201
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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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202
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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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203
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Abstract
Recent advances have demonstrated that bacterial cells have an exquisitely organized and dynamic subcellular architecture. Like their eukaryotic counterparts, bacteria employ a full complement of cytoskeletal proteins, localize proteins and DNA to specific subcellular addresses at specific times, and use intercellular signaling to coordinate multicellular events. The striking conceptual and molecular similarities between prokaryotic and eukaryotic cell biology thus make bacteria powerful model systems for studying fundamental cellular questions.
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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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204
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Thanbichler M, Viollier PH, Shapiro L. The structure and function of the bacterial chromosome. Curr Opin Genet Dev 2005; 15:153-62. [PMID: 15797198 DOI: 10.1016/j.gde.2005.01.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Advances in microscopic and cell biological techniques have considerably improved our understanding of bacterial chromosome organization and dynamics. The nucleoid was formerly perceived to be an amorphous entity divided into ill-defined domains of supercoiling that are randomly deposited in the cell. Recent work, however, has demonstrated a remarkable degree of spatial organization. A highly ordered chromosome structure, established while DNA replication and partitioning are in progress, is maintained and propagated during growth. Duplication of the chromosome and partitioning of the newly generated daughter strands are interwoven processes driven by the dynamic interplay between the synthesis, segregation and condensation of DNA. These events are intimately coupled with the bacterial cell cycle and exhibit a previously unanticipated complexity reminiscent of eukaryotic systems.
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Affiliation(s)
- Martin Thanbichler
- Department of Developmental Biology, Stanford University School of Medicine, Beckman Center B300, 279 Campus Drive, Stanford, CA 94305-5329, USA
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205
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Migocki MD, Lewis PJ, Wake RG, Harry EJ. The midcell replication factory in Bacillus subtilis is highly mobile: implications for coordinating chromosome replication with other cell cycle events. Mol Microbiol 2005; 54:452-63. [PMID: 15469516 DOI: 10.1111/j.1365-2958.2004.04267.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
During vegetative growth, rod-shaped bacterial cells such as Escherichia coli and Bacillus subtilis divide precisely at midcell. It is the Z ring that defines the position of the division site. We previously demonstrated that the early stages of chromosome replication are linked to midcell Z ring assembly in B. subtilis and proposed a direct role for the centrally located replication factory in masking and subsequently unmasking the midcell site for Z ring assembly. We now show that the replication factory is significantly more scattered about the cell centre than the Z ring in both vegetative cells and outgrown spores of B. subtilis. This finding is inconsistent with the midcell replication factory acting as a direct physical block to Z ring assembly. Time-lapse experiments demonstrated that the lower precision of replication factory positioning results from its high mobility around the cell centre. Various aspects of this mobility are presented and the results are discussed in the light of current views on the determinants of positional information required for accurate chromosome segregation and cell division.
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Affiliation(s)
- Margaret D Migocki
- School of Molecular and Microbial Biosciences, University of Sydney, Sydney, NSW 2006, Australia
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206
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Abstract
In rod-shaped bacteria, a surprisingly large number of proteins are localized to the cell poles. Polar positioning of proteins is crucial to many fundamental cellular processes. Formation of the pole occurs at the time of a prior cell division event and involves coordination of the cell division machinery with septal placement of newly-synthesized peptidoglycan. Development of polar peptidoglycan and outer membrane depends on the formation of the cytokinetic FtsZ ring at midcell. By contrast, positioning of at least two polar proteins depends on signals independent of both the assembly of the FtsZ ring and the synthesis of septal and polar peptidoglycan. We propose a model for distinct but interrelated developmental pathways for polar cell envelope synthesis and positional information recognized by polar proteins.
