1
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Letzkus M, Trela C, Mera PE. Three factors ParA, TipN, and DnaA-mediated chromosome replication initiation are contributors of centromere segregation in Caulobacter crescentus. Mol Biol Cell 2024; 35:ar68. [PMID: 38568781 PMCID: PMC11151105 DOI: 10.1091/mbc.e23-12-0503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/05/2024] [Accepted: 03/25/2024] [Indexed: 04/05/2024] Open
Abstract
The ability of bacteria to maintain chromosomal integrity throughout their life cycle is crucial for survival. In Caulobacter crescentus, the polar factor TipN has been proposed to be involved with the partitioning system ParABS. Cells with tipN knocked out display subtle segregation defects of the centromere-like region parS. We hypothesized that TipN's role with parS segregation is obscured by other forces that are ParABS-independent. To test our hypothesis, we removed one of those forces - chromosome replication - and analyzed the role of TipN with ParA. We first confirm that ParA retains its ability to transport the centromeric region parS from the stalked pole to the opposite pole in the absence of chromosome replication. Our data revealed that in the absence of chromosome replication, TipN becomes essential for ParA's ability to transport parS. Furthermore, we identify a potential connection between the replication initiator DnaA and TipN. Although TipN is not essential for viability, tipN knockout cells lose viability when the regulation of DnaA levels is altered. Our data suggest that the DnaA-dependent susceptibility of tipN knockout cells is connected to parS segregation. Collectively, this work provides insights into the complex regulation involved in the coordination of chromosome replication and segregation in bacteria.
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Affiliation(s)
- Morgan Letzkus
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Corey Trela
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Paola E. Mera
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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2
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Letzkus M, Trela C, Mera PE. TipN's involvement with centromere segregation in Caulobacter crescentus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.20.572679. [PMID: 38187783 PMCID: PMC10769339 DOI: 10.1101/2023.12.20.572679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Bacteria's ability to maintain chromosomal integrity throughout their life cycle is crucial for their survival. In Caulobacter crescentus, the polar factor TipN has been proposed to be involved with the partitioning system ParABS. However, cells with tipN knocked out display subtle parS segregation defects. We hypothesized that TipN's role with parS segregation is obscured by other forces that are ParABS-independent. To test our hypothesis, we removed one of those forces - chromosome replication - and analyzed the role of TipN with ParA. We first demonstrate that ParA retains its ability to transport the centromeric region parS from the stalked pole to the opposite pole in the absence of chromosome replication. Our data revealed that in the absence of chromosome replication, TipN becomes essential for ParA's ability to transport parS. Furthermore, we identify a potential connection between the replication initiator DnaA and TipN. Although TipN is not essential for viability, tipN knockout cells lose viability when the regulation of DnaA levels is altered. Our data suggest that the DnaA-dependent susceptibility of tipN knockout cells is connected to parS segregation. Collectively, this work provides insights into the complex regulation involved in the coordination of chromosome replication and segregation in bacteria.
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Affiliation(s)
- Morgan Letzkus
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Corey Trela
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Paola E. Mera
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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3
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The structure of the bacterial DNA segregation ATPase filament reveals the conformational plasticity of ParA upon DNA binding. Nat Commun 2021; 12:5166. [PMID: 34453062 PMCID: PMC8397727 DOI: 10.1038/s41467-021-25429-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 08/11/2021] [Indexed: 02/02/2023] Open
Abstract
The efficient segregation of replicated genetic material is an essential step for cell division. Bacterial cells use several evolutionarily-distinct genome segregation systems, the most common of which is the type I Par system. It consists of an adapter protein, ParB, that binds to the DNA cargo via interaction with the parS DNA sequence; and an ATPase, ParA, that binds nonspecific DNA and mediates cargo transport. However, the molecular details of how this system functions are not well understood. Here, we report the cryo-EM structure of the Vibrio cholerae ParA2 filament bound to DNA, as well as the crystal structures of this protein in various nucleotide states. These structures show that ParA forms a left-handed filament on DNA, stabilized by nucleotide binding, and that ParA undergoes profound structural rearrangements upon DNA binding and filament assembly. Collectively, our data suggest the structural basis for ParA’s cooperative binding to DNA and the formation of high ParA density regions on the nucleoid. ParA is an ATPase involved in the segregation of newly replicated DNA in bacteria. Here, structures of a ParA filament bound to DNA and of ParA in various nucleotide states offer insight into its conformational changes upon DNA binding and filament assembly, including the basis for ParA’s cooperative binding to DNA.
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4
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Decombe S, Loll F, Caccianini L, Affannoukoué K, Izeddin I, Mozziconacci J, Escudé C, Lopes J. Epigenetic rewriting at centromeric DNA repeats leads to increased chromatin accessibility and chromosomal instability. Epigenetics Chromatin 2021; 14:35. [PMID: 34321103 PMCID: PMC8317386 DOI: 10.1186/s13072-021-00410-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 07/18/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Centromeric regions of human chromosomes contain large numbers of tandemly repeated α-satellite sequences. These sequences are covered with constitutive heterochromatin which is enriched in trimethylation of histone H3 on lysine 9 (H3K9me3). Although well studied using artificial chromosomes and global perturbations, the contribution of this epigenetic mark to chromatin structure and genome stability remains poorly known in a more natural context. RESULTS Using transcriptional activator-like effectors (TALEs) fused to a histone lysine demethylase (KDM4B), we were able to reduce the level of H3K9me3 on the α-satellites repeats of human chromosome 7. We show that the removal of H3K9me3 affects chromatin structure by increasing the accessibility of DNA repeats to the TALE protein. Tethering TALE-demethylase to centromeric repeats impairs the recruitment of HP1α and proteins of Chromosomal Passenger Complex (CPC) on this specific centromere without affecting CENP-A loading. Finally, the epigenetic re-writing by the TALE-KDM4B affects specifically the stability of chromosome 7 upon mitosis, highlighting the importance of H3K9me3 in centromere integrity and chromosome stability, mediated by the recruitment of HP1α and the CPC. CONCLUSION Our cellular model allows to demonstrate the direct role of pericentromeric H3K9me3 epigenetic mark on centromere integrity and function in a natural context and opens interesting possibilities for further studies regarding the role of the H3K9me3 mark.
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Affiliation(s)
- Sheldon Decombe
- Laboratoire Structure et Instabilité des Génomes, INSERM U1154, CNRS UM7196, Muséum National d'Histoire Naturelle, 43 rue Cuvier, 75005, Paris, France.,DCCBR, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - François Loll
- Laboratoire Structure et Instabilité des Génomes, INSERM U1154, CNRS UM7196, Muséum National d'Histoire Naturelle, 43 rue Cuvier, 75005, Paris, France.,INSERM, UMR 1229, Regenerative Medicine and Skeleton, Université de Nantes, ONIRIS, 44042, Nantes, France
| | - Laura Caccianini
- Laboratoire Physico-Chimie, Institut Curie, CNRS UMR168, Paris-Science Lettres, Sorbonne Université, 75005, Paris, France
| | - Kévin Affannoukoué
- Institut Langevin, ESPCI Paris, PSL Université, CNRS, 75005, Paris, France.,Institut Fresnel, Aix Marseille Université CNRS Centrale Marseille, Marseille, France
| | - Ignacio Izeddin
- Institut Langevin, ESPCI Paris, PSL Université, CNRS, 75005, Paris, France
| | - Julien Mozziconacci
- Laboratoire Structure et Instabilité des Génomes, INSERM U1154, CNRS UM7196, Muséum National d'Histoire Naturelle, 43 rue Cuvier, 75005, Paris, France
| | - Christophe Escudé
- Laboratoire Structure et Instabilité des Génomes, INSERM U1154, CNRS UM7196, Muséum National d'Histoire Naturelle, 43 rue Cuvier, 75005, Paris, France
| | - Judith Lopes
- Laboratoire Structure et Instabilité des Génomes, INSERM U1154, CNRS UM7196, Muséum National d'Histoire Naturelle, 43 rue Cuvier, 75005, Paris, France.
