromosomal territories to maintain harmony between the two major cellular functions in fast-growing cells. Our study suggests that bacterial chromosomes are spatially and functionally organized, analogous to eukaryotes.
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Affiliation(s)
| | | | - Ding Jun Jin
- To whom correspondence should be addressed. Tel: +1 301 846 7684; Fax: +1 301 846 1489;
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5
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Adachi S, Murakawa Y, Hiraga S. Dynamic nature of SecA and its associated proteins in Escherichia coli. Front Microbiol 2015; 6:75. [PMID: 25713567 PMCID: PMC4322705 DOI: 10.3389/fmicb.2015.00075] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 01/21/2015] [Indexed: 11/13/2022] Open
Abstract
Mechanical properties such as physical constraint and pushing of chromosomes are thought to be important for chromosome segregation in Escherichia coli and it could be mediated by a hypothetical molecular "tether." However, the actual tether that mediates these features is not known. We previously described that SecA (Secretory A) and Secretory Y (SecY), components of the membrane protein translocation machinery, and AcpP (Acyl carrier protein P) were involved in chromosome segregation and homeostasis of DNA topology. In the present work, we performed three-dimensional deconvolution of microscopic images and time-lapse experiments of these proteins together with MukB and DNA topoisomerases, and found that these proteins embraced the structures of tortuous nucleoids with condensed regions. Notably, SecA, SecY, and AcpP dynamically localized in cells, which was interdependent on each other requiring the ATPase activity of SecA. Our findings imply that the membrane protein translocation machinery plays a role in the maintenance of proper chromosome partitioning, possibly through "tethering" of MukB [a functional homolog of structural maintenance of chromosomes (SMC) proteins], DNA gyrase, DNA topoisomerase IV, and SeqA (Sequestration A).
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Affiliation(s)
- Shun Adachi
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University Kyoto, Japan
| | - Yasuhiro Murakawa
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University Kyoto, Japan
| | - Sota Hiraga
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University Kyoto, Japan
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6
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Mika JT, Vanhecke A, Dedecker P, Swings T, Vangindertael J, Van den Bergh B, Michiels J, Hofkens J. A study of SeqA subcellular localization in Escherichia coli using photo-activated localization microscopy. Faraday Discuss 2015; 184:425-50. [DOI: 10.1039/c5fd00058k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Escherichia coli (E. coli) cells replicate their genome once per cell cycle to pass on genetic information to the daughter cells. The SeqA protein binds the origin of replication, oriC, after DNA replication initiation and sequesters it from new initiations in order to prevent overinitiation. Conventional fluorescence microscopy studies of SeqA localization in bacterial cells have shown that the protein is localized to discrete foci. In this study we have used photo-activated localization microscopy (PALM) to determine the localization of SeqA molecules, tagged with fluorescent proteins, with a localization precision of 20–30 nm with the aim to visualize the SeqA subcellular structures in more detail than previously possible. SeqA–PAmCherry was imaged in wild type E. coli, expressed from plasmid or genetically engineered into the bacterial genome, replacing the native seqA gene. Unsynchronized cells as well as cells with a synchronized cell cycle were imaged at various time points, in order to investigate the evolution of SeqA localization during the cell cycle. We found that SeqA indeed localized into discrete foci but these were not the only subcellular localizations of the protein. A significant amount of SeqA–PAmCherry molecules was localized outside the foci and in a fraction of cells we saw patterns indicating localization at the membrane. Using quantitative PALM, we counted protein copy numbers per cell, protein copy numbers per focus, the numbers of foci per cell and the sizes of the SeqA clusters. The data showed broad cell-to-cell variation and we did not observe a correlation between SeqA–PAmCherry protein numbers and the cell cycle under the experimental conditions of this study. The numbers of SeqA–PAmCherry molecules per focus as well as the foci sizes also showed broad distributions indicating that the foci are likely not characterized by a fixed number of molecules. We also imaged an E. coli strain devoid of the dam methylase (Δdam) and observed that SeqA–PAmCherry no longer formed foci, and was dispersed throughout the cell and localized to the plasma membrane more readily. We discuss our results in the context of the limitations of the technique.
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Affiliation(s)
- Jacek T. Mika
- Department of Chemistry
- KU Leuven
- 3001 Heverlee
- Belgium
| | | | | | - Toon Swings
- Centre of Microbial and Plant Genetics (CMPG)
- KU Leuven
- 3001 Leuven
- Belgium
| | | | - Bram Van den Bergh
- Centre of Microbial and Plant Genetics (CMPG)
- KU Leuven
- 3001 Leuven
- Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics (CMPG)
- KU Leuven
- 3001 Leuven
- Belgium
| | - Johan Hofkens
- Department of Chemistry
- KU Leuven
- 3001 Heverlee
- Belgium
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7
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Kuwada NJ, Traxler B, Wiggins PA. Genome-scale quantitative characterization of bacterial protein localization dynamics throughout the cell cycle. Mol Microbiol 2014; 95:64-79. [PMID: 25353361 PMCID: PMC4309519 DOI: 10.1111/mmi.12841] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2014] [Indexed: 11/28/2022]
Abstract
Bacterial cells display both spatial and temporal organization, and this complex structure is known to play a central role in cellular function. Although nearly one-fifth of all proteins in Escherichia coli localize to specific subcellular locations, fundamental questions remain about how cellular-scale structure is encoded at the level of molecular-scale interactions. One significant limitation to our understanding is that the localization behavior of only a small subset of proteins has been characterized in detail. As an essential step toward a global model of protein localization in bacteria, we capture and quantitatively analyze spatial and temporal protein localization patterns throughout the cell cycle for nearly every protein in E. coli that exhibits nondiffuse localization. This genome-scale analysis reveals significant complexity in patterning, notably in the behavior of DNA-binding proteins. Complete cell-cycle imaging also facilitates analysis of protein partitioning to daughter cells at division, revealing a broad and robust assortment of asymmetric partitioning behaviors.
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Affiliation(s)
- Nathan J Kuwada
- Department of Physics, University of Washington, Seattle, WA, 98195, USA; Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
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8
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Fossum-Raunehaug S, Helgesen E, Stokke C, Skarstad K. Escherichia coli SeqA structures relocalize abruptly upon termination of origin sequestration during multifork DNA replication. PLoS One 2014; 9:e110575. [PMID: 25333813 PMCID: PMC4204900 DOI: 10.1371/journal.pone.0110575] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 09/22/2014] [Indexed: 01/23/2023] Open
Abstract
The Escherichia coli SeqA protein forms complexes with new, hemimethylated DNA behind replication forks and is important for successful replication during rapid growth. Here, E. coli cells with two simultaneously replicating chromosomes (multifork DNA replication) and YFP tagged SeqA protein was studied. Fluorescence microscopy showed that in the beginning of the cell cycle cells contained a single focus at midcell. The focus was found to remain relatively immobile at midcell for a period of time equivalent to the duration of origin sequestration. Then, two abrupt relocalization events occurred within 2-6 minutes and resulted in SeqA foci localized at each of the cell's quarter positions. Imaging of cells containing an additional fluorescent tag in the origin region showed that SeqA colocalizes with the origin region during sequestration. This indicates that the newly replicated DNA of first one chromosome, and then the other, is moved from midcell to the quarter positions. At the same time, origins are released from sequestration. Our results illustrate that newly replicated sister DNA is segregated pairwise to the new locations. This mode of segregation is in principle different from that of slowly growing bacteria where the newly replicated sister DNA is partitioned to separate cell halves and the decatenation of sisters a prerequisite for, and possibly a mechanistic part of, segregation.