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Affiliation(s)
- Anuradha Janakiraman
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital/Harvard Medical School, 65 Landsdowne St., Cambridge, MA 02139, USA
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207
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Barillà D, Rosenberg MF, Nobbmann U, Hayes F. Bacterial DNA segregation dynamics mediated by the polymerizing protein ParF. EMBO J 2005; 24:1453-64. [PMID: 15775965 PMCID: PMC1142544 DOI: 10.1038/sj.emboj.7600619] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2004] [Accepted: 02/15/2005] [Indexed: 11/09/2022] Open
Abstract
Prokaryotic DNA segregation most commonly involves members of the Walker-type ParA superfamily. Here we show that the ParF partition protein specified by the TP228 plasmid is a ParA ATPase that assembles into extensive filaments in vitro. Polymerization is potentiated by ATP binding and does not require nucleotide hydrolysis. Analysis of mutations in conserved residues of the Walker A motif established a functional coupling between filament dynamics and DNA partitioning. The partner partition protein ParG plays two separable roles in the ParF polymerization process. ParF is unrelated to prokaryotic polymerizing proteins of the actin or tubulin families, but is a homologue of the MinD cell division protein, which also assembles into filaments. The ultrastructures of the ParF and MinD polymers are remarkably similar. This points to an evolutionary parallel between DNA segregation and cytokinesis in prokaryotic cells, and reveals a potential molecular mechanism for plasmid and chromosome segregation mediated by the ubiquitous ParA-type proteins.
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Affiliation(s)
- Daniela Barillà
- Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Mark F Rosenberg
- Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Ulf Nobbmann
- Malvern Instruments Ltd, Malvern, Worcestershire, UK
| | - Finbarr Hayes
- Faculty of Life Sciences, University of Manchester, Manchester, UK
- Faculty of Life Sciences, The University of Manchester, PO Box 88, Sackville Street, Manchester M60 1QD, UK. Tel.: +44 161 200 8934; Fax: +44 161 236 0409; E-mail:
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208
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Bacillus subtilis actin-like protein MreB influences the positioning of the replication machinery and requires membrane proteins MreC/D and other actin-like proteins for proper localization. BMC Cell Biol 2005; 6:10. [PMID: 15745453 PMCID: PMC555950 DOI: 10.1186/1471-2121-6-10] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2004] [Accepted: 03/03/2005] [Indexed: 11/25/2022] Open
Abstract
Background Bacterial actin-like proteins have been shown to perform essential functions in several aspects of cellular physiology. They affect cell growth, cell shape, chromosome segregation and polar localization of proteins, and localize as helical filaments underneath the cell membrane. Bacillus subtilis MreB and Mbl have been shown to perform dynamic motor like movements within cells, extending along helical tracks in a time scale of few seconds. Results In this work, we show that Bacillus subtilis MreB has a dual role, both in the formation of rod cell shape, and in chromosome segregation, however, its function in cell shape is distinct from that of MreC. Additionally, MreB is important for the localization of the replication machinery to the cell centre, which becomes aberrant soon after depletion of MreB. 3D image reconstructions suggest that frequently, MreB filaments consist of several discontinuous helical filaments with varying length. The localization of MreB was abnormal in cells with decondensed chromosomes, as well as during depletion of Mbl, MreBH and of the MreC/MreD proteins, which we show localize to the cell membrane. Thus, proper positioning of MreB filaments depends on and is affected by a variety of factors in the cell. Conclusion Our data provide genetic and cytological links between MreB and the membrane, as well as with other actin like proteins, and further supports the connection of MreB with the chromosome. The functional dependence on MreB of the localization of the replication machinery suggests that the replisome is not anchored at the cell centre, but is positioned in a dynamic manner.
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209
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Champion M. Spiraled origins. Mol Cell 2005; 17:475-7. [PMID: 15721251 DOI: 10.1016/j.molcel.2005.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Recent studies have established that the eukaryotic actin-based cytoskeleton has prokaryotic origins. In addition to regulating cell shape and polarity, Gitai et al. (2005) provide convincing evidence that the Caulobacter actin homolog MreB also mediates the early segregation of the chromosomal origin, a typical functional role of the eukaryotic tubulin-based cytoskeleton.
