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Tomares DT, Whitlock S, Mann M, DiBernardo E, Childers WS. Repurposing Peptide Nanomaterials as Synthetic Biomolecular Condensates in Bacteria. ACS Synth Biol 2022; 11:2154-2162. [PMID: 35658421 DOI: 10.1021/acssynbio.2c00078] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptide nanomaterials exhibit diverse applications in vitro, such as drug delivery. Here, we consider the utility of de novo peptide nanomaterials to organize biochemistry within the bacterial cytoplasm. Toward this goal, we discovered that ABC coiled-coil triblock peptides form gel-like biomolecular condensates with a csat of 10 μM in addition to their well-known hydrogel-forming capabilities. Expression of the coiled-coil triblock peptides in bacteria leads to cell pole accumulation via a nucleoid occlusion mechanism. We then provide a proof of principle that these synthetic biomolecular condensates could sequester clients at the cell pole. Finally, we demonstrate that triblock peptides and another biomolecular condensate, RNase E, phase-separate as distinct protein-rich assemblies in vitro and in vivo. These results reveal the potential of using peptide nanomaterials to divide the bacterial cytoplasm into distinct subcellular zones with future metabolic engineering and synthetic biology applications.
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Affiliation(s)
- Dylan T Tomares
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Sara Whitlock
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Matthew Mann
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Emma DiBernardo
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - W Seth Childers
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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2
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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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3
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Misra HS, Maurya GK, Kota S, Charaka VK. Maintenance of multipartite genome system and its functional significance in bacteria. J Genet 2018. [DOI: 10.1007/s12041-018-0969-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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4
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Maturation of the [Ni-4Fe-4S] active site of carbon monoxide dehydrogenases. J Biol Inorg Chem 2018; 23:613-620. [PMID: 29445873 PMCID: PMC6006190 DOI: 10.1007/s00775-018-1541-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 01/30/2018] [Indexed: 12/11/2022]
Abstract
Nickel-containing enzymes are diverse in terms of function and active site structure. In many cases, the biosynthesis of the active site depends on accessory proteins which transport and insert the Ni ion. We review and discuss the literature related to the maturation of carbon monoxide dehydrogenases (CODH) which bear a nickel-containing active site consisting of a [Ni–4Fe–4S] center called the C-cluster. The maturation of this center has been much less studied than that of other nickel-containing enzymes such as urease and NiFe hydrogenase. Several proteins present in certain CODH operons, including the nickel-binding proteins CooT and CooJ, still have unclear functions. We question the conception that the maturation of all CODH depends on the accessory protein CooC described as essential for nickel insertion into the active site. The available literature reveals biological variations in CODH active site biosynthesis.
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5
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Grangeasse C. Rewiring the Pneumococcal Cell Cycle with Serine/Threonine- and Tyrosine-kinases. Trends Microbiol 2016; 24:713-724. [DOI: 10.1016/j.tim.2016.04.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Revised: 03/23/2016] [Accepted: 04/07/2016] [Indexed: 12/14/2022]
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6
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Joh RI, Palmieri CM, Hill IT, Motamedi M. Regulation of histone methylation by noncoding RNAs. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:1385-94. [PMID: 24954181 DOI: 10.1016/j.bbagrm.2014.06.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 05/30/2014] [Accepted: 06/09/2014] [Indexed: 12/19/2022]
Abstract
Cells can adapt to their environment and develop distinct identities by rewiring their transcriptional networks to regulate the output of key biological pathways without concomitant mutations to the underlying genes. These alterations, called epigenetic changes, persist stably through mitotic or, in some instances, meiotic cell divisions. In eukaryotes, heritable changes to chromatin structure are a prominent, but not exclusive, mechanism by which epigenetic changes are mediated. These changes are initiated by sequence-specific events, which trigger a cascade of molecular interactions resulting in feedback mechanisms, alterations in chromatin structure, histone posttranslational modifications (PTMs), and ultimately establishment of distinct transcriptional states. In recent years, advances in next generation sequencing have led to the discovery of several novel classes of noncoding RNAs (ncRNAs). In addition to their well-established cytoplasmic roles in posttranscriptional regulation of gene expression, ncRNAs have emerged as key regulators of epigenetic changes via chromatin-dependent mechanisms in organisms ranging from yeast to man. They function by affecting chromatin structure, histone PTMs, and the recruitment of transcriptional activating or repressing complexes. Among histone PTMs, lysine methylation serves as the binding substrate for the recruitment of key protein complexes involved in the regulation of genome architecture, stability, and gene expression. In this review, we will outline the known mechanisms by which ncRNAs of different origins regulate histone methylation, and in doing so contribute to a variety of genome regulatory functions in eukaryotes.