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5
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Benler S, Yutin N, Antipov D, Rayko M, Shmakov S, Gussow AB, Pevzner P, Koonin EV. Thousands of previously unknown phages discovered in whole-community human gut metagenomes. MICROBIOME 2021; 9:78. [PMID: 33781338 PMCID: PMC8008677 DOI: 10.1186/s40168-021-01017-w] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 02/02/2021] [Indexed: 05/07/2023]
Abstract
BACKGROUND Double-stranded DNA bacteriophages (dsDNA phages) play pivotal roles in structuring human gut microbiomes; yet, the gut virome is far from being fully characterized, and additional groups of phages, including highly abundant ones, continue to be discovered by metagenome mining. A multilevel framework for taxonomic classification of viruses was recently adopted, facilitating the classification of phages into evolutionary informative taxonomic units based on hallmark genes. Together with advanced approaches for sequence assembly and powerful methods of sequence analysis, this revised framework offers the opportunity to discover and classify unknown phage taxa in the human gut. RESULTS A search of human gut metagenomes for circular contigs encoding phage hallmark genes resulted in the identification of 3738 apparently complete phage genomes that represent 451 putative genera. Several of these phage genera are only distantly related to previously identified phages and are likely to found new families. Two of the candidate families, "Flandersviridae" and "Quimbyviridae", include some of the most common and abundant members of the human gut virome that infect Bacteroides, Parabacteroides, and Prevotella. The third proposed family, "Gratiaviridae," consists of less abundant phages that are distantly related to the families Autographiviridae, Drexlerviridae, and Chaseviridae. Analysis of CRISPR spacers indicates that phages of all three putative families infect bacteria of the phylum Bacteroidetes. Comparative genomic analysis of the three candidate phage families revealed features without precedent in phage genomes. Some "Quimbyviridae" phages possess Diversity-Generating Retroelements (DGRs) that generate hypervariable target genes nested within defense-related genes, whereas the previously known targets of phage-encoded DGRs are structural genes. Several "Flandersviridae" phages encode enzymes of the isoprenoid pathway, a lipid biosynthesis pathway that so far has not been known to be manipulated by phages. The "Gratiaviridae" phages encode a HipA-family protein kinase and glycosyltransferase, suggesting these phages modify the host cell wall, preventing superinfection by other phages. Hundreds of phages in these three and other families are shown to encode catalases and iron-sequestering enzymes that can be predicted to enhance cellular tolerance to reactive oxygen species. CONCLUSIONS Analysis of phage genomes identified in whole-community human gut metagenomes resulted in the delineation of at least three new candidate families of Caudovirales and revealed diverse putative mechanisms underlying phage-host interactions in the human gut. Addition of these phylogenetically classified, diverse, and distinct phages to public databases will facilitate taxonomic decomposition and functional characterization of human gut viromes. Video abstract.
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Affiliation(s)
- Sean Benler
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland 20894 USA
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland 20894 USA
| | - Dmitry Antipov
- Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, 199004 Russia
| | - Mikhail Rayko
- Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, 199004 Russia
| | - Sergey Shmakov
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland 20894 USA
| | - Ayal B. Gussow
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland 20894 USA
| | - Pavel Pevzner
- Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, 199004 Russia
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093 USA
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland 20894 USA
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6
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Chien HL, Huang WZ, Tsai MY, Cheng CH, Liu CT. Overexpression of the Chromosome Partitioning Gene parA in Azorhizobium caulinodans ORS571 Alters the Bacteroid Morphotype in Sesbania rostrata Stem Nodules. Front Microbiol 2019; 10:2422. [PMID: 31749773 PMCID: PMC6842974 DOI: 10.3389/fmicb.2019.02422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 10/07/2019] [Indexed: 11/13/2022] Open
Abstract
Azorhizobium caulinodans ORS571 is a diazotroph that forms N2-fixing nodules on the roots and stems of the tropical legume Sesbania rostrata. Deletion of the parA gene of this bacterium results in cell cycle defects, pleiomorphic cell shape, and formation of immature stem nodules on its host plant. In this study, we constructed a parA overexpression mutant (PnptII-parA) to complement a previous study and provide new insights into bacteroid formation. We found that overproduction of ParA did not affect growth, cell morphology, chromosome partitioning, or vegetative nitrogen fixation in the free-living state. Under symbiosis, however, distinctive features, such as a single swollen bacteroid in one symbiosome, relatively narrow symbiosome space, and polyploid cells were observed. The morphotype of the PnptII-parA bacteroid is reminiscent of terminal differentiation in some IRLC indeterminate nodules, but S. rostrata is not thought to produce the NCR peptides that induce terminal differentiation in rhizobia. In addition, the transcript patterns of many symbiosis-related genes elicited by PnptII-parA were different from those elicited by the wild type. Accordingly, we propose that the particular symbiosome formation in PnptII-parA stem-nodules is due to cell cycle disruption caused by excess ParA protein in the symbiotic cells during nodulation.
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Affiliation(s)
- Hsiao-Lin Chien
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Wan-Zhen Huang
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Ming-Yen Tsai
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Chiung-Hsiang Cheng
- Institute of Molecular and Comparative Pathobiology, School of Veterinary Medicine, National Taiwan University, Taipei, Taiwan
| | - Chi-Te Liu
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
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7
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Hürtgen D, Murray SM, Mascarenhas J, Sourjik V. DNA Segregation in Natural and Synthetic Minimal Systems. ACTA ACUST UNITED AC 2019; 3:e1800316. [DOI: 10.1002/adbi.201800316] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/18/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Daniel Hürtgen
- MPI for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (Synmikro) Marburg 35043 Germany
| | - Seán M. Murray
- MPI for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (Synmikro) Marburg 35043 Germany
| | - Judita Mascarenhas
- MPI for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (Synmikro) Marburg 35043 Germany
| | - Victor Sourjik
- MPI for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (Synmikro) Marburg 35043 Germany
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8
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Scutigliani EM, Scholl ER, Grootemaat AE, Khanal S, Kochan JA, Krawczyk PM, Reits EA, Garzan A, Ngo HX, Green KD, Garneau-Tsodikova S, Ruijter JM, van Veen HA, van der Wel NN. Interfering With DNA Decondensation as a Strategy Against Mycobacteria. Front Microbiol 2018; 9:2034. [PMID: 30233521 PMCID: PMC6135046 DOI: 10.3389/fmicb.2018.02034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 08/13/2018] [Indexed: 12/31/2022] Open
Abstract
Tuberculosis is once again a major global threat, leading to more than 1 million deaths each year. Treatment options for tuberculosis patients are limited, expensive and characterized by severe side effects, especially in the case of multidrug-resistant forms. Uncovering novel vulnerabilities of the pathogen is crucial to generate new therapeutic strategies. Using high resolution microscopy techniques, we discovered one such vulnerability of Mycobacterium tuberculosis. We demonstrate that the DNA of M. tuberculosis can condense under stressful conditions such as starvation and antibiotic treatment. The DNA condensation is reversible and specific for viable bacteria. Based on these observations, we hypothesized that blocking the recovery from the condensed state could weaken the bacteria. We showed that after inducing DNA condensation, and subsequent blocking of acetylation of DNA binding proteins, the DNA localization in the bacteria is altered. Importantly under these conditions, Mycobacterium smegmatis did not replicate and its survival was significantly reduced. Our work demonstrates that agents that block recovery from the condensed state of the nucleoid can be exploited as antibiotic. The combination of fusidic acid and inhibition of acetylation of DNA binding proteins, via the Eis enzyme, potentiate the efficacy of fusidic acid by 10 and the Eis inhibitor to 1,000-fold. Hence, we propose that successive treatment with antibiotics and drugs interfering with recovery from DNA condensation constitutes a novel approach for treatment of tuberculosis and related bacterial infections.