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Affiliation(s)
- Mia Champion
- Cell Press, 1100 Massachusetts Avenue, Cambridge, MA 02138, USA
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210
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Wagner JK, Galvani CD, Brun YV. Caulobacter crescentus requires RodA and MreB for stalk synthesis and prevention of ectopic pole formation. J Bacteriol 2005; 187:544-53. [PMID: 15629926 PMCID: PMC543564 DOI: 10.1128/jb.187.2.544-553.2005] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Caulobacter crescentus cells treated with amdinocillin, an antibiotic which specifically inhibits the cell elongation transpeptidase penicillin binding protein 2 in Escherichia coli, exhibit defects in stalk elongation and morphology, indicating that stalk synthesis may be a specialized form of cell elongation. In order to investigate this possibility further, we examined the roles of two other proteins important for cell elongation, RodA and MreB. We show that, in C. crescentus, the rodA gene is essential and that RodA depletion leads to a loss of control over stalk and cell body diameter and a stalk elongation defect. In addition, we demonstrate that MreB depletion leads to a stalk elongation defect and conclude that stalk elongation is a more constrained form of cell elongation. Our results strongly suggest that MreB by itself does not determine the diameter of the cell body or stalk. Finally, we show that cells recovering from MreB depletion exhibit a strong budding and branching cell body phenotype and possess ectopic poles, as evidenced by the presence of multiple, misplaced, and sometimes highly branched stalks at the ends of these buds and branches. This phenotype is also seen to a lesser extent in cells recovering from RodA depletion and amdinocillin treatment. We conclude that MreB, RodA, and the target(s) of amdinocillin all contribute to the maintenance of cellular polarity in C. crescentus.
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Affiliation(s)
- Jennifer K Wagner
- Department of Biology, Indiana University, Bloomington, IN 47405-3700, USA
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211
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Gitai Z, Dye NA, Reisenauer A, Wachi M, Shapiro L. MreB Actin-Mediated Segregation of a Specific Region of a Bacterial Chromosome. Cell 2005; 120:329-41. [PMID: 15707892 DOI: 10.1016/j.cell.2005.01.007] [Citation(s) in RCA: 282] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2004] [Revised: 12/22/2004] [Accepted: 01/06/2005] [Indexed: 10/25/2022]
Abstract
Faithful chromosome segregation is an essential component of cell division in all organisms. The eukaryotic mitotic machinery uses the cytoskeleton to move specific chromosomal regions. To investigate the potential role of the actin-like MreB protein in bacterial chromosome segregation, we first demonstrate that MreB is the direct target of the small molecule A22. We then demonstrate that A22 completely blocks the movement of newly replicated loci near the origin of replication but has no qualitative or quantitative effect on the segregation of other loci if added after origin segregation. MreB selectively interacts, directly or indirectly, with origin-proximal regions of the chromosome, arguing that the origin-proximal region segregates via an MreB-dependent mechanism not used by the rest of the chromosome.
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Affiliation(s)
- Zemer Gitai
- Department of Developmental Biology, Beckman Center, School of Medicine, Stanford University, California 94305, USA.
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212
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Pastoret S, Fraipont C, den Blaauwen T, Wolf B, Aarsman MEG, Piette A, Thomas A, Brasseur R, Nguyen-Distèche M. Functional analysis of the cell division protein FtsW of Escherichia coli. J Bacteriol 2005; 186:8370-9. [PMID: 15576787 PMCID: PMC532424 DOI: 10.1128/jb.186.24.8370-8379.2004] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Site-directed mutagenesis experiments combined with fluorescence microscopy shed light on the role of Escherichia coli FtsW, a membrane protein belonging to the SEDS family that is involved in peptidoglycan assembly during cell elongation, division, and sporulation. This essential cell division protein has 10 transmembrane segments (TMSs). It is a late recruit to the division site and is required for subsequent recruitment of penicillin-binding protein 3 (PBP3) catalyzing peptide cross-linking. The results allow identification of several domains of the protein with distinct functions. The localization of PBP3 to the septum was found to be dependent on the periplasmic loop located between TMSs 9 and 10. The E240-A249 amphiphilic peptide in the periplasmic loop between TMSs 7 and 8 appears to be a key element in the functioning of FtsW in the septal peptidoglycan assembly machineries. The intracellular loop (containing the R166-F178 amphiphilic peptide) between TMSs 4 and 5 and Gly 311 in TMS 8 are important components of the amino acid sequence-folding information.