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Affiliation(s)
- Richard I Joh
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School,149 13th Street, Charlestown, MA 02129, USA
| | - Christina M Palmieri
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School,149 13th Street, Charlestown, MA 02129, USA
| | - Ian T Hill
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School,149 13th Street, Charlestown, MA 02129, USA; PhD Program in Biological and Biomedical Sciences, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Mo Motamedi
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School,149 13th Street, Charlestown, MA 02129, USA.
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7
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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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8
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How to get (a)round: mechanisms controlling growth and division of coccoid bacteria. Nat Rev Microbiol 2013; 11:601-14. [PMID: 23949602 DOI: 10.1038/nrmicro3088] [Citation(s) in RCA: 193] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Bacteria come in a range of shapes, including round, rod-shaped, curved and spiral cells. This morphological diversity implies that different mechanisms exist to guide proper cell growth, division and chromosome segregation. Although the majority of studies on cell division have focused on rod-shaped cells, the development of new genetic and cell biology tools has provided mechanistic insight into the cell cycles of bacteria with different shapes, allowing us to appreciate the underlying molecular basis for their morphological diversity. In this Review, we discuss recent progress that has advanced our knowledge of the complex mechanisms for chromosome segregation and cell division in bacteria which have, deceptively, the simplest possible shape: the cocci.
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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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10
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Lopez-Vernaza MA, Leach DRF. WITHDRAWN: Symmetries and Asymmetries Associated with Non-Random Segregation of Sister DNA Strands in Escherichia coli. Semin Cell Dev Biol 2013:S1084-9521(13)00077-3. [PMID: 23692810 DOI: 10.1016/j.semcdb.2013.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 05/06/2013] [Indexed: 11/19/2022]
Abstract
The Publisher regrets that this article is an accidental duplication of an article that has already been published, http://dx.doi.org/10.1016/j.semcdb.2013.05.010. The duplicate article has therefore been withdrawn.
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Affiliation(s)
- Manuel A Lopez-Vernaza
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JR, United Kingdom
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Lopez-Vernaza MA, Leach DRF. Symmetries and asymmetries associated with non-random segregation of sister DNA strands in Escherichia coli. Semin Cell Dev Biol 2013; 24:610-7. [PMID: 23685127 DOI: 10.1016/j.semcdb.2013.05.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The successful inheritance of genetic information across generations is a complex process requiring replication of the genome and its faithful segregation into two daughter cells. At each replication cycle there is a risk that new DNA strands incorporate genetic changes caused by miscopying of parental information. By contrast the parental strands retain the original information. This raises the intriguing possibility that specific cell lineages might inherit "immortal" parental DNA strands via non-random segregation. If so, this requires an understanding of the mechanisms of non-random segregation. Here, we review several aspects of asymmetry in the very symmetrical cell, Escherichia coli, in the interest of exploring the potential basis for non-random segregation of leading- and lagging-strand replicated chromosome arms. These considerations lead us to propose a model for DNA replication that integrates chromosome segregation and genomic localisation with non-random strand segregation.