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Affiliation(s)
- Enzo M Scutigliani
- Electron Microscopy Center Amsterdam, Academic Medical Center, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Medical Biology, Academic Medical Center, Amsterdam, Netherlands
| | - Edwin R Scholl
- Electron Microscopy Center Amsterdam, Academic Medical Center, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Medical Biology, Academic Medical Center, Amsterdam, Netherlands
| | - Anita E Grootemaat
- Electron Microscopy Center Amsterdam, Academic Medical Center, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Medical Biology, Academic Medical Center, Amsterdam, Netherlands
| | - Sadhana Khanal
- Electron Microscopy Center Amsterdam, Academic Medical Center, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Medical Biology, Academic Medical Center, Amsterdam, Netherlands
| | - Jakub A Kochan
- Medical Biology, Academic Medical Center, Amsterdam, Netherlands
| | | | - Eric A Reits
- Medical Biology, Academic Medical Center, Amsterdam, Netherlands
| | - Atefeh Garzan
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, United States
| | - Huy X Ngo
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, United States
| | - Keith D Green
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, United States
| | | | - Jan M Ruijter
- Medical Biology, Academic Medical Center, Amsterdam, Netherlands
| | - Henk A van Veen
- Electron Microscopy Center Amsterdam, Academic Medical Center, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Medical Biology, Academic Medical Center, Amsterdam, Netherlands
| | - Nicole N van der Wel
- Electron Microscopy Center Amsterdam, Academic Medical Center, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Medical Biology, Academic Medical Center, Amsterdam, Netherlands
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9
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Misra HS, Maurya GK, Chaudhary R, Misra CS. Interdependence of bacterial cell division and genome segregation and its potential in drug development. Microbiol Res 2018; 208:12-24. [DOI: 10.1016/j.micres.2017.12.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 12/05/2017] [Accepted: 12/31/2017] [Indexed: 11/28/2022]
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10
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Wang Y. Spatial distribution of high copy number plasmids in bacteria. Plasmid 2017; 91:2-8. [PMID: 28263761 DOI: 10.1016/j.plasmid.2017.02.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 02/27/2017] [Accepted: 02/27/2017] [Indexed: 11/26/2022]
Abstract
Plasmids play essential roles in bacterial metabolism, evolution, and pathogenesis. The maintenance of plasmids is of great importance both scientifically and practically. In this mini-review, I look at the problem from a slightly different point of view and focus on the spatial distribution of high copy number plasmids, for which no active segregation mechanism has been identified. I review several distribution models and summarize the direct and indirect evidence in the literature, including the most recent progress on measuring the spatial distribution of high copy number plasmids using emerging super-resolution fluorescence microscopy. It is concluded that many open questions remain in the field and that in-depth studies on the spatial distribution of plasmids could shed light on the understanding of the maintenance of plasmids in bacteria.
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Affiliation(s)
- Yong Wang
- Department of Physics, University of Arkansas, Fayetteville, AR 72701, United States; Microelectronics and Photonics Program, University of Arkansas, Fayetteville, AR 72701, United States; Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, United States.
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11
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The antimicrobial polymer PHMB enters cells and selectively condenses bacterial chromosomes. Sci Rep 2016; 6:23121. [PMID: 26996206 PMCID: PMC4800398 DOI: 10.1038/srep23121] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 02/29/2016] [Indexed: 11/08/2022] Open
Abstract
To combat infection and antimicrobial resistance, it is helpful to elucidate drug mechanism(s) of action. Here we examined how the widely used antimicrobial polyhexamethylene biguanide (PHMB) kills bacteria selectively over host cells. Contrary to the accepted model of microbial membrane disruption by PHMB, we observed cell entry into a range of bacterial species, and treated bacteria displayed cell division arrest and chromosome condensation, suggesting DNA binding as an alternative antimicrobial mechanism. A DNA-level mechanism was confirmed by observations that PHMB formed nanoparticles when mixed with isolated bacterial chromosomal DNA and its effects on growth were suppressed by pairwise combination with the DNA binding ligand Hoechst 33258. PHMB also entered mammalian cells, but was trapped within endosomes and excluded from nuclei. Therefore, PHMB displays differential access to bacterial and mammalian cellular DNA and selectively binds and condenses bacterial chromosomes. Because acquired resistance to PHMB has not been reported, selective chromosome condensation provides an unanticipated paradigm for antimicrobial action that may not succumb to resistance.
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12
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Versatile plasmid-based expression systems for Gram-negative bacteria—General essentials exemplified with the bacterium Ralstonia eutropha H16. N Biotechnol 2015; 32:552-8. [DOI: 10.1016/j.nbt.2015.03.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 03/12/2015] [Accepted: 03/20/2015] [Indexed: 12/13/2022]
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13
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Schumacher MA, Tonthat NK, Lee J, Rodriguez-Castañeda FA, Chinnam NB, Kalliomaa-Sanford AK, Ng IW, Barge MT, Shaw PLR, Barillà D. Structures of archaeal DNA segregation machinery reveal bacterial and eukaryotic linkages. Science 2015; 349:1120-4. [PMID: 26339031 PMCID: PMC4844061 DOI: 10.1126/science.aaa9046] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Although recent studies have provided a wealth of information about archaeal biology, nothing is known about the molecular basis of DNA segregation in these organisms. Here, we unveil the machinery and assembly mechanism of the archaeal Sulfolobus pNOB8 partition system. This system uses three proteins: ParA; an atypical ParB adaptor; and a centromere-binding component, AspA. AspA utilizes a spreading mechanism to create a DNA superhelix onto which ParB assembles. This supercomplex links to the ParA motor, which contains a bacteria-like Walker motif. The C domain of ParB harbors structural similarity to CenpA, which dictates eukaryotic segregation. Thus, this archaeal system combines bacteria-like and eukarya-like components, which suggests the possible conservation of DNA segregation principles across the three domains of life.
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Affiliation(s)
- Maria A Schumacher
- Department of Biochemistry, Duke University School of Medicine, 243 Nanaline H. Duke, Box 3711, Durham, NC 27710, USA.
| | - Nam K Tonthat
- Department of Biochemistry, Duke University School of Medicine, 243 Nanaline H. Duke, Box 3711, Durham, NC 27710, USA
| | - Jeehyun Lee
- Department of Biochemistry, Duke University School of Medicine, 243 Nanaline H. Duke, Box 3711, Durham, NC 27710, USA
| | | | - Naga Babu Chinnam
- Department of Biochemistry, Duke University School of Medicine, 243 Nanaline H. Duke, Box 3711, Durham, NC 27710, USA
| | | | - Irene W Ng
- Department of Biology, University of York, York YO10 5DD, UK
| | - Madhuri T Barge
- Department of Biology, University of York, York YO10 5DD, UK
| | - Porsha L R Shaw
- Department of Biochemistry, Duke University School of Medicine, 243 Nanaline H. Duke, Box 3711, Durham, NC 27710, USA
| | - Daniela Barillà
- Department of Biology, University of York, York YO10 5DD, UK.
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14
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Abstract
Evolutionary selection for optimal genome preservation, replication, and expression should yield similar chromosome organizations in any type of cells. And yet, the chromosome organization is surprisingly different between eukaryotes and prokaryotes. The nuclear versus cytoplasmic accommodation of genetic material accounts for the distinct eukaryotic and prokaryotic modes of genome evolution, but it falls short of explaining the differences in the chromosome organization. I propose that the two distinct ways to organize chromosomes are driven by the differences between the global-consecutive chromosome cycle of eukaryotes and the local-concurrent chromosome cycle of prokaryotes. Specifically, progressive chromosome segregation in prokaryotes demands a single duplicon per chromosome, while other "precarious" features of the prokaryotic chromosomes can be viewed as compensations for this severe restriction.
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15
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Abstract
In both eukaryotes and prokaryotes, chromosomal DNA undergoes replication, condensation-decondensation and segregation, sequentially, in some fixed order. Other conditions, like sister-chromatid cohesion (SCC), may span several chromosomal events. One set of these chromosomal transactions within a single cell cycle constitutes the 'chromosome cycle'. For many years it was generally assumed that the prokaryotic chromosome cycle follows major phases of the eukaryotic one: -replication-condensation-segregation-(cell division)-decondensation-, with SCC of unspecified length. Eventually it became evident that, in contrast to the strictly consecutive chromosome cycle of eukaryotes, all stages of the prokaryotic chromosome cycle run concurrently. Thus, prokaryotes practice 'progressive' chromosome segregation separated from replication by a brief SCC, and all three transactions move along the chromosome at the same fast rate. In other words, in addition to replication forks, there are 'segregation forks' in prokaryotic chromosomes. Moreover, the bulk of prokaryotic DNA outside the replication-segregation transition stays compacted. I consider possible origins of this concurrent replication-segregation and outline the 'nucleoid administration' system that organizes the dynamic part of the prokaryotic chromosome cycle.