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Affiliation(s)
- Soumya Pastoret
- Centre d'Ingénierie des Protéines, Institut de Chimie, Bât. allée de la Chimie, 3, B-4000 Liège, Belgium
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213
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Slovak PM, Wadhams GH, Armitage JP. Localization of MreB in Rhodobacter sphaeroides under conditions causing changes in cell shape and membrane structure. J Bacteriol 2005; 187:54-64. [PMID: 15601688 PMCID: PMC538805 DOI: 10.1128/jb.187.1.54-64.2005] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
MreB is thought to be a bacterial actin homolog that defines the morphology of rod-shaped bacteria. Rhodobacter sphaeroides changes shape, from a rod to coccobacillus, and undergoes extensive cytoplasmic membrane invagination when it switches from aerobic to photoheterotrophic growth. The role of MreB in defining R. sphaeroides shape was therefore investigated. Attempts at deleting or insertionally inactivating mreB were unsuccessful under all growth conditions. Immunofluorescence microscopy showed MreB localized to mid-cell in elongating cells under both aerobic and photoheterotrophic conditions. Three-dimensional reconstruction showed that MreB formed a ring at mid-cell. MreB remained at mid-cell as septation began but localized to new sites in the daughter cells before the completion of septation. MreB localized to putative septation sites in cephalexin-treated filamentous cells. Genomic single-copy mreB was replaced with gfp-mreB, and green fluorescent protein (GFP)-MreB localized in the same pattern, as seen with immunofluorescence microscopy. Some of the cells expressing GFP-MreB were abnormal, principally displaying an increase in cell width, suggesting that the fusion was not fully functional in all cells. GFP-MreB localized to swellings at mid-cell in cells treated with the penicillin-binding protein 2 inhibitor amdinocillin. These data suggest that MreB is essential in R. sphaeroides, performing a role at mid-cell in elongating cells, and in early septation, putatively in the cytoplasmic control of the peptidoglycan synthetic complexes.
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Affiliation(s)
- Peter M Slovak
- Department of Biochemistry, University of Oxford, South Parks Rd., Oxford, OX1 3QU United Kingdom
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214
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Thanbichler M, Wang SC, Shapiro L. The bacterial nucleoid: A highly organized and dynamic structure. J Cell Biochem 2005; 96:506-21. [PMID: 15988757 DOI: 10.1002/jcb.20519] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Recent advances in bacterial cell biology have revealed unanticipated structural and functional complexity, reminiscent of eukaryotic cells. Particular progress has been made in understanding the structure, replication, and segregation of the bacterial chromosome. It emerged that multiple mechanisms cooperate to establish a dynamic assembly of supercoiled domains, which are stacked in consecutive order to adopt a defined higher-level organization. The position of genetic loci on the chromosome is thereby linearly correlated with their position in the cell. SMC complexes and histone-like proteins continuously remodel the nucleoid to reconcile chromatin compaction with DNA replication and gene regulation. Moreover, active transport processes ensure the efficient segregation of sister chromosomes and the faithful restoration of nucleoid organization while DNA replication and condensation are in progress.
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Affiliation(s)
- Martin Thanbichler
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305-5329, USA
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215
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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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216
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Abstract
It has become clear recently that bacteria contain all of the cytoskeletal elements that are found in eukaryotic cells, demonstrating that the cytoskeleton has not been a eukaryotic invention, but evolved early in evolution. Several proteins that are involved in cell division, cell structure and DNA partitioning have been found to form highly dynamic ring structures or helical filaments underneath the cell membrane or throughout the length of the cell. These exciting findings indicate that several highly dynamic processes occur within prokaryotic cells, during growth or differentiation, that are vital for a wide range of cellular tasks.
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Affiliation(s)
- Peter L Graumann
- Biochemie, Fachbereich Chemie, Hans-Meerwein-Strasse, Philipps-Universität Marburg, 35032 Marburg, Germany.
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217
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218
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Abstract
Dynamic instability-the switching of a two-state polymer between phases of steady elongation and rapid shortening-is essential to the cellular function of eukaryotic microtubules, especially during chromosome segregation. Since the discovery of dynamic instability 20 years ago, no other biological polymer has been found to exhibit this behavior. Using total internal reflection fluorescence microscopy and fluorescence resonance energy transfer, we observe that the prokaryotic actin homolog ParM, whose assembly is required for the segregation of large, low-copy number plasmids, displays both dynamic instability and symmetrical, bidirectional polymerization. The dynamic instability of ParM is regulated by adenosine triphosphate (ATP) hydrolysis, and filaments are stabilized by a cap of ATP-bound monomers. ParM is not related to tubulin, so its dynamic instability must have arisen by convergent evolution driven by a set of common constraints on polymer-based segregation of DNA.