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Affiliation(s)
- Solveig Fossum-Raunehaug
- Department of Cell Biology, Institute for Cancer Research, Oslo University Hospital, the Norwegian Radium Hospital, Oslo, Norway
- School of Pharmacy, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Emily Helgesen
- Department of Cell Biology, Institute for Cancer Research, Oslo University Hospital, the Norwegian Radium Hospital, Oslo, Norway
| | - Caroline Stokke
- Department of Cell Biology, Institute for Cancer Research, Oslo University Hospital, the Norwegian Radium Hospital, Oslo, Norway
| | - Kirsten Skarstad
- Department of Cell Biology, Institute for Cancer Research, Oslo University Hospital, the Norwegian Radium Hospital, Oslo, Norway
- School of Pharmacy, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
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9
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Odsbu I, Skarstad K. DNA compaction in the early part of the SOS response is dependent on RecN and RecA. MICROBIOLOGY-SGM 2014; 160:872-882. [PMID: 24615185 DOI: 10.1099/mic.0.075051-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The nucleoids of undamaged Escherichia coli cells have a characteristic shape and number, which is dependent on the growth medium. Upon induction of the SOS response by a low dose of UV irradiation an extensive reorganization of the nucleoids occurred. Two distinct phases were observed by fluorescence microscopy. First, the nucleoids were found to change shape and fuse into compact structures at midcell. The compaction of the nucleoids lasted for 10-20 min and was followed by a phase where the DNA was dispersed throughout the cells. This second phase lasted for ~1 h. The compaction was found to be dependent on the recombination proteins RecA, RecO and RecR as well as the SOS-inducible, SMC (structural maintenance of chromosomes)-like protein RecN. RecN protein is produced in high amounts during the first part of the SOS response. It is possible that the RecN-mediated 'compact DNA' stage at the beginning of the SOS response serves to stabilize damaged DNA prior to recombination and repair.
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Affiliation(s)
- Ingvild Odsbu
- Department of Cell Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Kirsten Skarstad
- Department of Cell Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
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10
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Asakawa H, Hiraoka Y, Haraguchi T. A method of correlative light and electron microscopy for yeast cells. Micron 2014; 61:53-61. [PMID: 24792447 DOI: 10.1016/j.micron.2014.02.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 02/11/2014] [Accepted: 02/11/2014] [Indexed: 11/25/2022]
Abstract
Correlative light and electron microscopy (CLEM) is a method of imaging in which the same specimen is observed by both light microscopy and electron microscopy. Specifically, CLEM compares images obtained by light and electron microscopy and makes a correlation between them. After the advent of fluorescent proteins, CLEM was extended by combining electron microscopy with fluorescence microscopy to enable molecular-specific imaging of subcellular structures with a resolution at the nanometer level. This method is a powerful tool that is used to determine the localization of specific molecules of interest in the context of subcellular structures. Knowledge of the localization of target proteins coupled with the functions of the structures to which they are localized yields valuable information about the molecular functions of these proteins. However, this method has been mostly applied to adherent cells due to technical difficulties in immobilizing non-adherent target cells, such as yeasts, during sample preparation. We have developed a method of CLEM applicable to yeast cells. In this report, we detail this method and present its extension to Live CLEM. The Live CLEM method enabled us to link the dynamic properties of molecules of interest to cellular ultrastructures in the yeast cell. Since yeasts are premier organisms in molecular genetics, combining CLEM with yeast genetics promises to provide important new findings for understanding the molecular basis of the function of cellular structures.
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Affiliation(s)
- Haruhiko Asakawa
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Yasushi Hiraoka
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan; Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, 588-2 Iwaoka, Iwaoka-cho, Nishi-ku, Kobe 651-2492, Japan; Graduate School of Science, Osaka University, Toyonaka 560-0043, Japan
| | - Tokuko Haraguchi
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan; Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, 588-2 Iwaoka, Iwaoka-cho, Nishi-ku, Kobe 651-2492, Japan; Graduate School of Science, Osaka University, Toyonaka 560-0043, Japan.
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11
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Intracellular locations of replication proteins and the origin of replication during chromosome duplication in the slowly growing human pathogen Helicobacter pylori. J Bacteriol 2013; 196:999-1011. [PMID: 24363345 DOI: 10.1128/jb.01198-13] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
We followed the position of the replication complex in the pathogenic bacterium Helicobacter pylori using antibodies raised against the single-stranded DNA binding protein (HpSSB) and the replicative helicase (HpDnaB). The position of the replication origin, oriC, was also localized in growing cells by fluorescence in situ hybridization (FISH) with fluorescence-labeled DNA sequences adjacent to the origin. The replisome assembled at oriC near one of the cell poles, and the two forks moved together toward the cell center as replication progressed in the growing cell. Termination and resolution of the forks occurred near midcell, on one side of the septal membrane. The duplicated copies of oriC did not separate until late in elongation, when the daughter chromosomes segregated into bilobed nucleoids, suggesting sister chromatid cohesion at or near the oriC region. Components of the replication machinery, viz., HpDnaB and HpDnaG (DNA primase), were found associated with the cell membrane. A model for the assembly and location of the H. pylori replication machinery during chromosomal duplication is presented.
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12
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Regulation of sister chromosome cohesion by the replication fork tracking protein SeqA. PLoS Genet 2013; 9:e1003673. [PMID: 23990792 PMCID: PMC3749930 DOI: 10.1371/journal.pgen.1003673] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 06/12/2013] [Indexed: 01/12/2023] Open
Abstract
Analogously to chromosome cohesion in eukaryotes, newly replicated DNA in E. coli is held together by inter-sister linkages before partitioning into daughter nucleoids. In both cases, initial joining is apparently mediated by DNA catenation, in which replication-induced positive supercoils diffuse behind the fork, causing newly replicated duplexes to twist around each other. Type-II topoisomerase-catalyzed sister separation is delayed by the well-characterized cohesin complex in eukaryotes, but cohesion control in E. coli is not currently understood. We report that the abundant fork tracking protein SeqA is a strong positive regulator of cohesion, and is responsible for markedly prolonged cohesion observed at “snap” loci. Epistasis analysis suggests that SeqA stabilizes cohesion by antagonizing Topo IV-mediated sister resolution, and possibly also by a direct bridging mechanism. We show that variable cohesion observed along the E. coli chromosome is caused by differential SeqA binding, with oriC and snap loci binding disproportionally more SeqA. We propose that SeqA binding results in loose inter-duplex junctions that are resistant to Topo IV cleavage. Lastly, reducing cohesion by genetic manipulation of Topo IV or SeqA resulted in dramatically slowed sister locus separation and poor nucleoid partitioning, indicating that cohesion has a prominent role in chromosome segregation. Sister chromosome cohesion in eukaryotes maintains genome stability by mediating chromosome segregation and homologous recombination-dependent DNA repair. Here we have investigated the mechanism of cohesion regulation in E. coli by measuring cohesion timing in a broad set of candidate mutant strains. Using a sensitive DNA replication and segregation assay, we show that cohesion is controlled by the conserved DNA decatenation enzyme Topo IV and the abundant DNA binding protein SeqA. Results suggest that cohesion occurs in E. coli by twisting of replicated duplexes around each other behind the replication fork, and immediate resolution of cohered regions is blocked by SeqA. SeqA binds to a sliding 300–400 kb window of hemimethylated DNA behind the fork, and regions binding more SeqA experience longer cohesion periods. An analogous decatenation inhibition function is carried out by the cohesin complex in eukaryotes, indicating that cells mediate pairing and separation of replicated DNA by a conserved mechanism. In both cases, mismanaged cohesion results in failed or inefficient chromosome segregation.
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13
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Merrikh H, Grossman AD. Control of the replication initiator DnaA by an anti-cooperativity factor. Mol Microbiol 2011; 82:434-46. [PMID: 21895792 DOI: 10.1111/j.1365-2958.2011.07821.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proper coordination of DNA replication with cell growth and division is critical for production of viable progeny. In bacteria, coordination of DNA replication with cell growth is generally achieved by controlling activity of the replication initiator DnaA and its access to the chromosomal origin of replication, oriC. Here we describe a previously unknown mechanism for regulation of DnaA. YabA, a negative regulator of replication initiation in Bacillus subtilis, interacts with DnaA and DnaN, the sliding (processivity) clamp of DNA polymerase. We found that in vivo, YabA associated with the oriC region in a DnaA-dependent manner and limited the amount of DnaA at oriC. In vitro, purified YabA altered binding of DnaA to DNA by inhibiting cooperativity. Although previously undescribed, proteins that directly inhibit cooperativity may be a common mechanism for regulating replication initiation. Conditions that cause release of DnaN from the replisome, or overproduction of DnaN, caused decreased association of YabA and increased association of DnaA with oriC. This effect of DnaN, either directly or indirectly, is likely responsible, in part, for enabling initiation of a new round of replication following completion of a previous round.
