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Wasim A, Gupta A, Mondal J. A Hi-C data-integrated model elucidates E. coli chromosome's multiscale organization at various replication stages. Nucleic Acids Res 2021; 49:3077-3091. [PMID: 33660781 PMCID: PMC8034658 DOI: 10.1093/nar/gkab094] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 01/31/2021] [Accepted: 02/17/2021] [Indexed: 11/13/2022] Open
Abstract
The chromosome of Escherichia coli is riddled with multi-faceted complexity. The emergence of chromosome conformation capture techniques are providing newer ways to explore chromosome organization. Here we combine a beads-on-a-spring polymer-based framework with recently reported Hi-C data for E. coli chromosome, in rich growth condition, to develop a comprehensive model of its chromosome at 5 kb resolution. The investigation focuses on a range of diverse chromosome architectures of E. coli at various replication states corresponding to a collection of cells, individually present in different stages of cell cycle. The Hi-C data-integrated model captures the self-organization of E. coli chromosome into multiple macrodomains within a ring-like architecture. The model demonstrates that the position of oriC is dependent on architecture and replication state of chromosomes. The distance profiles extracted from the model reconcile fluorescence microscopy and DNA-recombination assay experiments. Investigations into writhe of the chromosome model reveal that it adopts helix-like conformation with no net chirality, earlier hypothesized in experiments. A genome-wide radius of gyration map captures multiple chromosomal interaction domains and identifies the precise locations of rrn operons in the chromosome. We show that a model devoid of Hi-C encoded information would fail to recapitulate most genomic features unique to E. coli.
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Affiliation(s)
- Abdul Wasim
- Tata Institute of Fundamental Research, Centre for Interdisciplinary Sciences, Hyderabad 500046, India
| | - Ankit Gupta
- Tata Institute of Fundamental Research, Centre for Interdisciplinary Sciences, Hyderabad 500046, India
| | - Jagannath Mondal
- Tata Institute of Fundamental Research, Centre for Interdisciplinary Sciences, Hyderabad 500046, India
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2
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Ramachandran R, Jha J, Chattoraj DK. Chromosome segregation in Vibrio cholerae. J Mol Microbiol Biotechnol 2015; 24:360-70. [PMID: 25732338 DOI: 10.1159/000368853] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The study of chromosome segregation is currently one of the most exciting research frontiers in cell biology. In this review, we discuss our current knowledge of the chromosome segregation process in Vibrio cholerae, based primarily on findings from fluorescence microscopy experiments. This bacterium is of special interest because of its eukaryotic feature of having a divided genome, a feature shared with 10% of known bacteria. We also discuss how the segregation mechanisms of V. cholerae compare with those in other bacteria, and highlight some of the remaining questions regarding the process of bacterial chromosome segregation.
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Affiliation(s)
- Revathy Ramachandran
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Md., USA
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3
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Chen AH, Afonso B, Silver PA, Savage DF. Spatial and temporal organization of chromosome duplication and segregation in the cyanobacterium Synechococcus elongatus PCC 7942. PLoS One 2012; 7:e47837. [PMID: 23112856 PMCID: PMC3480399 DOI: 10.1371/journal.pone.0047837] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2012] [Accepted: 09/21/2012] [Indexed: 01/02/2023] Open
Abstract
The spatial and temporal control of chromosome duplication and segregation is crucial for proper cell division. While this process is well studied in eukaryotic and some prokaryotic organisms, relatively little is known about it in prokaryotic polyploids such as Synechococcus elongatus PCC 7942, which is known to possess one to eight copies of its single chromosome. Using a fluorescent repressor-operator system, S. elongatus chromosomes and chromosome replication forks were tagged and visualized. We found that chromosomal duplication is asynchronous and that the total number of chromosomes is correlated with cell length. Thus, replication is independent of cell cycle and coupled to cell growth. Replication events occur in a spatially random fashion. However, once assembled, replisomes move in a constrained manner. On the other hand, we found that segregation displays a striking spatial organization in some cells. Chromosomes transiently align along the major axis of the cell and timing of alignment was correlated to cell division. This mechanism likely contributes to the non-random segregation of chromosome copies to daughter cells.