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Affiliation(s)
- Ethan C Garner
- University of California, 600 16th Street, San Francisco, CA 94107, USA
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219
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Abstract
MreB, a major component of the bacterial cytoskeleton, exhibits high structural homology to its eukaryotic counterpart actin. Live cell microscopy studies suggest that MreB molecules organize into large filamentous spirals that support the cell membrane and play a key shape-determining function. However, the basic properties of MreB filament assembly remain unknown. Here, we studied the assembly of Thermotoga maritima MreB triggered by ATP in vitro and compared it to the well-studied assembly of actin. These studies show that MreB filament ultrastructure and polymerization depend crucially on temperature as well as the ions present on solution. At the optimal growth temperature of T. maritima, MreB assembly proceeded much faster than that of actin, without nucleation (or nucleation is highly favorable and fast) and with little or no contribution from filament end-to-end annealing. MreB exhibited rates of ATP hydrolysis and phosphate release similar to that of F-actin, however, with a critical concentration of approximately 3 nm, which is approximately 100-fold lower than that of actin. Furthermore, MreB assembled into filamentous bundles that have the ability to spontaneously form ring-like structures without auxiliary proteins. These findings suggest that despite high structural homology, MreB and actin display significantly different assembly properties.
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Affiliation(s)
- Osigwe Esue
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland 21218, USA
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220
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Abstract
The biochemical steps by which bacterial topoisomerases alter the topology of DNA are well known. However, it has been a more vexing task to establish physiological roles and sites of action of the different topoisomerases within the context of the bacterial cell cycle. This difficulty can be attributed in part to the redundancy among the activities of the different enzymes. In this microreview, we will focus on recent progress in understanding the topological structure of the chromosome, analysis of topoisomerase mechanism in single-molecule assays and recent data on the regulation and integration of topoisomerase activity within the cell cycle that have all brought a new perspective to the action of topoisomerases in the bacterial cell.
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Affiliation(s)
- Olivier Espeli
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA
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221
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Amos LA, van den Ent F, Löwe J. Structural/functional homology between the bacterial and eukaryotic cytoskeletons. Curr Opin Cell Biol 2004; 16:24-31. [PMID: 15037301 DOI: 10.1016/j.ceb.2003.11.005] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Structural proteins are now known to be as necessary for controlling cell division and cell shape in prokaryotes as they are in eukaryotes. Bacterial ParM and MreB not only have atomic structures that resemble eukaryotic actin and form similar filaments, but they are also equivalent in function: the assembly of ParM drives intracellular motility and MreB maintains the shape of the cell. FtsZ resembles tubulin in structure and in its dynamic assembly, and is similarly controlled by accessory proteins. Bacterial MinD and eukaryotic dynamin appear to have similar functions in membrane control. In dividing eukaryotic organelles of bacterial origin, bacterial and eukaryotic proteins work together.
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Affiliation(s)
- Linda A Amos
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.
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222
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Abstract
Traditional textbook representations of the prokaryotic cytoplasm show an amorphous, unstructured amalgamation of proteins and small molecules in which a randomly arranged chromosome resides. The development and application of a swathe of microscopic techniques over the last 10 years in particular, has shown this image of the microbial cell to be incorrect: the cytoplasm is highly structured with many proteins carrying out their assigned functions at specific subcellular locations; bacteria contain cytoskeletal elements including microtubule, actin and intermediate filament homologues; the chromosome is not randomly folded and is organized in such a way as to facilitate efficient segregation upon cell division. This review will concentrate on recent advances in our understanding of subcellular architecture and the techniques that have led to these discoveries.
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Affiliation(s)
- Peter J Lewis
- School of Environmental and Life Sciences, Biological Sciences, University of Newcastle, Callaghan, NSW 2308, Australia.
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223
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Johnson AS, van Horck S, Lewis PJ. Dynamic localization of membrane proteins in Bacillus subtilis. Microbiology (Reading) 2004; 150:2815-2824. [PMID: 15347741 DOI: 10.1099/mic.0.27223-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The subcellular localization of membrane proteins in Bacillus subtilis was examined by using fluorescent protein fusions. ATP synthase and succinate dehydrogenase were found to localize within discrete domains on the membrane rather than being homogeneously distributed around the cell periphery as expected. Dual labelling of cells indicated partial colocalization of ATP synthase and succinate dehydrogenase. Further analysis using an ectopically expressed phage protein gave the same localization patterns as ATP synthase and succinate dehydrogenase, implying that membrane proteins are restricted to domains within the membrane. 3D reconstruction of images of the localization of ATP synthase showed that domains were not regular and there was no bias for localization to cell poles or any other positions. Further analysis revealed that this localization was highly dynamic, but random, implying that integral membrane proteins are free to diffuse two-dimensionally around the cytoplasmic membrane.