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Affiliation(s)
- Manuel A Lopez-Vernaza
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
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12
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13
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Abstract
In dividing cells, chromosome duplication once per generation must be coordinated with faithful segregation of newly replicated chromosomes and with cell growth and division. Many of the mechanistic details of bacterial replication elongation are well established. However, an understanding of the complexities of how replication initiation is controlled and coordinated with other cellular processes is emerging only slowly. In contrast to eukaryotes, in which replication and segregation are separate in time, the segregation of most newly replicated bacterial genetic loci occurs sequentially soon after replication. We compare the strategies used by chromosomes and plasmids to ensure their accurate duplication and segregation and discuss how these processes are coordinated spatially and temporally with growth and cell division. We also describe what is known about the three conserved families of ATP-binding proteins that contribute to chromosome segregation and discuss their inter-relationships in a range of disparate bacteria.
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14
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Goldman AD, Landweber LF. Oxytricha as a modern analog of ancient genome evolution. Trends Genet 2012; 28:382-8. [PMID: 22622227 DOI: 10.1016/j.tig.2012.03.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2012] [Revised: 03/16/2012] [Accepted: 03/19/2012] [Indexed: 12/20/2022]
Abstract
Several independent lines of evidence suggest that the modern genetic system was preceded by the 'RNA world' in which RNA genes encoded RNA catalysts. Current gaps in our conceptual framework of early genetic systems make it difficult to imagine how a stable RNA genome may have functioned and how the transition to a DNA genome could have taken place. Here we use the single-celled ciliate, Oxytricha, as an analog to some of the genetic and genomic traits that may have been present in organisms before and during the establishment of a DNA genome. Oxytricha and its close relatives have a unique genome architecture involving two differentiated nuclei, one of which encodes the genome on small, linear nanochromosomes. While its unique genomic characteristics are relatively modern, some physiological processes related to the genomes and nuclei of Oxytricha may exemplify primitive states of the developing genetic system.
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Affiliation(s)
- Aaron David Goldman
- Department of Ecology and Evolutionary Biology, Princeton University, Guyot Hall, Princeton, NJ 08544, USA.
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15
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Guacci V, Koshland D. Cohesin-independent segregation of sister chromatids in budding yeast. Mol Biol Cell 2012; 23:729-39. [PMID: 22190734 PMCID: PMC3279399 DOI: 10.1091/mbc.e11-08-0696] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Revised: 12/01/2011] [Accepted: 12/12/2011] [Indexed: 12/02/2022] Open
Abstract
Cohesin generates cohesion between sister chromatids, which enables chromosomes to form bipolar attachments to the mitotic spindle and segregate. Cohesin also functions in chromosome condensation, transcriptional regulation, and DNA damage repair. Here we analyze the role of acetylation in modulating cohesin functions and how it affects budding yeast viability. Previous studies show that cohesion establishment requires Eco1p-mediated acetylation of the cohesin subunit Smc3p at residue K113. Smc3p acetylation was proposed to promote establishment by merely relieving Wpl1p inhibition because deletion of WPL1 bypasses the lethality of an ECO1 deletion (eco1Δ wpl1Δ). We find that little, if any, cohesion is established in eco1Δ wpl1Δ cells, indicating that Eco1p performs a function beyond antagonizing Wpl1p. Cohesion also fails to be established when SMC3 acetyl-mimics (K113Q or K112R,K113Q) are the sole functional SMC3s in cells. These results suggest that Smc3p acetylation levels affect establishment. It is remarkable that, despite their severe cohesion defect, eco1Δ wpl1Δ and smc3-K112R,K113Q strains are viable because a cohesin-independent mechanism enables bipolar attachment and segregation. This alternative mechanism is insufficient for smc3-K113Q strain viability. Smc3-K113Q is defective for condensation, whereas eco1Δ wpl1Δ and smc3-K112R,K113Q strains are competent for condensation. We suggest that Smc3p acetylation and Wpl1p antagonistically regulate cohesin's essential role in condensation.