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Affiliation(s)
- Anna H. Chen
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Bruno Afonso
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Pamela A. Silver
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
| | - David F. Savage
- Department of Molecular and Cell Biology and Department of Chemistry, University of California, Berkeley, California, United States of America
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4
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Mierzejewska J, Jagura-Burdzy G. Prokaryotic ParA-ParB-parS system links bacterial chromosome segregation with the cell cycle. Plasmid 2011; 67:1-14. [PMID: 21924286 DOI: 10.1016/j.plasmid.2011.08.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Revised: 08/23/2011] [Accepted: 08/24/2011] [Indexed: 12/17/2022]
Abstract
While the essential role of episomal par loci in plasmid DNA partitioning has long been appreciated, the function of chromosomally encoded par loci is less clear. The chromosomal parA-parB genes are conserved throughout the bacterial kingdom and encode proteins homologous to those of the plasmidic Type I active partitioning systems. The third conserved element, the centromere-like sequence called parS, occurs in several copies in the chromosome. Recent studies show that the ParA-ParB-parS system is a key player of a mitosis-like process ensuring proper intracellular localization of certain chromosomal regions such as oriC domain and their active and directed segregation. Moreover, the chromosomal par systems link chromosome segregation with initiation of DNA replication and the cell cycle.
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Affiliation(s)
- Jolanta Mierzejewska
- The Institute of Biochemistry and Biophysics, PAS, 02-106 Warsaw, Pawinskiego 5A, Poland
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5
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Reyes-Lamothe R, Wang X, Sherratt D. Escherichia coli and its chromosome. Trends Microbiol 2008; 16:238-45. [DOI: 10.1016/j.tim.2008.02.003] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2007] [Revised: 02/23/2008] [Accepted: 02/29/2008] [Indexed: 01/22/2023]
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6
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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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7
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Yao S, Helinski DR, Toukdarian A. Localization of the naturally occurring plasmid ColE1 at the cell pole. J Bacteriol 2006; 189:1946-53. [PMID: 17158664 PMCID: PMC1855736 DOI: 10.1128/jb.01451-06] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The naturally occurring plasmid ColE1 was found to localize as a cluster in one or both of the cell poles of Escherichia coli. In addition to the polar localization of ColE1 in most cells, movement of the plasmid to the midcell position was observed in time-lapse studies. ColE1 could be displaced from its polar location by the p15A replicon, pBAD33, but not by plasmid RK2. The displacement of ColE1 by pBAD33 resulted in an almost random positioning of ColE1 foci in the cell and also in a loss of segregational stability, as evidenced by the large number of cells carrying pBAD33 with no visible ColE1 focus and as confirmed by ColE1 stability studies. The addition of the active partitioning systems of the F plasmid (sopABC) or RK2 (O(B1) incC korB) resulted in movement of the ColE1 replicon from the cell pole to within the nucleoid region. This repositioning did not result in destabilization but did result in an increase in the number of plasmid foci, most likely due to partial declustering. These results are consistent with the importance of par regions to the localization of plasmids to specific regions of the cell and demonstrate both localization and dynamic movement for a naturally occurring plasmid that does not encode a replication initiation protein or a partitioning system that is required for plasmid stability.
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Affiliation(s)
- Shiyin Yao
- Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0322, USA
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8
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Hazan R, Ronen H, Ben-Yehuda S, Sigal BY. Resolving chromosome segregation in bacteria. J Mol Microbiol Biotechnol 2006; 11:126-39. [PMID: 16983190 DOI: 10.1159/000094049] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Bacterial chromosomes are evenly distributed between daughter cells, however no equivalent eukaryotic mitotic apparatus has been identified yet. Nevertheless, an advance in our understanding of the dynamics of the bacterial chromosome has been accomplished in recent years by adopting fluorescence microscopy techniques to visualize living bacterial cells. Here, some of the most recent studies that yield new insights into the nature of bacterial chromosome dynamics are described. In addition, we review in detail the current models that attempt to illuminate the mechanism of chromosome segregation in bacteria and discuss the possibility that a bacterial mitotic apparatus does indeed exist.