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Affiliation(s)
- Andrei Kuzminov
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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16
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Okibe N, Suzuki N, Inui M, Yukawa H. pCGR2 copy number depends on the par
locus that forms a ParC-ParB-DNA partition complex in Corynebacterium glutamicum. J Appl Microbiol 2013; 115:495-508. [DOI: 10.1111/jam.12257] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 04/12/2013] [Accepted: 04/29/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Naoko Okibe
- Research Institute of Innovative Technology for the Earth; Kizugawa Kyoto Japan
| | - Nobuaki Suzuki
- Research Institute of Innovative Technology for the Earth; Kizugawa Kyoto Japan
| | - Masayuki Inui
- Research Institute of Innovative Technology for the Earth; Kizugawa Kyoto Japan
| | - Hideaki Yukawa
- Research Institute of Innovative Technology for the Earth; Kizugawa Kyoto Japan
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17
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Liu CT, Lee KB, Wang YS, Peng MH, Lee KT, Suzuki S, Suzuki T, Oyaizu H. Involvement of the azorhizobial chromosome partition gene (parA) in the onset of bacteroid differentiation during Sesbania rostrata stem nodule development. Appl Environ Microbiol 2011; 77:4371-82. [PMID: 21571889 PMCID: PMC3127717 DOI: 10.1128/aem.02327-10] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Accepted: 05/03/2011] [Indexed: 12/17/2022] Open
Abstract
A parA gene in-frame deletion mutant of Azorhizobium caulinodans ORS571 (ORS571-ΔparA) was constructed to evaluate the roles of the chromosome-partitioning gene on various bacterial traits and on the development of stem-positioned nodules. The ΔparA mutant showed a pleiomorphic cell shape phenotype and was polyploid, with differences in nucleoid sizes due to dramatic defects in chromosome partitioning. Upon inoculation of the ΔparA mutant onto the stem of Sesbania rostrata, three types of immature nodule-like structures with impaired nitrogen-fixing activity were generated. Most showed signs of bacteroid early senescence. Moreover, the ΔparA cells within the nodule-like structures exhibited multiple developmental-stage phenotypes. Since the bacA gene has been considered an indicator for bacteroid formation, we applied the expression pattern of bacA as a nodule maturity index in this study. Our data indicate that the bacA gene expression is parA dependent in symbiosis. The presence of the parA gene transcript was inversely correlated with the maturity of nodule; the transcript was switched off in fully mature bacteroids. In summary, our experimental evidence demonstrates that the parA gene not only plays crucial roles in cellular development when the microbe is free-living but also negatively regulates bacteroid formation in S. rostrata stem nodules.
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Affiliation(s)
- Chi-Te Liu
- Institute of Biotechnology, National Taiwan University, R412, No. 81, Chang-Xing St., Taipei 106, Taiwan.
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18
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Prevalence and significance of plasmid maintenance functions in the virulence plasmids of pathogenic bacteria. Infect Immun 2011; 79:2502-9. [PMID: 21555398 DOI: 10.1128/iai.00127-11] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Virulence functions of pathogenic bacteria are often encoded on large extrachromosomal plasmids. These plasmids are maintained at low copy number to reduce the metabolic burden on their host. Low-copy-number plasmids risk loss during cell division. This is countered by plasmid-encoded systems that ensure that each cell receives at least one plasmid copy. Plasmid replication and recombination can produce plasmid multimers that hinder plasmid segregation. These are removed by multimer resolution systems. Equitable distribution of the resulting monomers to daughter cells is ensured by plasmid partition systems that actively segregate plasmid copies to daughter cells in a process akin to mitosis in higher organisms. Any plasmid-free cells that still arise due to occasional failures of replication, multimer resolution, or partition are eliminated by plasmid-encoded postsegregational killing systems. Here we argue that all of these three systems are essential for the stable maintenance of large low-copy-number plasmids. Thus, they should be found on all large virulence plasmids. Where available, well-annotated sequences of virulence plasmids confirm this. Indeed, virulence plasmids often appear to contain more than one example conforming to each of the three system classes. Since these systems are essential for virulence, they can be regarded as ubiquitous virulence factors. As such, they should be informative in the search for new antibacterial agents and drug targets.
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19
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Babu M, Beloglazova N, Flick R, Graham C, Skarina T, Nocek B, Gagarinova A, Pogoutse O, Brown G, Binkowski A, Phanse S, Joachimiak A, Koonin EV, Savchenko A, Emili A, Greenblatt J, Edwards AM, Yakunin AF. A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair. Mol Microbiol 2011; 79:484-502. [PMID: 21219465 PMCID: PMC3071548 DOI: 10.1111/j.1365-2958.2010.07465.x] [Citation(s) in RCA: 214] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) and the associated proteins (Cas) comprise a system of adaptive immunity against viruses and plasmids in prokaryotes. Cas1 is a CRISPR-associated protein that is common to all CRISPR-containing prokaryotes but its function remains obscure. Here we show that the purified Cas1 protein of Escherichia coli (YgbT) exhibits nuclease activity against single-stranded and branched DNAs including Holliday junctions, replication forks and 5'-flaps. The crystal structure of YgbT and site-directed mutagenesis have revealed the potential active site. Genome-wide screens show that YgbT physically and genetically interacts with key components of DNA repair systems, including recB, recC and ruvB. Consistent with these findings, the ygbT deletion strain showed increased sensitivity to DNA damage and impaired chromosomal segregation. Similar phenotypes were observed in strains with deletion of CRISPR clusters, suggesting that the function of YgbT in repair involves interaction with the CRISPRs. These results show that YgbT belongs to a novel, structurally distinct family of nucleases acting on branched DNAs and suggest that, in addition to antiviral immunity, at least some components of the CRISPR-Cas system have a function in DNA repair.
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Affiliation(s)
- Mohan Babu
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada
| | - Natalia Beloglazova
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada
| | - Robert Flick
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada
| | - Chris Graham
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada
| | - Tatiana Skarina
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada
| | - Boguslaw Nocek
- Midwest Center for Structural Genomics and Structural Biology Center, Department of Biosciences, Argonne National Laboratory, Argonne, IL 60439
| | - Alla Gagarinova
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada
| | - Oxana Pogoutse
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada
| | - Greg Brown
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada
| | - Andrew Binkowski
- Midwest Center for Structural Genomics and Structural Biology Center, Department of Biosciences, Argonne National Laboratory, Argonne, IL 60439
| | - Sadhna Phanse
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics and Structural Biology Center, Department of Biosciences, Argonne National Laboratory, Argonne, IL 60439
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| | - Alexei Savchenko
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada
| | - Andrew Emili
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Jack Greenblatt
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Aled M. Edwards
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada
- Midwest Center for Structural Genomics and Structural Biology Center, Department of Biosciences, Argonne National Laboratory, Argonne, IL 60439
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Alexander F. Yakunin
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5G 1L6, Canada
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20
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Abstract
Non-essential extra-chromosomal DNA elements such as plasmids are responsible for their own propagation in dividing host cells, and one means to ensure this is to carry a miniature active segregation system reminiscent of the mitotic spindle. Plasmids that are maintained at low numbers in prokaryotic cells have developed a range of such active partitioning systems, which are characterized by an impressive simplicity and efficiency and which are united by the use of dynamic, nucleotide-driven filaments to separate and position DNA molecules. A comparison of different plasmid segregation systems reveals (i) how unrelated filament-forming and DNA-binding proteins have been adopted and modified to create a range of simple DNA segregating complexes and (ii) how subtle changes in the few components of these DNA segregation machines has led to a remarkable diversity in the molecular mechanisms of closely related segregation systems. Here, our current understanding of plasmid segregation systems is reviewed and compared with other DNA segregation systems, and this is extended by a discussion of basic principles of plasmid segregation systems, evolutionary implications and the relationship between an autonomous DNA element and its host cell.
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Affiliation(s)
- Jeanne Salje
- MRC Laboratory of Molecular Biology, Cambridge, UK.