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Affiliation(s)
- Vincent Guacci
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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16
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Genome engineering in Vibrio cholerae: a feasible approach to address biological issues. PLoS Genet 2012; 8:e1002472. [PMID: 22253612 PMCID: PMC3257285 DOI: 10.1371/journal.pgen.1002472] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Accepted: 11/24/2011] [Indexed: 01/10/2023] Open
Abstract
Although bacteria with multipartite genomes are prevalent, our knowledge of the mechanisms maintaining their genome is very limited, and much remains to be learned about the structural and functional interrelationships of multiple chromosomes. Owing to its bi-chromosomal genome architecture and its importance in public health, Vibrio cholerae, the causative agent of cholera, has become a preferred model to study bacteria with multipartite genomes. However, most in vivo studies in V. cholerae have been hampered by its genome architecture, as it is difficult to give phenotypes to a specific chromosome. This difficulty was surmounted using a unique and powerful strategy based on massive rearrangement of prokaryotic genomes. We developed a site-specific recombination-based engineering tool, which allows targeted, oriented, and reciprocal DNA exchanges. Using this genetic tool, we obtained a panel of V. cholerae mutants with various genome configurations: one with a single chromosome, one with two chromosomes of equal size, and one with both chromosomes controlled by identical origins. We used these synthetic strains to address several biological questions--the specific case of the essentiality of Dam methylation in V. cholerae and the general question concerning bacteria carrying circular chromosomes--by looking at the effect of chromosome size on topological issues. In this article, we show that Dam, RctB, and ParA2/ParB2 are strictly essential for chrII origin maintenance, and we formally demonstrate that the formation of chromosome dimers increases exponentially with chromosome size.
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17
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Zhang D, Sweredoski MJ, Graham RLJ, Hess S, Shan SO. Novel proteomic tools reveal essential roles of SRP and importance of proper membrane protein biogenesis. Mol Cell Proteomics 2011; 11:M111.011585. [PMID: 22030350 DOI: 10.1074/mcp.m111.011585] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The signal recognition particle (SRP), which mediates cotranslational protein targeting to cellular membranes, is universally conserved and essential for bacterial and mammalian cells. However, the current understanding of the role of SRP in cell physiology and pathology is still poor, and the reasons behind its essential role in cell survival remain unclear. Here, we systematically analyzed the consequences of SRP loss in E. coli using time-resolved quantitative proteomic analyses. A series of snapshots of the steady-state and newly synthesized proteome unveiled three stages of cellular responses to SRP depletion, and demonstrated essential roles of SRP in metabolism, membrane potential, and protein and energy homeostasis in both the membrane and cytoplasm. We also identified a group of periplasmic proteins, including key molecular chaperones, whose localization was impaired by the loss of SRP; this and additional results showed that SRP is crucial for protein homeostasis in the bacterial envelope. These results reveal the extensive roles that SRP plays in bacterial physiology, emphasize the importance of proper membrane protein biogenesis, and demonstrate the ability of time-resolved quantitative proteomic analysis to provide new biological insights.
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Affiliation(s)
- Dawei Zhang
- Division of Chemistry and Chemical Engineering, Beckman Institute, California Institute of Technology, Pasadena, California 91125, USA.
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18
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Contribution of SMC (structural maintenance of chromosomes) and SpoIIIE to chromosome segregation in Staphylococci. J Bacteriol 2010; 192:4067-73. [PMID: 20525833 DOI: 10.1128/jb.00010-10] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In contrast to rod-shaped bacteria, little is known about chromosomal maintenance and segregation in the spherical Staphylococcus aureus. The analysis of chromosomal segregation in smc (structural maintenance of chromosomes) and spoIIIE single and double mutants unravels differences in the chromosome dynamics in the spherical staphylococcal cells compared to the model in rods.