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Affiliation(s)
- Ronen Hazan
- Department of Molecular Biology, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
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9
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Berkmen MB, Grossman AD. Subcellular positioning of the origin region of the Bacillus subtilis chromosome is independent of sequences within oriC, the site of replication initiation, and the replication initiator DnaA. Mol Microbiol 2006; 63:150-65. [PMID: 17140409 DOI: 10.1111/j.1365-2958.2006.05505.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Regions of bacterial chromosomes occupy characteristic locations within the cell. In Bacillus subtilis, the origin of replication, oriC, is located at 0 degrees /360 degrees on the circular chromosome. After duplication, sister 0 degrees regions rapidly move to and then reside near the cell quarters. It has been hypothesized that origin function or oriC sequences contribute to positioning and movement of the 0 degrees region. We found that the position of a given chromosomal region does not depend on initiation of replication from the 0 degrees region. In an oriC mutant strain that replicates from a heterologous origin (oriN) at 257 degrees , the position of both the 0 degrees and 257 degrees regions was similar to that in wild-type cells. Thus, positioning of chromosomal regions appears to be independent of which region is replicated first. Furthermore, we found that neither oriC sequences nor the replication initiator DnaA is required or sufficient for positioning a region near the cell quarters. A sequence within oriC previously proposed to play a critical role in chromosome positioning and partitioning was found to make little, if any, contribution. We propose that uncharacterized sites outside of oriC are involved in moving and/or maintaining the 0 degrees region near the cell quarters.
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Affiliation(s)
- Melanie B Berkmen
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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10
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Dubarry N, Pasta F, Lane D. ParABS systems of the four replicons of Burkholderia cenocepacia: new chromosome centromeres confer partition specificity. J Bacteriol 2006; 188:1489-96. [PMID: 16452432 PMCID: PMC1367244 DOI: 10.1128/jb.188.4.1489-1496.2006] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Most bacterial chromosomes carry an analogue of the parABS systems that govern plasmid partition, but their role in chromosome partition is ambiguous. parABS systems might be particularly important for orderly segregation of multipartite genomes, where their role may thus be easier to evaluate. We have characterized parABS systems in Burkholderia cenocepacia, whose genome comprises three chromosomes and one low-copy-number plasmid. A single parAB locus and a set of ParB-binding (parS) centromere sites are located near the origin of each replicon. ParA and ParB of the longest chromosome are phylogenetically similar to analogues in other multichromosome and monochromosome bacteria but are distinct from those of smaller chromosomes. The latter form subgroups that correspond to the taxa of their hosts, indicating evolution from plasmids. The parS sites on the smaller chromosomes and the plasmid are similar to the "universal" parS of the main chromosome but with a sequence specific to their replicon. In an Escherichia coli plasmid stabilization test, each parAB exhibits partition activity only with the parS of its own replicon. Hence, parABS function is based on the independent partition of individual chromosomes rather than on a single communal system or network of interacting systems. Stabilization by the smaller chromosome and plasmid systems was enhanced by mutation of parS sites and a promoter internal to their parAB operons, suggesting autoregulatory mechanisms. The small chromosome ParBs were found to silence transcription, a property relevant to autoregulation.
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Affiliation(s)
- Nelly Dubarry
- Laboratoire de Microbiologie et Génétique Moléculaire, Centre National de Recherche Scientifique, 118 route de Narbonne, 31062 Toulouse, France
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11
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Zhao J, Lambowitz AM. A bacterial group II intron-encoded reverse transcriptase localizes to cellular poles. Proc Natl Acad Sci U S A 2005; 102:16133-40. [PMID: 16186487 PMCID: PMC1283441 DOI: 10.1073/pnas.0507057102] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Lactococcus lactis Ll.LtrB group II intron encodes a reverse transcriptase (LtrA protein) that binds the intron RNA to promote RNA splicing and intron mobility. Here, we used LtrA-GFP fusions and immunofluorescence microscopy to show that LtrA localizes to cellular poles in Escherichia coli and Lactococcus lactis. This polar localization occurs with or without coexpression of Ll.LtrB intron RNA, is observed over a wide range of cellular growth rates and expression levels, and is independent of replication origin function. The same localization pattern was found for three nonoverlapping LtrA subsegments, possibly reflecting dependence on common redundant signals and/or protein physical properties. When coexpressed in E. coli, LtrA interferes with the polar localization of the Shigella IcsA protein, which mediates polarized actin tail assembly, suggesting competition for a common localization determinant. The polar localization of LtrA could account for the preferential insertion of the Ll.LtrB intron in the origin and terminus regions of the E. coli chromosome, may facilitate access to exposed DNA in these regions, and could potentially link group II intron mobility to the host DNA replication and/or cell division machinery.