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Affiliation(s)
- Houra Merrikh
- Department of Biology, Building 68-530, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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14
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Stokke C, Waldminghaus T, Skarstad K. Replication patterns and organization of replication forks in Vibrio cholerae. MICROBIOLOGY-SGM 2010; 157:695-708. [PMID: 21163839 DOI: 10.1099/mic.0.045112-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We have investigated the replication patterns of the two chromosomes of the bacterium Vibrio cholerae grown in four different media. By combining flow cytometry and quantitative real-time PCR with computer simulations, we show that in rich media, V. cholerae cells grow with overlapping replication cycles of both the large chromosome (ChrI) and the small chromosome (ChrII). In Luria-Bertani (LB) medium, initiation occurs at four copies of the ChrI origin and two copies of the ChrII origin. Replication of ChrII was found to occur at the end of the ChrI replication period in all four growth conditions. Novel cell-sorting experiments with marker frequency analysis support these conclusions. Incubation with protein synthesis inhibitors indicated that the potential for initiation of replication of ChrII was present at the same time as that of ChrI, but was actively delayed until much of ChrI was replicated. Investigations of the localization of SeqA bound to new DNA at replication forks indicated that the forks were co-localized in pairs when cells grew without overlapping replication cycles and in higher-order structures during more rapid growth. The increased degree of fork organization during rapid growth may be a means by which correct segregation of daughter molecules is facilitated.
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Affiliation(s)
- Caroline Stokke
- Department of Cell Biology, Institute for Cancer Research, The Norwegian Radiumhospital, Oslo University Hospital, Oslo, Norway
| | - Torsten Waldminghaus
- Department of Cell Biology, Institute for Cancer Research, The Norwegian Radiumhospital, Oslo University Hospital, Oslo, Norway
| | - Kirsten Skarstad
- Department of Cell Biology, Institute for Cancer Research, The Norwegian Radiumhospital, Oslo University Hospital, Oslo, Norway
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15
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A mathematical model for timing the release from sequestration and the resultant Brownian migration of SeqA clusters in E. coli. Bull Math Biol 2010; 73:1271-91. [PMID: 20640526 DOI: 10.1007/s11538-010-9558-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2009] [Accepted: 06/04/2010] [Indexed: 10/19/2022]
Abstract
DNA replication in Escherichia coli is initiated by DnaA binding to oriC, the replication origin. During the process of assembly of the replication factory, the DnaA is released back into the cytoplasm, where it is competent to reinitiate replication. Premature reinitiation is prevented by binding SeqA to newly formed GATC sites near the replication origin. Resolution of the resulting SeqA cluster is one aspect of timing for reinitiation. A Markov model accounting for the competition between SeqA binding and methylation for one or several GATC sites relates the timing to reaction rates, and consequently to the concentrations of SeqA and methylase. A model is proposed for segregation, the motion of the two daughter DNAs into opposite poles of the cell before septation. This model assumes that the binding of SeqA and its subsequent clustering results in loops from both daughter nucleoids attached to the SeqA cluster at the GATC sites. As desequestration occurs, the cluster is divided in two, one associated with each daughter. As the loops of DNA uncoil, the two subclusters migrate apart due to the Brownian ratchet effect of the DNA loop.
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16
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Aloui A, Mihoub M, Sethom MM, Chatti A, Feki M, Kaabachi N, Landoulsi A. Effects ofdamand/orseqAMutations on the Fatty Acid and Phospholipid Membrane Composition ofSalmonella entericaSerovar Typhimurium. Foodborne Pathog Dis 2010; 7:573-83. [DOI: 10.1089/fpd.2009.0385] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Amine Aloui
- Biochemistry Unit of Lipids and Interactions of Macromolecules in Biology, Laboratory of Biochemistry and Molecular Biology, Faculty of Sciences of Bizerte, Zarzouna, Tunisia
| | - Mouadh Mihoub
- Biochemistry Unit of Lipids and Interactions of Macromolecules in Biology, Laboratory of Biochemistry and Molecular Biology, Faculty of Sciences of Bizerte, Zarzouna, Tunisia
| | | | - Abdelwaheb Chatti
- Biochemistry Unit of Lipids and Interactions of Macromolecules in Biology, Laboratory of Biochemistry and Molecular Biology, Faculty of Sciences of Bizerte, Zarzouna, Tunisia
| | - Moncef Feki
- Research Laboratory, Biochemistry Department, LaRabta Hospital, Tunis, Tunisia
| | - Naziha Kaabachi
- Research Laboratory, Biochemistry Department, LaRabta Hospital, Tunis, Tunisia
| | - Ahmed Landoulsi
- Biochemistry Unit of Lipids and Interactions of Macromolecules in Biology, Laboratory of Biochemistry and Molecular Biology, Faculty of Sciences of Bizerte, Zarzouna, Tunisia
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Katayama T, Ozaki S, Keyamura K, Fujimitsu K. Regulation of the replication cycle: conserved and diverse regulatory systems for DnaA and oriC. Nat Rev Microbiol 2010; 8:163-70. [PMID: 20157337 DOI: 10.1038/nrmicro2314] [Citation(s) in RCA: 225] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Chromosomal replication must be limited to once and only once per cell cycle. This is accomplished by multiple regulatory pathways that govern initiator proteins and replication origins. A principal feature of DNA replication is the coupling of the replication reaction to negative-feedback regulation. Some of the factors that are important in this process have been discovered, including the clamp (DNA polymerase III subunit-beta (DnaN)), the datA locus, SeqA, DnaA homologue protein (Hda) and YabA, as well as factors that are involved at other stages of the regulatory mechanism, such as DnaA initiator-associating protein (DiaA), the DnaA-reactivating sequence (DARS) loci and Soj. Here, we describe the regulation of DnaA, one of the central proteins involved in bacterial DNA replication, by these factors in Escherichia coli, Bacillus subtilis and Caulobacter crescentus.
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Affiliation(s)
- Tsutomu Katayama
- Department of Molecular Biology, Kyushu University Graduate School of Pharmaceutical Sciences, Fukuoka 812-8582, Japan.
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18
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A reduction in ribonucleotide reductase activity slows down the chromosome replication fork but does not change its localization. PLoS One 2009; 4:e7617. [PMID: 19898675 PMCID: PMC2773459 DOI: 10.1371/journal.pone.0007617] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2009] [Accepted: 10/04/2009] [Indexed: 11/25/2022] Open
Abstract
Background It has been proposed that the enzymes of nucleotide biosynthesis may be compartmentalized or concentrated in a structure affecting the organization of newly replicated DNA. Here we have investigated the effect of changes in ribonucleotide reductase (RNR) activity on chromosome replication and organization of replication forks in Escherichia coli. Methodology/Principal Findings Reduced concentrations of deoxyribonucleotides (dNTPs) obtained by reducing the activity of wild type RNR by treatment with hydroxyurea or by mutation, resulted in a lengthening of the replication period. The replication fork speed was found to be gradually reduced proportionately to moderate reductions in nucleotide availability. Cells with highly extended C periods showed a “delay” in cell division i.e. had a higher cell mass. Visualization of SeqA structures by immunofluorescence indicated no change in organization of the new DNA upon moderate limitation of RNR activity. Severe nucleotide limitation led to replication fork stalling and reversal. Well defined SeqA structures were not found in situations of extensive replication fork repair. In cells with stalled forks obtained by UV irradiation, considerable DNA compaction was observed, possibly indicating a reorganization of the DNA into a “repair structure” during the initial phase of the SOS response. Conclusion/Significance The results indicate that the replication fork is slowed down in a controlled manner during moderate nucleotide depletion and that a change in the activity of RNR does not lead to a change in the organization of newly replicated DNA. Control of cell division but not control of initiation was affected by the changes in replication elongation.
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Felczak MM, Kaguni JM. DnaAcos hyperinitiates by circumventing regulatory pathways that control the frequency of initiation in Escherichia coli. Mol Microbiol 2009; 72:1348-63. [PMID: 19432804 DOI: 10.1111/j.1365-2958.2009.06724.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Mutants of dnaAcos are inviable at 30 degrees C because DnaAcos hyperinitiates, leading to new replication forks that apparently collide from behind with stalled forks, thereby generating lethal double-strand breaks. By comparison, an elevated level of DnaA also induces extra initiations, but lethality occurs only in strains defective in repairing double-strand breaks. To explore the model that the chromosomal level of DnaAcos, or the increased abundance of DnaA, increases initiation frequency by, escaping or overcoming pathways that control initiation, respectively, we developed a genetic selection and identified seqA, datA, dnaN and hda, which function in pathways that either act at oriC or modulate DnaA activity. To assess each pathway's relative effectiveness, we used genetically inactivated strains, and quantified initiation frequency after elevating the level of DnaA. The results indicate that the hda-dependent pathway has a stronger effect on initiation than pathways involving seqA and datA. Testing the model that DnaAcos overinitiates because it fails to respond to one or more regulatory mechanisms, we show that dnaAcos is unresponsive to hda and dnaN, which encodes the beta clamp, and also datA, a locus proposed to titer excess DnaA. These results explain how DnaAcos hyperinitiates to interfere with viability.