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Löwe J, Ellonen A, Allen MD, Atkinson C, Sherratt DJ, Grainge I. Molecular mechanism of sequence-directed DNA loading and translocation by FtsK. Mol Cell 2008; 31:498-509. [PMID: 18722176 DOI: 10.1016/j.molcel.2008.05.027] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2007] [Revised: 03/10/2008] [Accepted: 05/29/2008] [Indexed: 11/17/2022]
Abstract
Dimeric circular chromosomes, formed by recombination between monomer sisters, cannot be segregated to daughter cells at cell division. XerCD site-specific recombination at the Escherichia coli dif site converts these dimers to monomers in a reaction that requires the DNA translocase FtsK. Short DNA sequences, KOPS (GGGNAGGG), which are polarized toward dif in the chromosome, direct FtsK translocation. FtsK interacts with KOPS through a C-terminal winged helix domain gamma. The crystal structure of three FtsKgamma domains bound to 8 bp KOPS DNA demonstrates how three gamma domains recognize KOPS. Using covalently linked dimers of FtsK, we infer that three gamma domains per hexamer are sufficient to recognize KOPS and load FtsK and subsequently activate recombination at dif. During translocation, FtsK fails to recognize an inverted KOPS sequence. Therefore, we propose that KOPS act solely as a loading site for FtsK, resulting in a unidirectionally oriented hexameric motor upon DNA.
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Affiliation(s)
- Jan Löwe
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.
| | - Antti Ellonen
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Mark D Allen
- Centre for Protein Engineering, MRC, Hills Road, Cambridge CB2 0QH, UK
| | - Claire Atkinson
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - David J Sherratt
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Ian Grainge
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
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20
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Yoshida N, Ide K. Plasmid DNA is released from nanosized acicular material surface by low molecular weight oligonucleotides: exogenous plasmid acquisition mechanism for penetration intermediates based on the Yoshida effect. Appl Microbiol Biotechnol 2008; 80:813-21. [PMID: 18704395 DOI: 10.1007/s00253-008-1637-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2008] [Revised: 07/24/2008] [Accepted: 07/30/2008] [Indexed: 10/21/2022]
Abstract
When a colloidal solution consisting of nanosized acicular material and bacterial cells is stimulated with sliding friction at the interface between the hydrogel and interface-forming material where the frictional coefficient increases rapidly, the nanosized acicular material accompanying the bacterial cells forms a penetration intermediate. This effect is known as the Yoshida effect in honor of its discoverer. Through the Yoshida effect, a novel property in which penetration intermediates incorporate exogenous plasmid DNA has been identified. This report proposes a possible mechanism for exogenous plasmid acquisition by penetration intermediates in the Yoshida effect. Escherichia coli cells, pUC18, and chrysotile were used as recipient cells, plasmid DNA, and nanosized acicular material, respectively. Even when repeatedly washing the mixture consisting of pUC18 and chrysotile, transformation efficiency by pUC18 was stable. Accordingly, pUC18 adsorbed onto chrysotile was introduced into recipient E. coli cells. At saturation, the amount of pUC18 adsorbed onto chrysotile was 0.8-1.2 microg/mg. To investigate whether pUC18 adsorbed on chrysotile is replicated by polymerase, polymerase chain reaction (PCR) was carried out with the chrysotile. Amplification of the beta-lactamase gene coded in pUC18, which was adsorbed onto chrysotile, was strongly inhibited. This suggests that DNA adsorbed onto chrysotile is not replicated in vivo. When we searched for substances to release pUC18 adsorbed onto chrysotile, we found that a 300-bp single- or double-stranded segment of DNA releases pUC18 from chrysotile. Competitive adsorption onto chrysotile between double-stranded DNA and pUC18 was then examined through the Yoshida effect. The 310- and 603-bp double-stranded nucleotides caused 50% competitive inhibition at the same molar ratio with pUC18. Hence, the adsorbed region of pUC18 is about 300 bp in length. As the culture period for recipient cells increases, transformation efficiency decreases while the expression levels of small RNA of 300-600 bp also decrease. These results suggest that pUC18 adsorbed onto chrysotile can be released by 300-bp small RNA, replicated by DNA polymerase, and transferred to daughter cells.