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Affiliation(s)
- Junhua Zhao
- Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry, and Section of Molecular Genetics and Microbiology, University of Texas, Austin, TX 78712, USA
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12
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Abstract
Eukaryotic chromosomes contain a locus, the centromere, at which force is applied to separate replicated chromosomes. A centromere analogue is also found in some bacterial plasmids and chromosomes, although not yet identified in the well-studied Escherichia coli chromosome. We aimed to identify centromere-like sequences in E. coli with the premise that such sequences would be the first to migrate towards the cell poles, away from the cell centre where DNA replication is believed to occur. We have labelled different loci on the chromosome by integrating arrays of binding sites for LacI-EYFP and phage lambdacI-ECFP and supplying these fusion proteins in trans. Comparison of such pairs of loci suggests the presence of a centromere-like site close to the origin of replication. Polar migration of the site was dependent on migS, a locus recently implicated in chromosome migration, thus providing strong support for migS being the E. coli centromere.
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Affiliation(s)
- Richard A Fekete
- Laboratory of Biochemistry, CCR, NCI, NIH, Bldg. 37, Bethesda, MD 20892-4255, USA
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13
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Bates D, Kleckner N. Chromosome and replisome dynamics in E. coli: loss of sister cohesion triggers global chromosome movement and mediates chromosome segregation. Cell 2005; 121:899-911. [PMID: 15960977 PMCID: PMC2973560 DOI: 10.1016/j.cell.2005.04.013] [Citation(s) in RCA: 249] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2004] [Revised: 03/03/2005] [Accepted: 04/01/2005] [Indexed: 11/29/2022]
Abstract
Chromosome and replisome dynamics were examined in synchronized E. coli cells undergoing a eukaryotic-like cell cycle. Sister chromosomes remain tightly colocalized for much of S phase and then separate, in a single coordinate transition. Origin and terminus regions behave differently, as functionally independent domains. During separation, sister loci move far apart and the nucleoid becomes bilobed. Origins and terminus regions also move. We infer that sisters are initially linked and that loss of cohesion triggers global chromosome reorganization. This reorganization creates the 2-fold symmetric, ter-in/ori-out conformation which, for E. coli, comprises sister segregation. Analogies with eukaryotic prometaphase suggest that this could be a primordial segregation mechanism to which microtubule-based processes were later added. We see no long-lived replication "factory"; replication initiation timing does not covary with cell mass, and we identify changes in nucleoid position and state that are tightly linked to cell division. We propose that cell division licenses the next round of replication initiation via these changes.
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Affiliation(s)
- David Bates
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
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14
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Prozorov AA. The Bacterial Cell Cycle: DNA Replication, Nucleoid Segregation, and Cell Division. Microbiology (Reading) 2005. [DOI: 10.1007/s11021-005-0077-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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15
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Leonard TA, Møller-Jensen J, Löwe J. Towards understanding the molecular basis of bacterial DNA segregation. Philos Trans R Soc Lond B Biol Sci 2005; 360:523-35. [PMID: 15897178 PMCID: PMC1569471 DOI: 10.1098/rstb.2004.1608] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Bacteria ensure the fidelity of genetic inheritance by the coordinated control of chromosome segregation and cell division. Here, we review the molecules and mechanisms that govern the correct subcellular positioning and rapid separation of newly replicated chromosomes and plasmids towards the cell poles and, significantly, the emergence of mitotic-like machineries capable of segregating plasmid DNA. We further describe surprising similarities between proteins involved in DNA partitioning (ParA/ParB) and control of cell division (MinD/MinE), suggesting a mechanism for intracellular positioning common to the two processes. Finally, we discuss the role that the bacterial cytoskeleton plays in DNA partitioning and the missing link between prokaryotes and eukaryotes that is bacterial mechano-chemical motor proteins.