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Affiliation(s)
- A S Johnson
- School of Environmental and Life Sciences, Biological Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - S van Horck
- School of Environmental and Life Sciences, Biological Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - P J Lewis
- School of Environmental and Life Sciences, Biological Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
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224
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Defeu Soufo HJ, Graumann PL. Dynamic movement of actin-like proteins within bacterial cells. EMBO Rep 2004; 5:789-94. [PMID: 15272301 PMCID: PMC1299120 DOI: 10.1038/sj.embor.7400209] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2004] [Revised: 06/25/2004] [Accepted: 06/25/2004] [Indexed: 11/09/2022] Open
Abstract
Actin proteins are present in pro- and eukaryotes, and have been shown to perform motor-like functions in eukaryotic cells in a variety of processes. Bacterial actin homologues are essential for cell viability and have been implicated in the formation of rod cell shape, as well as in segregation of plasmids and whole chromosomes. We have generated functional green fluorescent protein fusions of all three Bacillus subtilis actin-like proteins (MreB, Mbl and MreBH), and show that all three proteins form helical filaments underneath the cell membrane, the pattern of which is distinct for each protein. Time-lapse microscopy showed that the filaments are highly dynamic structures. A number of separate filaments of MreB and Mbl continuously move through the cell along helical tracks underneath the cell membrane. The speed of extension of the growing end of filaments is within the range of known actin polymerization (0.1 microm/s), generating a potential poleward or centreward pushing velocity at 0.24 microm/min for MreB or Mbl, respectively. During nutritional downshift and a block in topoisomerase IV activity, the filaments rapidly disintegrated, showing that movement occurs only in growing cells. Contrary to Mbl and MreBH filaments, MreB filaments were generally absent in cells lacking DNA, providing a further distinction between the three orthologues.
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Affiliation(s)
- Hervé Joël Defeu Soufo
- Biochemie, Fachbereich Chemie, Hans-Meerweinstraße, Philipps-Universität Marburg, 35032 Marburg, Germany
| | - Peter L Graumann
- Biochemie, Fachbereich Chemie, Hans-Meerweinstraße, Philipps-Universität Marburg, 35032 Marburg, Germany
- Tel: +49 6421 2825747; Fax: +49 6421 2822191; E-mail:
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225
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Affiliation(s)
- Aretha Fiebig
- Department of Biochemistry and of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305-5307, USA
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226
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Gitai Z, Dye N, Shapiro L. An actin-like gene can determine cell polarity in bacteria. Proc Natl Acad Sci U S A 2004; 101:8643-8. [PMID: 15159537 PMCID: PMC423248 DOI: 10.1073/pnas.0402638101] [Citation(s) in RCA: 246] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Achieving proper polarity is essential for cellular function. In bacteria, cell polarity has been observed by using both morphological and molecular markers; however, no general regulators of bacterial cell polarity have been identified. Here we investigate the effect on cell polarity of two cytoskeletal elements previously implicated in cell shape determination. We find that the actin-like MreB protein mediates global cell polarity in Caulobacter crescentus, although the intermediate filament-like CreS protein influences cell shape without affecting cell polarity. MreB is organized in an axial spiral that is dynamically rearranged during the cell cycle, and MreB dynamics may be critical for the determination of cell polarity. By examining depletion and overexpression strains, we demonstrate that MreB is required both for the polar localization of the chromosomal origin sequence and the dynamic localization of regulatory proteins to the correct cell pole. We propose that the molecular polarity inherent in an actin-like filament is translated into a mechanism for directing global cell polarity.
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Affiliation(s)
- Zemer Gitai
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
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227
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Ebersbach G, Gerdes K. Bacterial mitosis: partitioning protein ParA oscillates in spiral-shaped structures and positions plasmids at mid-cell. Mol Microbiol 2004; 52:385-98. [PMID: 15066028 DOI: 10.1111/j.1365-2958.2004.04002.x] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The par2 locus of Escherichia coli plasmid pB171 encodes oscillating ATPase ParA, DNA binding protein ParB and two cis-acting DNA regions to which ParB binds (parC1 and parC2). Three independent techniques were used to investigate the subcellular localization of plasmids carrying par2. In cells with a single plasmid focus, the focus located preferentially at mid-cell. In cells with two foci, these located at quarter-cell positions. In the absence of ParB and parC1/parC2, ParA-GFP formed stationary helices extending from one end of the nucleoid to the other. In the presence of ParB and parC1/parC2, ParA-GFP oscillated in spiral-shaped structures. Amino acid substitutions in ParA simultaneously abolished ParA spiral formation, oscillation and either plasmid localization or plasmid separation at mid-cell. Therefore, our results suggest that ParA spirals position plasmids at the middle of the bacterial nucleoid and subsequently separate them into daughter cells.