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Affiliation(s)
- Magdalena M Felczak
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-1319, USA
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20
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Morigen, Odsbu I, Skarstad K. Growth rate dependent numbers of SeqA structures organize the multiple replication forks in rapidly growing Escherichia coli. Genes Cells 2009; 14:643-57. [PMID: 19371375 DOI: 10.1111/j.1365-2443.2009.01298.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
When the bacterium Escherichia coli is grown in rich medium, the replication and segregation periods may span two, three or four generations and cells may contain up to 24 replication forks. The newly synthesized, hemimethylated DNA at each fork is bound by SeqA protein. The SeqA-DNA structures form distinct foci that can be observed by immunofluorescence microscopy. The numbers of foci were lower than the numbers of replication forks indicating fork co-localization. The extent of co-localization correlated with the extent of replication cycle overlap in wild-type cells. No abrupt increase in the numbers of foci occurred at the time of initiation of replication, suggesting that new replication forks bind to existing SeqA structures. Manipulations with replication control mechanisms that led to extension or reduction of the replication period and number of forks, did not lead to changes in the numbers of SeqA foci per cell. The results indicate that the number of SeqA foci is not directly governed by the number of replication forks, and supports the idea that new DNA may be 'captured' by existing SeqA structures.
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Affiliation(s)
- Morigen
- Department of Cell Biology, Institute for Cancer Research, Norwegian Radium Hospital, Rikshospitalet, University of Oslo, 0310 Oslo, Norway
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21
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Chung YS, Brendler T, Austin S, Guarné A. Structural insights into the cooperative binding of SeqA to a tandem GATC repeat. Nucleic Acids Res 2009; 37:3143-52. [PMID: 19304745 PMCID: PMC2691817 DOI: 10.1093/nar/gkp151] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
SeqA is a negative regulator of DNA replication in Escherichia coli and related bacteria that functions by sequestering the origin of replication and facilitating its resetting after every initiation event. Inactivation of the seqA gene leads to unsynchronized rounds of replication, abnormal localization of nucleoids and increased negative superhelicity. Excess SeqA also disrupts replication synchrony and affects cell division. SeqA exerts its functions by binding clusters of transiently hemimethylated GATC sequences generated during replication. However, the molecular mechanisms that trigger formation and disassembly of such complex are unclear. We present here the crystal structure of a dimeric mutant of SeqA [SeqAΔ(41–59)-A25R] bound to tandem hemimethylated GATC sites. The structure delineates how SeqA forms a high-affinity complex with DNA and it suggests why SeqA only recognizes GATC sites at certain spacings. The SeqA–DNA complex also unveils additional protein–protein interaction surfaces that mediate the formation of higher ordered complexes upon binding to newly replicated DNA. Based on this data, we propose a model describing how SeqA interacts with newly replicated DNA within the origin of replication and at the replication forks.
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Affiliation(s)
- Yu Seon Chung
- Department of Biochemistry and Biomedical Sciences, Health Sciences Center, McMaster University, 1200 Main Street West, Hamilton, ON L8N 3Z5, Canada
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22
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Waldminghaus T, Skarstad K. The Escherichia coli SeqA protein. Plasmid 2009; 61:141-50. [PMID: 19254745 DOI: 10.1016/j.plasmid.2009.02.004] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2008] [Revised: 02/12/2009] [Accepted: 02/19/2009] [Indexed: 10/21/2022]
Abstract
The Escherichia coli SeqA protein contributes to regulation of chromosome replication by preventing re-initiation at newly replicated origins. SeqA protein binds to new DNA which is hemimethylated at the adenine of GATC sequences. Most of the cellular SeqA is found complexed with the new DNA at the replication forks. In vitro the SeqA protein binds as a dimer to two GATC sites and is capable of forming a helical fiber of dimers through interactions of the N-terminal domain. SeqA can also bind, with less affinity, to fully methylated origins and affect timing of "primary" initiations. In addition to its roles in replication, the SeqA protein may also act in chromosome organization and gene regulation.
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Affiliation(s)
- Torsten Waldminghaus
- Department of Cell Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Rikshospitalet, University of Oslo, 0310 Oslo, Norway
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23
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Ferullo DJ, Lovett ST. The stringent response and cell cycle arrest in Escherichia coli. PLoS Genet 2008; 4:e1000300. [PMID: 19079575 PMCID: PMC2586660 DOI: 10.1371/journal.pgen.1000300] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2008] [Accepted: 11/07/2008] [Indexed: 11/18/2022] Open
Abstract
The bacterial stringent response, triggered by nutritional deprivation, causes an accumulation of the signaling nucleotides pppGpp and ppGpp. We characterize the replication arrest that occurs during the stringent response in Escherichia coli. Wild type cells undergo a RelA-dependent arrest after treatment with serine hydroxamate to contain an integer number of chromosomes and a replication origin-to-terminus ratio of 1. The growth rate prior to starvation determines the number of chromosomes upon arrest. Nucleoids of these cells are decondensed; in the absence of the ability to synthesize ppGpp, nucleoids become highly condensed, similar to that seen after treatment with the translational inhibitor chloramphenicol. After induction of the stringent response, while regions corresponding to the origins of replication segregate, the termini remain colocalized in wild-type cells. In contrast, cells arrested by rifampicin and cephalexin do not show colocalized termini, suggesting that the stringent response arrests chromosome segregation at a specific point. Release from starvation causes rapid nucleoid reorganization, chromosome segregation, and resumption of replication. Arrest of replication and inhibition of colony formation by ppGpp accumulation is relieved in seqA and dam mutants, although other aspects of the stringent response appear to be intact. We propose that DNA methylation and SeqA binding to non-origin loci is necessary to enforce a full stringent arrest, affecting both initiation of replication and chromosome segregation. This is the first indication that bacterial chromosome segregation, whose mechanism is not understood, is a step that may be regulated in response to environmental conditions.
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Affiliation(s)
- Daniel J. Ferullo
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Susan T. Lovett
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
- * E-mail:
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24
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Daghfous D, Chatti A, Hammami R, Landoulsi A. Modeling of the full-length Escherichia coli SeqA protein, in complex with DNA. ACTA ACUST UNITED AC 2008; 57:e61-6. [PMID: 18849124 DOI: 10.1016/j.patbio.2008.03.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2008] [Accepted: 03/18/2008] [Indexed: 11/27/2022]
Abstract
The Escherichia coli SeqA protein, a negative regulator of chromosome DNA replication, prevents the overinitiation of replication within one cell cycle by binding to hemimethylated GATC sequences in the replication origin, oriC. In addition to the hemimethylated DNA-binding activity, the SeqA protein has a self-association activity, which is also considered to be essential for its regulatory function in replication initiation. To study the SeqA protein biological activity, we performed a SeqA protein model to examine its architecture. SeqA has a bipartite structure composed of a large and small lobe. The SeqA spatial conformation contributes to its ability to bind to a pair of hemimethylated GATC sequences and to its cooperative behavior.
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Affiliation(s)
- D Daghfous
- Laboratoire de biochimie et de biologie moléculaire, faculté des sciences de Bizerte, 7021 Zarzouna, Tunisia.
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25
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Kato JI. Regulatory Network of the Initiation of Chromosomal Replication inEscherichia coli. Crit Rev Biochem Mol Biol 2008; 40:331-42. [PMID: 16338685 DOI: 10.1080/10409230500366090] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The bacterial chromosome is replicated once during the division cycle, a process ensured by the tight regulation of initiation at oriC. In prokaryotes, the initiator protein DnaA plays an essential role at the initiation step, and feedback control is critical in regulating initiation. Three systems have been identified that exert feedback control in Escherichia coli, all of which are necessary for tight strict regulation of the initiation step. In particular, the ATP-dependent control of DnaA activity is essential. A missing link in initiator activity regulation has been identified, facilitating analysis of the reaction mechanism. Furthermore, key components of this regulatory network have also been described. Because the eukaryotic initiator complex, ORC, is also regulated by ATP, the bacterial system provides an important model for understanding initiation in eukaryotes. This review summarizes recent studies on the regulation of initiator activity.