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21
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Philip DS, Sarovich DS, Pemberton JM. Complete sequence and analysis of the stability functions of pPSX, a vector that allows stable cloning and expression of Streptomycete genes in Escherichia coli K12. Plasmid 2009; 62:39-43. [PMID: 19303899 DOI: 10.1016/j.plasmid.2009.03.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2008] [Revised: 03/05/2009] [Accepted: 03/11/2009] [Indexed: 10/21/2022]
Abstract
The broad host range, cloning and expression vector pPSX has been completely sequenced and analysed. pPSX is 14.7kb in length and contains the fusion of two continuous segments of the parental 34kb, IncW plasmid pR388. pPSX appears to have retained at least three sets of gene/s which contribute in different ways to plasmid stability. The first of these parB, is a known participant in the partitioning of low-copy number plasmids. While the adjoining gene, orf35, has high homology with kfrA, a putative plasmid nucleoid organiser that is often associated with the ParAB family of proteins. The second set of genes; orfs18, 19, 20, whose exact functions are not clear, have homology to the stability operons of both IncW and IncN plasmids. The third is the resolvase, resP, which may resolve plasmid multimers that can lead to plasmid instability. pPSX is a small, stable cloning vector good for cloning and expression of a wide range of genes, including those from streptomycetes.
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Affiliation(s)
- Daniel S Philip
- Department of Microbiology and Parasitology, University of Queensland, Brisbane 4072, Australia
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22
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The tubulin-like RepX protein encoded by the pXO1 plasmid forms polymers in vivo in Bacillus anthracis. J Bacteriol 2009; 191:2493-500. [PMID: 19233922 DOI: 10.1128/jb.00027-09] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacillus anthracis contains two megaplasmids, pXO1 and pXO2, that are critical for its pathogenesis. Stable inheritance of pXO1 in B. anthracis is dependent upon the tubulin/FtsZ-like RepX protein encoded by this plasmid. Previously, we have shown that RepX undergoes GTP-dependent polymerization in vitro. However, the polymerization properties and localization pattern of RepX in vivo are not known. Here, we utilize a RepX-green fluorescent protein (GFP) fusion to show that RepX forms foci and three distinct forms of polymeric structures in B. anthracis in vivo, namely straight, curved, and helical filaments. Polymerization of RepX-GFP as well as the nature of polymers formed were dependent upon concentration of the protein inside the B. anthracis cells. RepX predominantly localized as polymers that were parallel to the length of the cell. RepX also formed polymers in Escherichia coli in the absence of other pXO1-encoded products, showing that in vivo polymerization is an inherent property of the protein and does not require either the pXO1 plasmid or proteins unique to B. anthracis. Overexpression of RepX did not affect the cell morphology of B. anthracis cells, whereas it drastically distorted the cell morphology of E. coli host cells. We discuss the significance of our observations in view of the plasmid-specific functions that have been proposed for RepX and related proteins encoded by several megaplasmids found in members of the Bacillus cereus group of bacteria.
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23
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Bouet JY, Lane D. Molecular basis of the supercoil deficit induced by the mini-F plasmid partition complex. J Biol Chem 2008; 284:165-173. [PMID: 19001378 DOI: 10.1074/jbc.m802752200] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Formation of a partition complex on plasmid F by binding of SopB protein to the sopC centromere is the first step in the partition process that ensures stability of F in dividing cells. Establishment of the complex enables nonspecific binding of SopB to neighboring DNA, which extends the partition complex and provokes reduction of negative supercoiling of the plasmid. This reduction is believed to reflect winding of DNA into positive supercoils about SopB to create a nucleoprotein structure of probable importance to partition. We have searched for evidence that SopB alters plasmid topology. Permutation analysis indicated only modest bending of linear DNA fragments, and in vivo DNase I footprinting revealed no enhanced cleavages indicating curvature. In vitro, SopB binding left no topological trace in relaxed-circular DNA treated with topoisomerase I or in nicked circles closed by ligase. In vivo, novobiocin-mediated inhibition of DNA gyrase relaxed a plasmid carrying the partition complex but left no residue of positive supercoils. Hence, SopB does not reduce plasmid supercoiling directly. We did observe that SopB partly prevented removal of negative supercoils from plasmid DNA by topoisomerase I and partly prevented ligation of nicked circles, indicating that it acts as a physical obstacle. The supercoil deficit is thus better explained as SopB recoating of just-replicated DNA, which shelters it from gyrase and from topological changes in SopB-free DNA. This topological simplicity distinguishes the Sop partition complex from other complexes described.
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Affiliation(s)
- Jean-Yves Bouet
- Laboratoire de Microbiologie et Gánátique Moláculaires, CNRS, F-31000 Toulouse, France and LMGM, Universitáde Toulouse, UPS, F-31000 Toulouse, France; Laboratoire de Microbiologie et Gánátique Moláculaires, CNRS, F-31000 Toulouse, France and LMGM, Universitáde Toulouse, UPS, F-31000 Toulouse, France.
| | - David Lane
- Laboratoire de Microbiologie et Gánátique Moláculaires, CNRS, F-31000 Toulouse, France and LMGM, Universitáde Toulouse, UPS, F-31000 Toulouse, France
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24
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Bacterial growth and cell division: a mycobacterial perspective. Microbiol Mol Biol Rev 2008; 72:126-56, table of contents. [PMID: 18322037 DOI: 10.1128/mmbr.00028-07] [Citation(s) in RCA: 271] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genus Mycobacterium is best known for its two major pathogenic species, M. tuberculosis and M. leprae, the causative agents of two of the world's oldest diseases, tuberculosis and leprosy, respectively. M. tuberculosis kills approximately two million people each year and is thought to latently infect one-third of the world's population. One of the most remarkable features of the nonsporulating M. tuberculosis is its ability to remain dormant within an individual for decades before reactivating into active tuberculosis. Thus, control of cell division is a critical part of the disease. The mycobacterial cell wall has unique characteristics and is impermeable to a number of compounds, a feature in part responsible for inherent resistance to numerous drugs. The complexity of the cell wall represents a challenge to the organism, requiring specialized mechanisms to allow cell division to occur. Besides these mycobacterial specializations, all bacteria face some common challenges when they divide. First, they must maintain their normal architecture during and after cell division. In the case of mycobacteria, that means synthesizing the many layers of complex cell wall and maintaining their rod shape. Second, they need to coordinate synthesis and breakdown of cell wall components to maintain integrity throughout division. Finally, they need to regulate cell division in response to environmental stimuli. Here we discuss these challenges and the mechanisms that mycobacteria employ to meet them. Because these organisms are difficult to study, in many cases we extrapolate from information known for gram-negative bacteria or more closely related GC-rich gram-positive organisms.
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25
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Pavlendová N, Muchová K, Barák I. Chromosome segregation in Bacillus subtilis. Folia Microbiol (Praha) 2008; 52:563-72. [PMID: 18450217 DOI: 10.1007/bf02932184] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacillus subtilis, a Gram-positive bacterium commonly found in soil, is an excellent model organism for the study of basic cell processes, such as cell division and cell differentiation, called sporulation. In B. subtilis the essential genetic information is carried on a single circular chromosome, the correct segregation of which is crucial for both vegetative growth and sporulation. The proper completion of life cycle requires each daughter cell to obtain identical genetic information. The consequences of inaccurate chromosome segregation can lead to formation of anucleate cells, cells with two chromosomes, or cells with incomplete chromosomes. Although bacteria miss the classical eukaryotic mitotic apparatus, the chromosome segregation is undeniably an active process tightly connected to other cell processes as DNA replication and compaction. To fully understand the chromosome segregation, it is necessary to study this process in a wider context and to examine the role of different proteins at various cell life cycle stages. The life cycle of B. subtilis is characteristic by its specific cell differentiation process where, two slightly different segregation mechanisms exist, specialized in vegetative growth and in sporulation.
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Affiliation(s)
- N Pavlendová
- Institute of Molecular Biology, Slovak Academy of Sciences, 845 51 Bratislava, Slovakia.