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Affiliation(s)
- N Yoshida
- Department of Biochemistry and Applied Biosciences, University of Miyazaki, Kibanadai-Nishi, Miyazaki, Japan.
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21
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22
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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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23
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Pogliano J. The bacterial cytoskeleton. Curr Opin Cell Biol 2008; 20:19-27. [PMID: 18243677 DOI: 10.1016/j.ceb.2007.12.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2007] [Revised: 12/17/2007] [Accepted: 12/18/2007] [Indexed: 11/27/2022]
Abstract
Bacteria contain a complex cytoskeleton that is more diverse than previously thought. Recent research provides insight into how bacterial actins, tubulins, and ParA proteins participate in a variety of cellular processes.
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Affiliation(s)
- Joe Pogliano
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093-0377, USA.
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24
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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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25
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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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26
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Abstract
Insertion sequences (ISs) are the smallest and most frequent transposable elements in prokaryotes where they play an important evolutionary role by promoting gene inactivation and genome plasticity. Their genomic abundance varies by several orders of magnitude for reasons largely unknown and widely speculated. The current availability of hundreds of genomes renders testable many of these hypotheses, notably that IS abundance correlates positively with the frequency of horizontal gene transfer (HGT), genome size, pathogenicity, nonobligatory ecological associations, and human association. We thus reannotated ISs in 262 prokaryotic genomes and tested these hypotheses showing that when using appropriate controls, there is no empirical basis for IS family specificity, pathogenicity, or human association to influence IS abundance or density. HGT seems necessary for the presence of ISs, but cannot alone explain the absence of ISs in more than 20% of the organisms, some of which showing high rates of HGT. Gene transfer is also not a significant determinant of the abundance of IS elements in genomes, suggesting that IS abundance is controlled at the level of transposition and ensuing natural selection and not at the level of infection. Prokaryotes engaging in obligatory associations have fewer ISs when controlled for genome size, but this may be caused by some being sexually isolated. Surprisingly, genome size is the only significant predictor of IS numbers and density. Alone, it explains over 40% of the variance of IS abundance. Because we find that genome size and IS abundance correlate negatively with minimal doubling times, we conclude that selection for rapid replication cannot account for the few ISs found in small genomes. Instead, we show evidence that IS numbers are controlled by the frequency of highly deleterious insertion targets. Indeed, IS abundance increases quickly with genome size, which is the exact inverse trend found for the density of genes under strong selection such as essential genes. Hence, for ISs, the bigger the genome the better.
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Affiliation(s)
- Marie Touchon
- Génétique des Génomes Bactériens, CNRS URA2171, Institut Pasteur, Paris, France.
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27
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Hayes F, Barillà D. Assembling the bacterial segrosome. Trends Biochem Sci 2006; 31:247-50. [PMID: 16584885 DOI: 10.1016/j.tibs.2006.03.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2006] [Revised: 03/07/2006] [Accepted: 03/20/2006] [Indexed: 11/27/2022]
Abstract
Genome segregation in prokaryotes is a highly ordered process that integrates with DNA replication, cytokinesis and other fundamental facets of the bacterial cell cycle. The segrosome is the nucleoprotein complex that mediates DNA segregation in bacteria, its assembly and organization is best understood for plasmid partition. The recent elucidation of structures of the ParB plasmid segregation protein bound to centromeric DNA, and of the tertiary structures of other segregation proteins, are key milestones in the path to deciphering the molecular basis of bacterial DNA segregation.
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Affiliation(s)
- Finbarr Hayes
- Faculty of Life Sciences and Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester M1 7ND, UK.