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Affiliation(s)
- Jun-ichi Kato
- Department of Biology, Graduate School of Science, Tokyo Metropolitan University, Minamiohsawa, Hachioji, Tokyo, Japan
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26
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Abstract
Summary It has been postulated that bacterial DNA replication occurs via a factory mechanism in which unreplicated DNA is spooled into a centrally located replisome and newly synthesized DNA is discharged towards opposite cell poles. Although there is considerable support for this view, it does not fit with many key observations. I review new findings, and provide alternative interpretations for old findings, which challenge this model. As a whole, current data suggest that the replisome, at least in slowly growing Escherichia coli cells, tracks along a stationary chromosome. These replisomes are not stationary, tethered or restricted in their movement, but rather travel throughout the nucleoid. One possibility is that the replisome navigates along a chromosome made up of looped domains as has been previously envisioned.
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Affiliation(s)
- David Bates
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
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27
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Chung YS, Guarné A. Crystallization and preliminary X-ray diffraction analysis of SeqA bound to a pair of hemimethylated GATC sites. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:567-71. [PMID: 18540078 DOI: 10.1107/s1744309108014851] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2008] [Accepted: 05/16/2008] [Indexed: 11/10/2022]
Abstract
Escherichia coli SeqA is a negative regulator of DNA replication. The SeqA protein forms a high-affinity complex with newly replicated DNA at the origin of replication and thus prevents premature re-initiation events. Beyond the origin, SeqA is found at the replication forks, where it organizes newly replicated DNA into higher ordered structures. These two functions depend on SeqA binding to multiple hemimethylated GATC sequences. In an effort to understand how SeqA forms a high-affinity complex with hemimethylated DNA, a dimeric variant of SeqA was overproduced, purified and crystallized bound to a DNA duplex containing two hemimethylated GATC sites. The preliminary X-ray analysis of crystals diffracting to 3 A resolution is presented here.
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Affiliation(s)
- Yu Seon Chung
- Department of Biochemistry and Biomedical Sciences, HSC-4N57A, McMaster University, Hamilton ON L8N 3Z5, Canada
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28
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Babic A, Lindner AB, Vulic M, Stewart EJ, Radman M. Direct visualization of horizontal gene transfer. Science 2008; 319:1533-6. [PMID: 18339941 DOI: 10.1126/science.1153498] [Citation(s) in RCA: 143] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Conjugation allows bacteria to acquire genes for antibiotic resistance, novel virulence attributes, and alternative metabolic pathways. Using a fluorescent protein fusion, SeqA-YFP, we have visualized this process in real time and in single cells of Escherichia coli. We found that the F pilus mediates DNA transfer at considerable cell-to-cell distances. Integration of transferred DNA by recombination occurred in up to 96% of recipients; in the remaining cells, the transferred DNA was fully degraded by the RecBCD helicase/nuclease. The acquired integrated DNA was tracked through successive replication rounds and was found to occasionally split and segregate with different chromosomes, leading to the inheritance of different gene clusters within the cell lineage. The incidence of DNA splitting corresponds to about one crossover per cell generation.
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29
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Adachi S, Fukushima T, Hiraga S. Dynamic events of sister chromosomes in the cell cycle of Escherichia coli. Genes Cells 2008; 13:181-97. [DOI: 10.1111/j.1365-2443.2007.01157.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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30
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Fossum S, Crooke E, Skarstad K. Organization of sister origins and replisomes during multifork DNA replication in Escherichia coli. EMBO J 2007; 26:4514-22. [PMID: 17914458 PMCID: PMC2063475 DOI: 10.1038/sj.emboj.7601871] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2007] [Accepted: 09/10/2007] [Indexed: 11/09/2022] Open
Abstract
The replication period of Escherichia coli cells grown in rich medium lasts longer than one generation. Initiation thus occurs in the 'mother-' or 'grandmother generation'. Sister origins in such cells were found to be colocalized for an entire generation or more, whereas sister origins in slow-growing cells were colocalized for about 0.1-0.2 generations. The role of origin inactivation (sequestration) by the SeqA protein in origin colocalization was studied by comparing sequestration-deficient mutants with wild-type cells. Cells with mutant, non-sequesterable origins showed wild-type colocalization of sister origins. In contrast, cells unable to sequester new origins due to loss of SeqA, showed aberrant localization of origins indicating a lack of organization of new origins. In these cells, aberrant replisome organization was also found. These results suggest that correct organization of sister origins and sister replisomes is dependent on the binding of SeqA protein to newly formed DNA at the replication forks, but independent of origin sequestration. In agreement, in vitro experiments indicate that SeqA is capable of pairing newly replicated DNA molecules.
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Affiliation(s)
- Solveig Fossum
- Department of Cell Biology, Institute of Cancer Research, The Norwegian Radium Hospital, Oslo, Norway
- Department of Biochemistry and Molecular & Cellular Biology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Elliott Crooke
- Department of Biochemistry and Molecular & Cellular Biology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Kirsten Skarstad
- Department of Cell Biology, Institute of Cancer Research, The Norwegian Radium Hospital, Oslo, Norway
- Department of Cell Biology, Institute of Cancer Research, The Norwegian Radium Hospital, Oslo 0310, Norway. Tel.: +47 229 34255; Fax: +47 229 34580; E-mail:
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Norris V, den Blaauwen T, Cabin-Flaman A, Doi RH, Harshey R, Janniere L, Jimenez-Sanchez A, Jin DJ, Levin PA, Mileykovskaya E, Minsky A, Saier M, Skarstad K. Functional taxonomy of bacterial hyperstructures. Microbiol Mol Biol Rev 2007; 71:230-53. [PMID: 17347523 PMCID: PMC1847379 DOI: 10.1128/mmbr.00035-06] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The levels of organization that exist in bacteria extend from macromolecules to populations. Evidence that there is also a level of organization intermediate between the macromolecule and the bacterial cell is accumulating. This is the level of hyperstructures. Here, we review a variety of spatially extended structures, complexes, and assemblies that might be termed hyperstructures. These include ribosomal or "nucleolar" hyperstructures; transertion hyperstructures; putative phosphotransferase system and glycolytic hyperstructures; chemosignaling and flagellar hyperstructures; DNA repair hyperstructures; cytoskeletal hyperstructures based on EF-Tu, FtsZ, and MreB; and cell cycle hyperstructures responsible for DNA replication, sequestration of newly replicated origins, segregation, compaction, and division. We propose principles for classifying these hyperstructures and finally illustrate how thinking in terms of hyperstructures may lead to a different vision of the bacterial cell.
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Affiliation(s)
- Vic Norris
- Department of Science, University of Rouen, 76821 Mont Saint Aignan Cedex, France.
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32
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Abstract
Escherichia coli cells depleted of the conserved GTPase, ObgE, show early chromosome-partitioning defects and accumulate replicated chromosomes in which the terminus regions are colocalized. Cells lacking ObgE continue to initiate replication, with a normal ratio of the origin to terminus. Localization of the SeqA DNA binding protein, normally seen as punctate foci, however, was disturbed. Depletion of ObgE also results in cell filamentation, with polyploid DNA content. Depletion of ObgE did not cause lethality, and cells recovered fully after expression of ObgE was restored. We propose a model in which ObgE is required to license chromosome segregation and subsequent cell cycle events.
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Affiliation(s)
- James J Foti
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454-9110, USA
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33
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Abstract
Escherichia coli is a model system to study the mechanism of DNA replication and its regulation during the cell cycle. One regulatory pathway ensures that initiation of DNA replication from the chromosomal origin, oriC, is synchronous and occurs at the proper time in the bacterial cell cycle. A major player in this pathway is SeqA protein and involves its ability to bind preferentially to oriC when it is hemi-methylated. The second pathway modulates DnaA activity by stimulating the hydrolysis of ATP bound to DnaA protein. The regulatory inactivation of DnaA function involves an interaction with Hda protein and the beta dimer, which functions as a sliding clamp for the replicase, DNA polymerase III holoenzyme. The datA locus represents a third mechanism, which appears to influence the availability of DnaA protein in supporting rifampicin-resistant initiations.