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26
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Abstract
Plasmid pSW100 is 1 of the 13 plasmids from Pantoea stewartii subsp. stewartii SW2 which has a replicon that resembles that of ColE1. This work uses a pSW100 derivative, pSW140K, to study how the pSW100 replicon is stably maintained in its hosts. Our results indicate that although pSW140K is stable in Escherichia coli HB101, the plasmid is rapidly lost in another E. coli strain, DH5alpha, indicating that the genetic background of an E. coli strain affects the stability of pSW140K. Mutagenesis of E. coli HB101 with EZ::TN <DHFR-1> revealed that mutations in traC, traF, traG, traN, and traV, which encode the components of the sex pilus assembly, reduce plasmid stability. Furthermore, this work identified that a 38-bp region located immediately upstream of the RNAII promoter is critical to the maintenance of plasmid stability in E. coli HB101. TraC binds to the region, and in addition, deleting the region destabilizes the plasmid. Furthermore, inserting this 38-bp fragment into a plasmid that contains the minimal replicon from pSW200 stabilizes the plasmid in E. coli HB101. Fluorescence in situ hybridization and immunofluorescence staining also revealed that derivatives of pSW100, pSW128A, and TraC are colocalized in cells, suggesting that pSW100 may use the sex pilus assembly as a partition apparatus to ensure the even distribution of the plasmid during cell division, which may thus maintain the plasmid's stability.
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27
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Derman AI, Lim-Fong G, Pogliano J. Intracellular mobility of plasmid DNA is limited by the ParA family of partitioning systems. Mol Microbiol 2008; 67:935-46. [PMID: 18208495 DOI: 10.1111/j.1365-2958.2007.06066.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The highly conserved ParA family of partitioning systems is responsible for positioning DNA and protein complexes in bacteria. In Escherichia coli, plasmids that rely upon these systems are positioned at mid-cell and are repositioned at the quarter-cell positions after replication. How they remain fixed at these positions throughout the cell cycle is unknown. We use fluorescence recovery after photobleaching and time-lapse microscopy to measure plasmid mobility in living E. coli cells. We find that a minimalized version of plasmid RK2 that lacks its Par system is highly mobile, that the intact RK2 plasmid is relatively immobile, and that the addition of a Par system to the minimalized RK2 plasmid limits its mobility to that of the intact RK2. Mobility is thus the default state, and Par systems are required not only to position plasmids, but also to hold them at these positions. The intervention of Par systems is required continuously throughout the cell cycle to restrict plasmid movement that would, if unrestricted, subvert the segregation process. Our results reveal an important function for Par systems in plasmid DNA segregation that is likely to be conserved in bacteria.
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Affiliation(s)
- Alan I Derman
- Division of Biological Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0377, USA
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28
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Anand SP, Akhtar P, Tinsley E, Watkins SC, Khan SA. GTP-dependent polymerization of the tubulin-like RepX replication protein encoded by the pXO1 plasmid of Bacillus anthracis. Mol Microbiol 2008; 67:881-90. [PMID: 18179418 DOI: 10.1111/j.1365-2958.2007.06100.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
RepX protein encoded by the pXO1 plasmid of Bacillus anthracis is required for plasmid replication. RepX harbours the tubulin signature motif and contains limited amino acid sequence homology to the bacterial cell division protein FtsZ. Although replication proteins are not known to polymerize, here we show by electron microscopy that RepX undergoes GTP-dependent polymerization into long filaments. RepX filaments assembled in the presence of GTPgammaS were more stable than those assembled in the presence of GTP, suggesting a role for GTP hydrolysis in the depolymerization of the filaments. Light scattering studies showed that RepX underwent rapid polymerization, and substitution of GTP with GTPgammaS stabilized the filaments. RepX exhibited GTPase activity and a mutation in the tubulin signature motif severely impaired its GTPase activity and its polymerization in vitro. Unlike FtsZ homologues, RepX harbours a highly basic carboxyl-terminal region and exhibits GTP-dependent, non-specific DNA binding activity. We speculate that RepX may be involved in both the replication and segregation of the pXO1 plasmid.
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Affiliation(s)
- Syam P Anand
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
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29
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Hoischen C, Bussiek M, Langowski J, Diekmann S. Escherichia coli low-copy-number plasmid R1 centromere parC forms a U-shaped complex with its binding protein ParR. Nucleic Acids Res 2007; 36:607-15. [PMID: 18056157 PMCID: PMC2241845 DOI: 10.1093/nar/gkm672] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Escherichia coli low-copy-number plasmid R1 contains a segregation machinery composed of parC, ParR and parM. The R1 centromere-like site parC contains two separate sets of repeats. By atomic force microscopy (AFM) we show here that ParR molecules bind to each of the 5-fold repeated iterons separately with the intervening sequence unbound by ParR. The two ParR protein complexes on parC do not complex with each other. ParR binds with a stoichiometry of about one ParR dimer per each single iteron. The measured DNA fragment lengths agreed with B-form DNA and each of the two parC 5-fold interon DNA stretches adopts a linear path in its complex with ParR. However, the overall parC/ParR complex with both iteron repeats bound by ParR forms an overall U-shaped structure: the DNA folds back on itself nearly completely, including an angle of ∼150°. Analysing linear DNA fragments, we never observed dimerized ParR complexes on one parC DNA molecule (intramolecular) nor a dimerization between ParR complexes bound to two different parC DNA molecules (intermolecular). This bacterial segrosome is compared to other bacterial segregation complexes. We speculate that partition complexes might have a similar overall structural organization and, at least in part, common functional properties.
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Affiliation(s)
- C Hoischen
- Molecular Biology, FLI, Leibniz-Institute for Age Research, Beutenbergstrasse 11, D-07745 Jena, Germany
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30
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Hatano T, Yamaichi Y, Niki H. Oscillating focus of SopA associated with filamentous structure guides partitioning of F plasmid. Mol Microbiol 2007; 64:1198-213. [PMID: 17542915 PMCID: PMC1974783 DOI: 10.1111/j.1365-2958.2007.05728.x] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The F plasmid is actively partitioned to daughter cells by the sopABC gene. To elucidate the partitioning mechanisms, we simultaneously analysed movements of the plasmid and the SopA ATPase in single living cells. SopA, which is a putative motor protein assembled densely near nucleoid borders and formed a single discrete focus associated with less dense filamentous distribution along the long axis of the cell. The dense SopA focus oscillates between cell poles. The direction of the plasmid motion switches as the SopA focus switches its position. The velocity of the plasmid motion stays constant while it oscillates moving towards the SopA focus. The low density filamentous distribution of SopA persisted throughout the SopA oscillation. The focus associated with filamentous distribution of SopA was also observed in a cell without nucleoid. The SopA filament may guide the movement of the plasmid as a railway track and lead it to cell quarters.
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Affiliation(s)
- Toshiyuki Hatano
- Microbial Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics1111 Yata, Mishima, Shizuoka 411-8540, Japan.
| | - Yoshiharu Yamaichi
- Microbial Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics1111 Yata, Mishima, Shizuoka 411-8540, Japan.
| | - Hironori Niki
- Microbial Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics1111 Yata, Mishima, Shizuoka 411-8540, Japan.
- Department of Genetics, SOKENDAI1111 Yata, Mishima Shizuoka 411-8540, Japan.
- *For correspondence. E-mail ; Tel. (+81) 55 981 6870; Fax (+81) 55 981 6826
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31
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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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32
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Van La M, Barbry P, Raoult D, Renesto P. Molecular basis of Tropheryma whipplei doxycycline susceptibility examined by transcriptional profiling. J Antimicrob Chemother 2007; 59:370-7. [PMID: 17289769 DOI: 10.1093/jac/dkl507] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVES AND METHODS Tropheryma whipplei is a poorly studied bacterium responsible for Whipple's disease. In this study, its susceptibility to doxycycline was investigated at a transcriptional level using a whole-genome DNA microarray. RESULTS Exposure of T. whipplei to the MIC of doxycycline (0.5 mg/L) induced antibiotic-specific primary expression profiles, while indirect effects were detected at 10 x MIC. In contrast to what was observed for several microorganisms exposed to antibiotics, the heat-shock proteins were not affected. Consistent with the mode of action of this translation inhibitor, genes encoding for ribosomal proteins and translation factors were differentially transcribed. This analysis also evidenced the regulation of genes that should account for cell growth arrest. Long-term survival of non-replicating bacteria is likely to be ensured by an increased level of ppGpp, the nucleotide effector of the stringent response. The gene expression profile observed with 10 x MIC was mainly characterized by the up-regulation of ABC transporters that possibly form efflux and detoxification systems, through which T. whipplei may limit the effects of this bacteriostatic compound. Obtained microarray data showed good agreement with real-time quantitative PCR (R2 = 0.969). CONCLUSIONS This work represents the first comprehensive genomic approach providing insights into the expression signature triggered by the exposure of T. whipplei to antibiotics.