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Affiliation(s)
- Thomas A Leonard
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.
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16
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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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17
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Lovett ST, Segall AM. New views of the bacterial chromosome. EMBO Rep 2005; 5:860-4. [PMID: 15319779 PMCID: PMC1299133 DOI: 10.1038/sj.embor.7400232] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2004] [Accepted: 07/21/2004] [Indexed: 11/09/2022] Open
Affiliation(s)
- Susan T Lovett
- Rosenstiel Basic Medical Research Sciences Center MS029, Brandeis University, Waltham, Massachusetts 02454-9110, USA.
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18
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Gitai Z, Dye NA, Reisenauer A, Wachi M, Shapiro L. MreB Actin-Mediated Segregation of a Specific Region of a Bacterial Chromosome. Cell 2005; 120:329-41. [PMID: 15707892 DOI: 10.1016/j.cell.2005.01.007] [Citation(s) in RCA: 282] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2004] [Revised: 12/22/2004] [Accepted: 01/06/2005] [Indexed: 10/25/2022]
Abstract
Faithful chromosome segregation is an essential component of cell division in all organisms. The eukaryotic mitotic machinery uses the cytoskeleton to move specific chromosomal regions. To investigate the potential role of the actin-like MreB protein in bacterial chromosome segregation, we first demonstrate that MreB is the direct target of the small molecule A22. We then demonstrate that A22 completely blocks the movement of newly replicated loci near the origin of replication but has no qualitative or quantitative effect on the segregation of other loci if added after origin segregation. MreB selectively interacts, directly or indirectly, with origin-proximal regions of the chromosome, arguing that the origin-proximal region segregates via an MreB-dependent mechanism not used by the rest of the chromosome.
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Affiliation(s)
- Zemer Gitai
- Department of Developmental Biology, Beckman Center, School of Medicine, Stanford University, California 94305, USA.
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19
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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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20
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Wang JD, Rokop ME, Barker MM, Hanson NR, Grossman AD. Multicopy plasmids affect replisome positioning in Bacillus subtilis. J Bacteriol 2004; 186:7084-90. [PMID: 15489419 PMCID: PMC523195 DOI: 10.1128/jb.186.21.7084-7090.2004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2004] [Accepted: 08/09/2004] [Indexed: 11/20/2022] Open
Abstract
The DNA replication machinery, various regions of the chromosome, and some plasmids occupy characteristic subcellular positions in bacterial cells. We visualized the location of a multicopy plasmid, pHP13, in living cells of Bacillus subtilis using an array of lac operators and LacI-green fluorescent protein (GFP). In the majority of cells, plasmids appeared to be highly mobile and randomly distributed. In a small fraction of cells, there appeared to be clusters of plasmids located predominantly at or near a cell pole. We also monitored the effects of the presence of multicopy plasmids on the position of DNA polymerase using a fusion of a subunit of DNA polymerase to GFP. Many of the plasmid-containing cells had extra foci of the replisome, and these were often found at uncharacteristic locations in the cell. Some of the replisome foci were dynamic and highly mobile, similar to what was observed for the plasmid. In contrast, replisome foci in plasmid-free cells were relatively stationary. Our results indicate that in B. subtilis, plasmid-associated replisomes are recruited to the subcellular position of the plasmid. Extending this notion to the chromosome, we postulated that the subcellular position of the chromosomally associated replisome is established by the subcellular location of oriC at the time of initiation of replication.