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Affiliation(s)
- Jon M Kaguni
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319, USA.
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34
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den Blaauwen T, Aarsman MEG, Wheeler LJ, Nanninga N. Pre‐replication assembly ofE. colireplisome components. Mol Microbiol 2006; 62:695-708. [PMID: 16999830 DOI: 10.1111/j.1365-2958.2006.05417.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The localization of SeqA, thymidylate synthase, DnaB (helicase) and the DNA polymerase components alpha and tau, has been studied by immunofluorescence microscopy. The origin has been labelled through GFP-LacI bound near oriC. SeqA was located in the cell centre for one replication factory (RF) and at 1/4 and 3/4 positions in pre-divisional cells harbouring two RFs. The transition of central to 1/4 and 3/4 positions of SeqA appeared abrupt. Labelled thymidylate synthetase was found all over the cell, thus not supporting the notion of a dNTP-synthesizing complex exclusively localized near the RF. More DnaB, alpha and tau foci were found than expected. We have hypothesized that extra foci arise at pre-replication assembly sites, where the number of sites equals the number of origins, i.e. the number of future RFs. A reasonable agreement was found between predicted and found foci. In the case of multifork replication the number of foci appeared consistent with the assumption that three RFs are grouped into a higher-order structure. The RF is probably separate from the foci containing SeqA and the hemi-methylated SeqA binding sites because these foci did not coincide significantly with DnaB as marker of the RF. Co-labelling of DnaB and oriC revealed limited colocalization, indicating that DnaB did not yet become associated with oriC at a pre-replication assembly site. DnaB and tau co-labelled in the cell centre, though not at presumed pre-replication assembly sites. By contrast, alpha and tau co-labelled consistently suggesting that they are already associated before replication starts.
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Affiliation(s)
- Tanneke den Blaauwen
- Molecular Cytology, Swammerdam Institute for Life Sciences, University of Amsterdam, Kruislaan 316, 1098 SM Amsterdam, the Netherlands
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35
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Odsbu I, Klungsøyr HK, Fossum S, Skarstad K. Specific N-terminal interactions of the Escherichia coli SeqA protein are required to form multimers that restrain negative supercoils and form foci. Genes Cells 2006; 10:1039-49. [PMID: 16236133 DOI: 10.1111/j.1365-2443.2005.00898.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Escherichia coli SeqA protein binds preferentially to hemimethylated DNA and is required for inactivation (sequestration) of newly formed origins. A mutant SeqA protein, SeqA4 (A25T), which is deficient in origin sequestration in vivo, was found here to have lost the ability to form multimers, but could bind as dimers with wild-type affinity to a pair of hemimethylated GATC sites. In vitro, binding of SeqA dimers to a plasmid first generates a topology change equivalent to a few positive supercoils, then the binding leads to a topology change in the "opposite" direction, resulting in a restraint of negative supercoils. Binding of SeqA4 mutant dimers produced the former effect, but not the latter, showing that a topology change equivalent to positive supercoiling is caused by the binding of single dimers, whereas restraint of negative supercoils requires multimerization via the N-terminus. In vivo, mutant SeqA4 protein was not capable of forming foci observed by immunofluorescence microscopy, showing that N-terminus-dependent multimerization is required for building SeqA foci. Overproduction of SeqA4 led to partially restored initiation synchrony, indicating that origin sequestration may not depend on efficient higher-order multimerization into foci, but do require a high local concentration of SeqA.
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Affiliation(s)
- Ingvild Odsbu
- Department of Cell Biology, Institute for Cancer Research, Montebello, 0310 Oslo, Norway
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36
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Abstract
DNA replication occurs at discrete sites in the cell. To gain insight into the spatial and temporal organization of the Bacillus subtilis replication cycle, we simultaneously visualized replication origins and the replication machinery (replisomes) inside live cells. We found that the origin of replication is positioned near midcell prior to replication. After initiation, the replisome colocalizes with the origin, confirming that replication initiates near midcell. The replisome remains near midcell after duplicated origins separate. Artificially mispositioning the origin region leads to mislocalization of the replisome indicating that the location of the origin at the time of initiation establishes the position of the replisome. Time-lapse microscopy revealed that a single replisome focus reversibly splits into two closely spaced foci every few seconds in many cells, including cells that recently initiated replication. Thus, sister replication forks are likely not intimately associated with each other throughout the replication cycle. Fork dynamics persisted when replication elongation was halted, and is thus independent of the relative movement of DNA through the replisome. Our results provide new insights into how the replisome is positioned in the cell and refine our current understanding of the spatial and temporal events of the B. subtilis replication cycle.
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Affiliation(s)
- Melanie B Berkmen
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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37
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Daghfous D, Chatti A, Marzouk B, Landoulsi A. Phospholipid changes in seqA and dam mutants of Escherichia coli. C R Biol 2006; 329:271-6. [PMID: 16644499 DOI: 10.1016/j.crvi.2006.02.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2005] [Revised: 01/05/2006] [Accepted: 02/14/2006] [Indexed: 11/28/2022]
Abstract
SeqA and Dam proteins were known to be responsible for regulating the initiation of replication and to affect the expression of many genes and metabolisms. We have examined here the fatty acids composition and phospholipids membrane in dam and/or seqA mutants. The dam mutant showed an accumulation of the acidic phospholipids cardiolipin, whereas, the seqA mutant showed a higher proportion of phosphatidylglycerol compared with the wild-type strain. The seqA dam double mutant showed an intermediate proportion of acidic phospholipids compared with the wild-type strain. Based on these observations, we discuss the role of Dam and SeqA proteins in the regulation of phospholipids synthesis.
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Affiliation(s)
- Douraid Daghfous
- Laboratoire de Biochimie et de Biologie Moléculaire, Faculté des Sciences de Bizerte, 7021 Zarzouna, Tunisie.
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38
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Elmore S, Müller M, Vischer N, Odijk T, Woldringh CL. Single-particle tracking of oriC-GFP fluorescent spots during chromosome segregation in Escherichia coli. J Struct Biol 2005; 151:275-87. [PMID: 16084110 DOI: 10.1016/j.jsb.2005.06.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2005] [Revised: 05/19/2005] [Accepted: 06/01/2005] [Indexed: 11/19/2022]
Abstract
DNA regions close to the origin of replication were visualized by the green fluorescent protein (GFP)-Lac repressor/lac operator system. The number of oriC-GFP fluorescent spots per cell and per nucleoid in batch-cultured cells corresponded to the theoretical DNA replication pattern. A similar pattern was observed in cells growing on microscope slides used for time-lapse experiments. The trajectories of 124 oriC-GFP spots were monitored by time-lapse microscopy of 31 cells at time intervals of 1, 2, and 3 min. Spot positions were determined along the short and long axis of cells. The lengthwise movement of spots was corrected for cell elongation. The step sizes of the spots showed a Gaussian distribution with a standard deviation of approximately 110 nm. Plots of the mean square displacement versus time indicated a free diffusion regime for spot movement along the long axis of the cell, with a diffusion coefficient of 4.3+/-2.6x10(-5) microm2/s. Spot movement along the short axis showed confinement in a region of the diameter of the nucleoid ( approximately 800 nm) with an effective diffusion coefficient of 2.9+/-1.7x10(-5) microm2/s. Confidence levels for the mean square displacement analysis were obtained from numerical simulations. We conclude from the analysis that within the experimental accuracy--the limits of which are indicated and discussed--there is no evidence that spot segregation requires any other mechanism than that of cell (length) growth.
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Affiliation(s)
- Steven Elmore
- Section Molecular Cytology, Swammerdam Institute for Life Sciences, BioCentrum Amsterdam, University of Amsterdam, Kruislaan 316, 1098 SM Amsterdam, The Netherlands
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39
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Abstract
What is biological complexity? How many sorts exist? Are there levels of complexity? How are they related to one another? How is complexity related to the emergence of new phenotypes? To try to get to grips with these questions, we consider the archetype of a complex biological system, Escherichia coli. We take the position that E. coli has been selected to survive adverse conditions and to grow in favourable ones and that many other complex systems undergo similar selection. We invoke the concept of hyperstructures which constitute a level of organisation intermediate between macromolecules and cells. We also invoke a new concept, competitive coherence, to describe how phenotypes are created by a competition between maintaining a consistent story over time and creating a response that is coherent with respect to both internal and external conditions. We suggest how these concepts lead to parameters suitable for describing the rich form of complexity termed hypercomplexity and we propose a relationship between competitive coherence and emergence.