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Affiliation(s)
- My Van La
- Unité des Rickettsies, CNRS-UMR6020, IFR48, Faculté de Médecine, 27 Bd Jean Moulin, Marseille, F13385, France
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Garcia-Russell N, Orchard SS, Segall AM. Probing nucleoid structure in bacteria using phage lambda integrase-mediated chromosome rearrangements. Methods Enzymol 2007; 421:209-26. [PMID: 17352925 DOI: 10.1016/s0076-6879(06)21017-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Conservative site-specific recombination has been adapted for a multitude of uses, in both prokaryotes and eukaryotes, including genetic engineering, expression technologies, and as probes of chromosome structure and organization. In this article, we give a specific example of the latter application, and a quick summary of some of the myriad other genetic and biotechnology applications of site-specific recombination.
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Abstract
Bacteria, like eukaryotic organisms, must compact the DNA molecule comprising their genome and form a functional chromosome. Yet, bacteria do it differently. A number of factors contribute to genome compaction and organization in bacteria, including entropic effects, supercoiling and DNA-protein interactions. A gamut of new experimental techniques have allowed new advances in the investigation of these factors, and spurred much interest in the dynamic response of the chromosome to environmental cues, segregation, and architecture, during both exponential and stationary phases. We review these recent developments with emphasis on the multifaceted roles that DNA-protein interactions play.
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Affiliation(s)
- Joel Stavans
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
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35
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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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36
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Bourhy P, Salaün L, Lajus A, Médigue C, Boursaux-Eude C, Picardeau M. A genomic island of the pathogen Leptospira interrogans serovar Lai can excise from its chromosome. Infect Immun 2006; 75:677-83. [PMID: 17118975 PMCID: PMC1828511 DOI: 10.1128/iai.01067-06] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An examination of the two Leptospira interrogans genomes sequenced so far reveals few genetic differences, including an extra DNA region, 54 kb in length, in L. interrogans serovar Lai. This locus contains 103 predicted coding sequences that are absent from the genome of L. interrogans serovar Copenhageni, of which only 20% had significant BLASTP hits in GenBank. By analyzing the L. interrogans serovar Lai genome by pulsed-field gel electrophoresis, we also found that this 54-kb DNA fragment exists as a circular plasmid. This was confirmed by amplification of a DNA fragment corresponding to that of the predicted fragment if this region excised from the chromosome and its left and right ends joined together. In addition, cloning of the putative rep gene of this DNA region was responsible for autonomous replication in Leptospira spp., therefore generating a new Escherichia coli-Leptospira sp. shuttle vector. Taken together, our results show that this genomic island can excise from the chromosome and form a replicative plasmid. Analysis of the distribution of this genomic island revealed that highly related sequences exist in other L. interrogans virulent strains. This genomic island, containing a high proportion of novel genes, may have an important role in spreading genes, including virulence factors, among bacterial populations.
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Affiliation(s)
- Pascale Bourhy
- Laboratoire des Spirochètes, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
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37
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Bell PJL. Sex and the eukaryotic cell cycle is consistent with a viral ancestry for the eukaryotic nucleus. J Theor Biol 2006; 243:54-63. [PMID: 16846615 DOI: 10.1016/j.jtbi.2006.05.015] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2005] [Revised: 04/11/2006] [Accepted: 05/20/2006] [Indexed: 12/31/2022]
Abstract
The origin of the eukaryotic cell cycle, including mitosis, meiosis, and sex are as yet unresolved aspects of the evolution of the eukaryotes. The wide phylogenetic distribution of both mitosis and meiosis suggest that these processes are integrally related to the origin of the earliest eukaryotic cells. According to the viral eukaryogenesis (VE) hypothesis, the eukaryotes are a composite of three phylogenetically unrelated organisms: a viral lysogen that evolved into the nucleus, an archaeal cell that evolved into the eukaryotic cytoplasm, and an alpha-proteobacterium that evolved into the mitochondria. In the extended VE hypothesis presented here, the eukaryotic cell cycle arises as a consequence of the derivation of the nucleus from a lysogenic DNA virus.
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Dmowski M, Sitkiewicz I, Ceglowski P. Characterization of a novel partition system encoded by the delta and omega genes from the streptococcal plasmid pSM19035. J Bacteriol 2006; 188:4362-72. [PMID: 16740943 PMCID: PMC1482978 DOI: 10.1128/jb.01922-05] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
High segregational stability of the streptococcal plasmid pSM19035 is achieved by the concerted action of systems involved in plasmid copy number control, multimer resolution, and postsegregational killing. In this study, we demonstrate the role of two genes, delta and omega, in plasmid stabilization by a partition mechanism. We show that these two genes can stabilize the native pSM19035 replicon as well as other theta- and sigma-type plasmids in Bacillus subtilis. In contrast to other known partition systems, in this case the two genes are transcribed separately; however, they are coregulated by the product of the parB-like gene omega. Analysis of mutants of the parA-like gene delta showed that the Walker A ATPase motif is necessary for plasmid stabilization. The ParB-like product of the omega gene binds to three regions containing repeated WATCACW heptamers, localized in the copS (regulation of plasmid copy number), delta, and omega promoter regions. We demonstrate that all three of these regions can cause partition-mediated incompatibility. Moreover, our data suggest that each of these could play the role of a centromere-like sequence. We conclude that delta and omega constitute a novel type of plasmid stabilization system.
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Affiliation(s)
- Michal Dmowski
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawiskiego 5A, 02-106 Warsaw, Poland.
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Abstract
The fundamental problems in duplicating and transmitting genetic information posed by the geometric and topological features of DNA, combined with its large size, are qualitatively similar for prokaryotic and eukaryotic chromosomes. The evolutionary solutions to these problems reveal common themes. However, depending on differences in their organization, ploidy, and copy number, chromosomes and plasmids display distinct segregation strategies as well. In bacteria, chromosome duplication, likely mediated by a stationary replication factory, is accompanied by rapid, directed migration of the daughter duplexes with assistance from DNA-compacting and perhaps translocating proteins. The segregation of unit-copy or low-copy bacterial plasmids is also regulated spatially and temporally by their respective partitioning systems. Eukaryotic chromosomes utilize variations of a basic pairing and unpairing mechanism for faithful segregation during mitosis and meiosis. Rather surprisingly, the yeast plasmid 2-micron circle also resorts to a similar scheme for equal partitioning during mitosis.
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Affiliation(s)
- Santanu Kumar Ghosh
- Section of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, Texas 78712-0612, USA.
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40
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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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41
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Nordström K. Plasmid R1--replication and its control. Plasmid 2005; 55:1-26. [PMID: 16199086 DOI: 10.1016/j.plasmid.2005.07.002] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2005] [Revised: 07/04/2005] [Accepted: 07/12/2005] [Indexed: 11/25/2022]
Abstract
Plasmid R1 is a low-copy-number plasmid belonging to the IncFII group. The genetics, biochemistry, molecular biology, and physiology of R1 replication and its control are summarised and discussed in the present communication. Replication of R1 starts at a unique origin, oriR1, and proceeds unidirectionally according to the Theta mode. Plasmid R1 replicates during the entire cell cycle and the R1 copies in the cell are members of a pool from which a plasmid copy at random is selected for replication. However, there is an eclipse period during which a newly replicated copy does not belong to this pool. Replication of R1 is controlled by an antisense RNA, CopA, that is unstable and formed constitutively; hence, its concentration is a measure of the concentration of the plasmid. CopA-RNA interacts with its complementary target, CopT-RNA, that is located upstream of the RepA message on the repA-mRNA. CopA-RNA post-transcriptionally inhibits translation of the repA-mRNA. CopA- and CopT-RNA interact in a bimolecular reaction which results in an inverse proportionality between the relative rate of replication (replications per plasmid copy and cell cycle) and the copy number; the number of replications per cell and cell cycle, n, is independent of the actual copy number in the individual cells, the so-called +n mode of control. Single base-pair substitutions in the copA/copT region of the plasmid genome may result in mutants that are compatible with the wild type. Loss of CopA activity results in (uncontrolled) so-called runaway replication, which is lethal to the host but useful for the production of proteins from cloned genes. Plasmid R1 also has an ancillary control system, CopB, that derepresses the synthesis of repA-mRNA in cells that happen to contain lower than normal number of copies. Plasmid R1, as other plasmids, form clusters in the cell and plasmid replication is assumed to take place in the centre of the cells; this requires traffic from the cluster to the replication factories and back to the clusters. The clusters are plasmid-specific and presumably based on sequence homology.