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Affiliation(s)
- Gitte Ebersbach
- Department of Biochemistry and Molecular Biology, Campusvej 55, DK-5230 Odense M, University of Southern Denmark, Denmark
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228
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Abstract
The bacterial actin homolog ParM catalyzes segregation of plasmid DNA in E. coli. Recent studies now suggest a model in which ParM forms actin-like filaments between two plasmid molecules, thereby providing the driving force for plasmid DNA separation.
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Affiliation(s)
- Joe Pogliano
- Division of Biological Sciences, University of California-San Diego, La Jolla, CA 92093, USA
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229
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Abstract
Bacterial cells exhibit a wide variety of shapes. Recent results indicate that the characteristic crescent shape of Caulobacter crescentus depends upon an inter-mediate filament-like protein that localizes to the concave side of the cell.
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Affiliation(s)
- William Margolin
- Department of Microbiology and Molecular Genetics, University of Texas Medical School, 6431 Fannin, Houston, Texas 77030, USA.
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230
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Ausmees N, Kuhn JR, Jacobs-Wagner C. The bacterial cytoskeleton: an intermediate filament-like function in cell shape. Cell 2004; 115:705-13. [PMID: 14675535 DOI: 10.1016/s0092-8674(03)00935-8] [Citation(s) in RCA: 272] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Various cell shapes are encountered in the prokaryotic world, but how they are achieved is poorly understood. Intermediate filaments (IFs) of the eukaryotic cytoskeleton play an important role in cell shape in higher organisms. No such filaments have been found in prokaryotes. Here, we describe a bacterial equivalent to IF proteins, named crescentin, whose cytoskeletal function is required for the vibrioid and helical shapes of Caulobacter crescentus. Without crescentin, the cells adopt a straight-rod morphology. Crescentin has characteristic features of IF proteins including the ability to assemble into filaments in vitro without energy or cofactor requirements. In vivo, crescentin forms a helical structure that colocalizes with the inner cell curvatures beneath the cytoplasmic membrane. We propose that IF-like filaments of crescentin assemble into a helical structure, which by applying its geometry to the cell, generates a vibrioid or helical cell shape depending on the length of the cell.
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Affiliation(s)
- Nora Ausmees
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
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231
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Abstract
Here, we review recent progress that yields fundamental new insight into the molecular mechanisms behind plasmid and chromosome segregation in prokaryotic cells. In particular, we describe how prokaryotic actin homologs form mitotic machineries that segregate DNA before cell division. Thus, the ParM protein of plasmid R1 forms F actin-like filaments that separate and move plasmid DNA from mid-cell to the cell poles. Evidence from three different laboratories indicate that the morphogenetic MreB protein may be involved in segregation of the bacterial chromosome.
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Affiliation(s)
- Kenn Gerdes
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, DK-5230 Odense M, Denmark.
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232
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Abstract
Actin performs structural as well as motor-like functions in eukaryotic cells. Orthologues of actin have also been identified in bacteria, where they perform an essential function during cell growth. Bacterial actins are implicated in the maintenance of rod-shaped cell morphology, and appear to form a cytoskeletal structure, localising as helical filaments underneath the cell membrane. Recently, a plasmid-borne actin orthologue has been shown to perform a mitotic-like function during segregation of a plasmid, and chromosomally encoded actin proteins were found to play an important role in chromosome segregation. Based on the findings that actin filaments are dynamic structures in two bacterial species, we propose that actins perform motor functions rather than a purely structural role in bacteria. We suggest that an intracellular motor exists in bacteria that could be derived from an ancestral actin motor that was present in cells early in evolution.
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Affiliation(s)
- Peter L Graumann
- Biochemie, Fachbereich Chemie, Philipps-Universität Marburg, Germany.
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