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Affiliation(s)
- Vic Norris
- Assemblages Moléculaires, Modélisation et Imagerie SIMS, FRE CNRS 2829, Faculté de Sciences et Techniques de Rouen, 76821, Mont Saint Aignan, France.
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40
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Adachi S, Kohiyama M, Onogi T, Hiraga S. Localization of replication forks in wild-type and mukB mutant cells of Escherichia coli. Mol Genet Genomics 2005; 274:264-71. [PMID: 16133165 DOI: 10.1007/s00438-005-0023-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2005] [Accepted: 05/18/2005] [Indexed: 10/25/2022]
Abstract
To examine the subcellular localization of the replication machinery in Escherichia coli, we have developed an immunofluorescence method that allows us to determine the subcellular location of newly synthesized DNA pulse-labeled with 5-bromo-2'-deoxyuridine (BrdU). Using this technique, we have analyzed growing cells. In wild-type cells that showed a single BrdU fluorescence signal, the focus was located in the middle of the cell; in cells with two signals, the foci were localized at positions equivalent to 1/4 and 3/4 of the cell length. The formation of BrdU foci was dependent upon ongoing chromosomal replication. A mutant lacking MukB, which is required for proper partitioning of sister chromosomes, failed to maintain the ordered localization of BrdU foci: (1) a single BrdU focus tended to be localized at a pole-proximal region of the nucleoid, and (2) a focus was often found to consist of two replicating chromosomes. Thus, the positioning of replication forks is affected by the disruption of the mukB gene.
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Affiliation(s)
- Shun Adachi
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Japan
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41
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Matoba K, Yamazoe M, Mayanagi K, Morikawa K, Hiraga S. Comparison of MukB homodimer versus MukBEF complex molecular architectures by electron microscopy reveals a higher-order multimerization. Biochem Biophys Res Commun 2005; 333:694-702. [PMID: 15979051 DOI: 10.1016/j.bbrc.2005.05.163] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2005] [Accepted: 05/31/2005] [Indexed: 11/24/2022]
Abstract
The complex of MukF, MukE, and MukB proteins participates in organization of sister chromosomes and partitioning into both daughter cells in Escherichia coli. We purified the MukB homodimer and the MukBEF complex and analyzed them by electron microscopy to compare both structures. A MukB homodimer shows a long rod-hinge-rod v-shape with small globular domains at both ends. The MukBEF complex shows a similar structure having larger globular domains than those of the MukB homodimer. These results suggest that MukF and MukE bind to the globular domains of a MukB homodimer. The globular domains of the MukBEF complex frequently associate with each other in an intramolecular fashion, forming a ring. In addition, MukBEF complex molecules tend to form multimers by the end-to-end joining with other MukBEF molecules in an intermolecular fashion, resulting in fibers and rosette-form structures in the absence of ATP and DNA in vitro.
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Affiliation(s)
- Kyoko Matoba
- Department of Structural Biology, Biomolecular Engineering Research Institute, 6-2-3 Furuedai, Suita-city, Osaka 565-0874, Japan
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42
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Yamazoe M, Adachi S, Kanaya S, Ohsumi K, Hiraga S. Sequential binding of SeqA protein to nascent DNA segments at replication forks in synchronized cultures of Escherichia coli. Mol Microbiol 2005; 55:289-98. [PMID: 15612935 DOI: 10.1111/j.1365-2958.2004.04389.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
To demonstrate that sequestration A (SeqA) protein binds preferentially to hemimethylated GATC sequences at replication forks and forms clusters in Escherichia coli growing cells, we analysed, by the chromatin immunoprecipitation (ChIP) assay using anti-SeqA antibody, a synchronized culture of a temperature-sensitive dnaC mutant strain in which only one round of chromosomal DNA replication was synchronously initiated. After synchronized initiation of chromosome replication, the replication origin oriC was first detected by the ChIP assay, and other six chromosomal regions having multiple GATC sequences were sequentially detected according to bidirectional replication of the chromosome. In contrast, DNA regions lacking the GATC sequence were not detected by the ChIP assay. These results indicate that SeqA binds hemimethylated nascent DNA segments according to the proceeding of replication forks in the chromosome, and SeqA releases from the DNA segments when fully methylated. Immunofluorescence microscopy reveals that a single SeqA focus containing paired replication apparatuses appears at the middle of the cell immediately after initiation of chromosome replication and the focus is subsequently separated into two foci that migrate to 1/4 and 3/4 cellular positions, when replication forks proceed bidirectionally an approximately one-fourth distance from the replication origin towards the terminus. This supports the translocating replication apparatuses model.
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Affiliation(s)
- Mitsuyoshi Yamazoe
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Konoe, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
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43
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Abstract
Despite decades of study, the exquisite temporal and spatial organization of bacterial chromosomes has only recently been appreciated. The direct visualization of specific chromosomal loci has revealed that bacteria condense, move and position their chromosomes in a reproducible fashion. The realization that bacterial chromosomes are actively translocated through the cell suggests the existence of specific mechanisms that direct this process. Here, we review bacterial chromosome dynamics and our understanding of the mechanisms that direct and coordinate them.
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Affiliation(s)
- Zemer Gitai
- Department of Developmental Biology, Beckman Center, School of Medicine, Stanford University, Stanford, CA 94305, USA.
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44
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Guarné A, Brendler T, Zhao Q, Ghirlando R, Austin S, Yang W. Crystal structure of a SeqA-N filament: implications for DNA replication and chromosome organization. EMBO J 2005; 24:1502-11. [PMID: 15933720 PMCID: PMC1142570 DOI: 10.1038/sj.emboj.7600634] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2004] [Accepted: 03/01/2005] [Indexed: 11/09/2022] Open
Abstract
Escherichia coli SeqA binds clusters of transiently hemimethylated GATC sequences and sequesters the origin of replication, oriC, from methylation and premature reinitiation. Besides oriC, SeqA binds and organizes newly synthesized DNA at replication forks. Binding to multiple GATC sites is crucial for the formation of stable SeqA-DNA complexes. Here we report the crystal structure of the oligomerization domain of SeqA (SeqA-N). The structural unit of SeqA-N is a dimer, which oligomerizes to form a filament. Mutations that disrupt filament formation lead to asynchronous DNA replication, but the resulting SeqA dimer can still bind two GATC sites separated from 5 to 34 base pairs. Truncation of the linker between the oligomerization and DNA-binding domains restricts SeqA to bind two GATC sites separated by one or two full turns. We propose a model of a SeqA filament interacting with multiple GATC sites that accounts for both origin sequestration and chromosome organization.
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Affiliation(s)
- Alba Guarné
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
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45
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Foti JJ, Schienda J, Sutera VA, Lovett ST. A bacterial G protein-mediated response to replication arrest. Mol Cell 2005; 17:549-60. [PMID: 15721258 DOI: 10.1016/j.molcel.2005.01.012] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2004] [Revised: 11/29/2004] [Accepted: 01/14/2005] [Indexed: 01/24/2023]
Abstract
To define factors in E. coli promoting survival to replication fork stress, we isolated insertion mutants sensitive to replication inhibitors. One insertion caused partial loss of the universally conserved GTPase, obgE/yhbZ gene. Although obgE is essential for growth, our insertion allele supported viability until challenged with various replication inhibitors. A mutation designed to negate the GTPase activity of the protein produced similar phenotypes, but was genetically dominant. Synergistic genetic interactions with recA and recB suggested that chromosome breaks and regressed forks accumulate in obgE mutants. Mutants in obgE also exhibited asynchronous overreplication during normal growth, as revealed by flow cytometry. ObgE overexpression caused SeqA foci, normally localized to replication forks, to spread extensively within the cell. We propose that ObgE defines a pathway analogous to the replication checkpoint response of eukaryotes and acts in a complementary way to the RecA-dependent SOS response to promote bacterial cell survival to replication fork arrest.