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Affiliation(s)
- Jue D Wang
- Department of Biology, Building 68-530, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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21
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Campo N, Dias MJ, Daveran-Mingot ML, Ritzenthaler P, Le Bourgeois P. Chromosomal constraints in Gram-positive bacteria revealed by artificial inversions. Mol Microbiol 2004; 51:511-22. [PMID: 14756790 DOI: 10.1046/j.1365-2958.2003.03847.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We used artificial chromosome inversions to investigate the chromosomal constraints that preserve genome organization in the Gram-positive bacterium Lactococcus lactis. Large inversions, 80-1260 kb in length, disturbing the symmetry of the origin and terminus of the replication axis to various extents, were constructed using the site-specific Cre-loxP recombination system. These inversions were all mechanistically feasible and fell into various classes according to stability and effect on cell fitness. The L. lactis chromosome supports only to some extent unbalance in length of its replication arms. The location of detrimental inversions allowed identification of two constrained chromosomal regions: a large domain covering one fifth of the genome that encompasses the origin of replication (Ori domain), and a smaller domain located at the opposite of the chromosome (Ter domain).
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Affiliation(s)
- N Campo
- Laboratoire de Microbiologie et Génétique Moléculaire du CNRS (UMR5100), Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse, France
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22
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Abstract
It is now clear that bacterial chromosomes rapidly separate in a manner independent of cell elongation, suggesting the existence of a mitotic apparatus in bacteria. Recent studies of bacterial cells reveal filamentous structures similar to the eukaryotic cytoskeleton, proteins that mediate polar chromosome anchoring during Bacillus subtilis sporulation, and SMC interacting proteins that are involved in chromosome condensation. A picture is thereby developing of how bacterial chromosomes are organized within the cell, how they are separated following duplication, and how these processes are coordinated with the cell cycle.
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Affiliation(s)
- Kit Pogliano
- Division of Biological Sciences, 9500 Gilman Drive, University of California-San Diego, La Jolla, CA 92093-0349, USA.
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23
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Abstract
Here, we review recent progress that yields fundamental new insight into the molecular mechanisms behind plasmid and chromosome segregation in prokaryotic cells. In particular, we describe how prokaryotic actin homologs form mitotic machineries that segregate DNA before cell division. Thus, the ParM protein of plasmid R1 forms F actin-like filaments that separate and move plasmid DNA from mid-cell to the cell poles. Evidence from three different laboratories indicate that the morphogenetic MreB protein may be involved in segregation of the bacterial chromosome.
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Affiliation(s)
- Kenn Gerdes
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, DK-5230 Odense M, Denmark.
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Yamaichi Y, Niki H. migS, a cis-acting site that affects bipolar positioning of oriC on the Escherichia coli chromosome. EMBO J 2003; 23:221-33. [PMID: 14685268 PMCID: PMC1271666 DOI: 10.1038/sj.emboj.7600028] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2003] [Accepted: 11/14/2003] [Indexed: 11/09/2022] Open
Abstract
During replication of the Escherichia coli chromosome, the replicated Ori domains migrate towards opposite cell poles, suggesting that a cis-acting site for bipolar migration is located in this region. To identify this cis-acting site, a series of mutants was constructed by splitting subchromosomes from the original chromosome. One mutant, containing a 720 kb subchromosome, was found to be defective in the bipolar positioning of oriC. The creation of deletion mutants allowed the identification of migS, a 25 bp sequence, as the cis-acting site for the bipolar positioning of oriC. When migS was located at the replication terminus, the chromosomal segment showed bipolar positioning. migS was able to rescue bipolar migration of plasmid DNA containing a mutation in the SopABC partitioning system. Interestingly, multiple copies of the migS sequence on a plasmid in trans inhibited the bipolar positioning of oriC. Taken together, these findings indicate that migS plays a crucial role in the bipolar positioning of oriC. In addition, real-time analysis of the dynamic morphological changes of nucleoids in wild-type and migS mutants suggests that bipolar positioning of the replicated oriC contributes to nucleoid organization.
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Affiliation(s)
- Yoshiharu Yamaichi
- Radioisotope Center, National Institute of Genetics, Yata 1111, Mishima 411-8540 Japan
- Graduate School of Medicine, Kumamoto University, Kuhonji 4-24-1, Kumamoto 862-0976, Japan
| | - Hironori Niki
- Radioisotope Center, National Institute of Genetics, Yata 1111, Mishima 411-8540 Japan
- National Institute of Genetics, Radioisotope Center, Yata 1111, Mishima 411-8540, Japan. Tel.: +81 55 981 6870; Fax: +81 55 981 6880/6871; E-mail:
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