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Affiliation(s)
- Kurt Nordström
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, P.O. Box 596, S-751 24 Uppsala, Sweden.
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42
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Meijer WJJ, Castilla-Llorente V, Villar L, Murray H, Errington J, Salas M. Molecular basis for the exploitation of spore formation as survival mechanism by virulent phage phi29. EMBO J 2005; 24:3647-57. [PMID: 16193065 PMCID: PMC1276709 DOI: 10.1038/sj.emboj.7600826] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2005] [Accepted: 09/01/2005] [Indexed: 11/09/2022] Open
Abstract
Phage phi29 is a virulent phage of Bacillus subtilis with no known lysogenic cycle. Indeed, lysis occurs rapidly following infection of vegetative cells. Here, we show that phi29 possesses a powerful strategy that enables it to adapt its infection strategy to the physiological conditions of the infected host to optimize its survival and proliferation. Thus, the lytic cycle is suppressed when the infected cell has initiated the process of sporulation and the infecting phage genome is directed into the highly resistant spore to remain dormant until germination of the spore. We have also identified two host-encoded factors that are key players in this adaptive infection strategy. We present evidence that chromosome segregation protein Spo0J is involved in spore entrapment of the infected phi29 genome. In addition, we demonstrate that Spo0A, the master regulator for initiation of sporulation, suppresses phi29 development by repressing the main early phi29 promoters via different and novel mechanisms and also by preventing activation of the single late phi29 promoter.
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Affiliation(s)
- Wilfried J J Meijer
- Instituto de Biología Molecular Eladio Viñuela (CSIC), Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma, Canto Blanco, Madrid, Spain.
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43
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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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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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45
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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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46
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Johnson EP, Yao S, Helinski DR. Gyrase inhibitors and thymine starvation disrupt the normal pattern of plasmid RK2 localization in Escherichia coli. J Bacteriol 2005; 187:3538-47. [PMID: 15866942 PMCID: PMC1112003 DOI: 10.1128/jb.187.10.3538-3547.2005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2004] [Accepted: 02/14/2005] [Indexed: 11/20/2022] Open
Abstract
Multicopy plasmids in Escherichia coli are not randomly distributed throughout the cell but exist as defined clusters that are localized at the mid-cell, or at the 1/4 and 3/4 cell length positions. To explore the factors that contribute to plasmid clustering and localization, E. coli cells carrying a plasmid RK2 derivative that can be tagged with a green fluorescent protein-LacI fusion protein were subjected to various conditions that interfere with plasmid superhelicity and/or DNA replication. The various treatments included thymine starvation and the addition of the gyrase inhibitors nalidixic acid and novobiocin. In each case, localization of plasmid clusters at the preferred positions was disrupted but the plasmids remained in clusters, suggesting that normal plasmid superhelicity and DNA synthesis in elongating cells are not required for the clustering of individual plasmid molecules. It was also observed that the inhibition of DNA replication by these treatments produced filaments in which the plasmid clusters were confined to one or two nucleoid bodies, which were located near the midline of the filament and were not evenly spaced throughout the filament, as is found in cells treated with cephalexin. Finally, the enhanced yellow fluorescent protein-RarA fusion protein was used to localize the replication complex in individual E. coli cells. Novobiocin and nalidixic acid treatment both resulted in rapid loss of RarA foci. Under these conditions the RK2 plasmid clusters were not disassembled, suggesting that a completely intact replication complex is not required for plasmid clustering.
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Affiliation(s)
- Erik P Johnson
- Center for Molecular Genetics and Division of Biological Sciences, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0322, USA
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47
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Real G, Autret S, Harry EJ, Errington J, Henriques AO. Cell division protein DivIB influences the Spo0J/Soj system of chromosome segregation in Bacillus subtilis. Mol Microbiol 2005; 55:349-67. [PMID: 15659156 DOI: 10.1111/j.1365-2958.2004.04399.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The initiation of the developmental process of sporulation in the rod-shaped bacterium Bacillus subtilis involves the activation of the Spo0A response regulator. Spo0A then drives the switch in the site of division septum formation from midcell to a polar position. Activated Spo0A is required for the transcription of key sporulation loci such as spoIIG, which are negatively regulated by the Soj protein. The transcriptional repressing activity of Soj is antagonized by Spo0J, and both proteins belong to the well-conserved Par family of partitioning proteins. Soj has been shown to jump from nucleoid to nucleoid via the cell pole. The dynamic behaviour of Soj is somehow controlled by Spo0J, which prevents the static association of Soj with the nucleoid, and presumably its transcriptional repression activity. Soj in turn is required for the proper condensation of Spo0J foci around the oriC region. The asymmetric partitioning of the sporangial cell requires DivIB and other proteins involved in vegetative (medial) division. We describe an allele of the cell division gene divIB (divIB80) that reduces the cellular levels of DivIB, and affects nucleoid structure and segregation in growing cells, yet has no major impact on cell division. In divIB80 cells Spo0J foci are not correctly condensed and Soj associates statically with the nucleoid. The divIB80 allele prevents transcription of spoIIG, and arrests sporulation prior to the formation of the asymmetric division septum. The defect in Spo0A-dependent gene expression, and the Spo- phenotype can be suppressed by expression of divIB in trans or by deletion of the soj-spo0J locus. However, deletion of the spo0J-soj region does not restore the normal cellular levels of DivIB. Therefore, the reduced levels of DivIB in the divIB80 mutant are sufficient for efficient cell division, but not to sustain a second, earlier function of DivIB related to the activity of the Spo0J/Soj system of chromosome segregation.
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Affiliation(s)
- Gonçalo Real
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, Apartado 127, 2781-901 Oeiras Codex, Portugal
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48
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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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49
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Leonard TA, Butler PJ, Löwe J. Bacterial chromosome segregation: structure and DNA binding of the Soj dimer--a conserved biological switch. EMBO J 2005; 24:270-82. [PMID: 15635448 PMCID: PMC545817 DOI: 10.1038/sj.emboj.7600530] [Citation(s) in RCA: 239] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2004] [Accepted: 11/29/2004] [Indexed: 11/08/2022] Open
Abstract
Soj and Spo0J of the Gram-negative hyperthermophile Thermus thermophilus belong to the conserved ParAB family of bacterial proteins implicated in plasmid and chromosome partitioning. Spo0J binds to DNA near the replication origin and localises at the poles following initiation of replication. Soj oscillates in the nucleoid region in an ATP- and Spo0J-dependent fashion. Here, we show that Soj undergoes ATP-dependent dimerisation in solution and forms nucleoprotein filaments with DNA. Crystal structures of Soj in three nucleotide states demonstrate that the empty and ADP-bound states are monomeric, while a hydrolysis-deficient mutant, D44A, is capable of forming a nucleotide 'sandwich' dimer. Soj ATPase activity is stimulated by Spo0J or the N-terminal 20 amino-acid peptide of Spo0J. Our analysis shows that dimerisation and activation involving a peptide containing a Lys/Arg is conserved for Soj, ParA and MinD and their modulators Spo0J, ParB and MinE, respectively. By homology to the nitrogenase iron protein and the GTPases Ffh/FtsY, we suggest that Soj dimerisation and regulation represent a conserved biological switch.
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50
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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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