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Affiliation(s)
- James J Foti
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454-9110, USA
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46
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Kang S, Han JS, Kim KP, Yang HY, Lee KY, Hong CB, Hwang DS. Dimeric configuration of SeqA protein bound to a pair of hemi-methylated GATC sequences. Nucleic Acids Res 2005; 33:1524-31. [PMID: 15767277 PMCID: PMC1065253 DOI: 10.1093/nar/gki289] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The binding of SeqA protein to hemi-methylated GATC sequences (hemi-sites) regulates chromosome initiation and the segregation of replicated chromosome in Escherichia coli. We have used atomic force microscopy to examine the architecture of SeqA and the mode of binding of one molecule of SeqA to a pair of hemi-sites in aqueous solution. SeqA has a bipartite structure composed of a large and a small lobe. Upon binding of a SeqA molecule to a pair of hemi-sites, the larger lobe becomes visibly separated into two DNA binding domains, each of which binds to one hemi-site. The two DNA binding domains are held together by association between the two multimerization domains that make up the smaller lobe. The binding of each DNA binding domain to a hemi-site leads to bending of the bound DNA inwards toward the bound protein. In this way, SeqA adopts a dimeric configuration when bound to a pair of hemi-sites. Mutational analysis of the multimerization domain indicates that, in addition to multimerization of SeqA polypeptides, this domain contributes to the ability of SeqA to bind to a pair of hemi-sites and to its cooperative behavior.
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Affiliation(s)
- Sukhyun Kang
- Institute of Molecular Biology and Genetics, Seoul National UniversitySeoul 151-742, Republic of Korea
| | - Joo Seok Han
- Institute of Molecular Biology and Genetics, Seoul National UniversitySeoul 151-742, Republic of Korea
| | - Keun Pill Kim
- Institute of Molecular Biology and Genetics, Seoul National UniversitySeoul 151-742, Republic of Korea
| | - Hye Yoon Yang
- Institute of Molecular Biology and Genetics, Seoul National UniversitySeoul 151-742, Republic of Korea
- School of Biological Sciences, Seoul National UniversitySeoul 151-742, Republic of Korea
| | - Kyung Yong Lee
- Institute of Molecular Biology and Genetics, Seoul National UniversitySeoul 151-742, Republic of Korea
| | - Choo Bong Hong
- Institute of Molecular Biology and Genetics, Seoul National UniversitySeoul 151-742, Republic of Korea
- School of Biological Sciences, Seoul National UniversitySeoul 151-742, Republic of Korea
| | - Deog Su Hwang
- Institute of Molecular Biology and Genetics, Seoul National UniversitySeoul 151-742, Republic of Korea
- School of Biological Sciences, Seoul National UniversitySeoul 151-742, Republic of Korea
- To whom correspondence should be addressed. Tel: +82 2 880 7524; Fax: +82 2 874 1206;
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47
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Molina F, Skarstad K. Replication fork and SeqA focus distributions in Escherichia coli suggest a replication hyperstructure dependent on nucleotide metabolism. Mol Microbiol 2005; 52:1597-612. [PMID: 15186411 DOI: 10.1111/j.1365-2958.2004.04097.x] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Replication from the origin of Escherichia coli has traditionally been visualized as two replisomes moving away from each other, each containing a leading and a lagging strand polymerase. Fluorescence microscopy studies of tagged polymerases or forks have, however, indicated that the polymerases may be confined to a single location (or a few locations in cells with overlapping replication cycles). Here, we have analysed the exact replication patterns of cells growing with four different growth and replication rates, and compared these with the distributions of SeqA foci. The SeqA foci represent replication forks because the SeqA protein binds to the newly formed hemimethylated DNA immediately following the forks. The results show that pairs of forks originating from the same origin stay coupled for most of the cell cycle and thus support the replication factory model. They also suggest that the factories consisting of four polymerases are, at the time immediately after initiation, organized into higher order structures consisting of eight or 12 polymerases. The organization into replication factories was lost when replication forks experienced a limitation in the supply of nucleotides or when the thymidylate synthetase gene was mutated. These results support the idea that the nucleotide synthesis apparatus co-localizes with the replisomes forming a 'hyperstructure' and further suggest that the integrity of the replication factories and hyperstructures is dependent on nucleotide metabolism.
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Affiliation(s)
- Felipe Molina
- Department of Cell Biology, Institute for Cancer Research, Montebello, 0310 Oslo, Norway
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48
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Bravo A, Serrano-Heras G, Salas M. Compartmentalization of prokaryotic DNA replication. FEMS Microbiol Rev 2005; 29:25-47. [PMID: 15652974 DOI: 10.1016/j.femsre.2004.06.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2004] [Revised: 06/15/2004] [Accepted: 06/17/2004] [Indexed: 11/22/2022] Open
Abstract
It becomes now apparent that prokaryotic DNA replication takes place at specific intracellular locations. Early studies indicated that chromosomal DNA replication, as well as plasmid and viral DNA replication, occurs in close association with the bacterial membrane. Moreover, over the last several years, it has been shown that some replication proteins and specific DNA sequences are localized to particular subcellular regions in bacteria, supporting the existence of replication compartments. Although the mechanisms underlying compartmentalization of prokaryotic DNA replication are largely unknown, the docking of replication factors to large organizing structures may be important for the assembly of active replication complexes. In this article, we review the current state of this subject in two bacterial species, Escherichia coli and Bacillus subtilis, focusing our attention in both chromosomal and extrachromosomal DNA replication. A comparison with eukaryotic systems is also presented.
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Affiliation(s)
- Alicia Bravo
- Instituto de Biología Molecular Eladio Viñuela (CSIC), Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma, Cantoblanco, 28049 Madrid, Spain.
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49
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Han JS, Kang S, Kim SH, Ko MJ, Hwang DS. Binding of SeqA protein to hemi-methylated GATC sequences enhances their interaction and aggregation properties. J Biol Chem 2004; 279:30236-43. [PMID: 15151991 DOI: 10.1074/jbc.m402612200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The SeqA protein regulates chromosome initiation and is involved in segregation in Escherichia coli. One SeqA protein binds to two hemi-methylated GATC sequences to form a stable SeqA-DNA complex. We found that binding induced DNA bending, which was pronounced when the two sequences were on the same face of the DNA. Two SeqA molecules bound cooperatively to each pair of hemi-methylated sites when the spacing between the sites was < or = 30 bp. This cooperative binding was able to stabilize the binding of a wild type to a single hemi-methylated site, or mutant form of SeqA protein to hemi-methylated sites, although such binding did not occur without cooperative interaction. Two cooperatively bound SeqA molecules interacted with another SeqA bound up to 185 bp away from the two bound SeqA proteins, and this was followed by aggregation of free SeqA proteins onto the bound proteins. These results suggest that the stepwise interaction of SeqA proteins with hemi-methylated GATC sites enhances their interaction and leads to the formation of SeqA aggregates. Cooperative interaction followed by aggregation may be the driving force for formation of the SeqA foci that appear to be located behind replication forks.
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Affiliation(s)
- Joo Seok Han
- School of Biological Sciences and Institute of Molecular Biology and Genetics, Seoul National University, Seoul 151-742, Korea
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50
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Sherratt DJ, Søballe B, Barre FX, Filipe S, Lau I, Massey T, Yates J. Recombination and chromosome segregation. Philos Trans R Soc Lond B Biol Sci 2004; 359:61-9. [PMID: 15065657 PMCID: PMC1693297 DOI: 10.1098/rstb.2003.1365] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The duplication of DNA and faithful segregation of newly replicated chromosomes at cell division is frequently dependent on recombinational processes. The rebuilding of broken or stalled replication forks is universally dependent on homologous recombination proteins. In bacteria with circular chromosomes, crossing over by homologous recombination can generate dimeric chromosomes, which cannot be segregated to daughter cells unless they are converted to monomers before cell division by the conserved Xer site-specific recombination system. Dimer resolution also requires FtsK, a division septum-located protein, which coordinates chromosome segregation with cell division, and uses the energy of ATP hydrolysis to activate the dimer resolution reaction. FtsK can also translocate DNA, facilitate synapsis of sister chromosomes and minimize entanglement and catenation of newly replicated sister chromosomes. The visualization of the replication/recombination-associated proteins, RecQ and RarA, and specific genes within living Escherichia coli cells, reveals further aspects of the processes that link replication with recombination, chromosome segregation and cell division, and provides new insight into how these may be coordinated.
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Affiliation(s)
- David J Sherratt
- Division of Molecular Genetics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
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