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28
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Dunning Hotopp JC, Lin M, Madupu R, Crabtree J, Angiuoli SV, Eisen JA, Eisen J, Seshadri R, Ren Q, Wu M, Utterback TR, Smith S, Lewis M, Khouri H, Zhang C, Niu H, Lin Q, Ohashi N, Zhi N, Nelson W, Brinkac LM, Dodson RJ, Rosovitz MJ, Sundaram J, Daugherty SC, Davidsen T, Durkin AS, Gwinn M, Haft DH, Selengut JD, Sullivan SA, Zafar N, Zhou L, Benahmed F, Forberger H, Halpin R, Mulligan S, Robinson J, White O, Rikihisa Y, Tettelin H. Comparative genomics of emerging human ehrlichiosis agents. PLoS Genet 2006; 2:e21. [PMID: 16482227 PMCID: PMC1366493 DOI: 10.1371/journal.pgen.0020021] [Citation(s) in RCA: 341] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2005] [Accepted: 01/09/2006] [Indexed: 11/25/2022] Open
Abstract
Anaplasma (formerly Ehrlichia) phagocytophilum, Ehrlichia chaffeensis, and Neorickettsia (formerly Ehrlichia) sennetsu are intracellular vector-borne pathogens that cause human ehrlichiosis, an emerging infectious disease. We present the complete genome sequences of these organisms along with comparisons to other organisms in the Rickettsiales order. Ehrlichia spp. and Anaplasma spp. display a unique large expansion of immunodominant outer membrane proteins facilitating antigenic variation. All Rickettsiales have a diminished ability to synthesize amino acids compared to their closest free-living relatives. Unlike members of the Rickettsiaceae family, these pathogenic Anaplasmataceae are capable of making all major vitamins, cofactors, and nucleotides, which could confer a beneficial role in the invertebrate vector or the vertebrate host. Further analysis identified proteins potentially involved in vacuole confinement of the Anaplasmataceae, a life cycle involving a hematophagous vector, vertebrate pathogenesis, human pathogenesis, and lack of transovarial transmission. These discoveries provide significant insights into the biology of these obligate intracellular pathogens. Ehrlichiosis is an acute disease that triggers flu-like symptoms in both humans and animals. It is caused by a range of bacteria transmitted by ticks or flukes. Because these bacteria are difficult to culture, however, the organisms are poorly understood. The genomes of three emerging human pathogens causing ehrlichiosis were sequenced. A database was designed to allow the comparison of these three genomes to sixteen other bacteria with similar lifestyles. Analysis from this database reveals new species-specific and disease-specific genes indicating niche adaptations, pathogenic traits, and other features. In particular, one of the organisms contains more than 100 copies of a single gene involved in interactions with the host(s). These comparisons also enabled a reconstruction of the metabolic potential of five representative genomes from these bacteria and their close relatives. With this work, scientists can study these emerging pathogens in earnest.
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29
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Willoughby K, Nettleton PF, Quirie M, Maley MA, Foster G, Toszeghy M, Newell DG. A multiplex polymerase chain reaction to detect and differentiate Campylobacter fetus subspecies fetus and Campylobacter fetus -species venerealis: use on UK isolates of C. fetus and other Campylobacter spp. J Appl Microbiol 2006; 99:758-66. [PMID: 16162226 DOI: 10.1111/j.1365-2672.2005.02680.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
AIMS Subspeciation of Campylobacter fetus subsp. fetus (CFF) and Campylobacter fetus subsp. venerealis (CFV) is important for international animal import regulations. Phenotyping can be unreliable, and genotyping by techniques like pulsed field gel electrophoresis is difficult in routine diagnostic laboratories. A PCR subspeciation technique has been reported [Aust Vet J (1997) 75, 827]; we aimed to develop this PCR and investigate its use on UK C. fetus isolates. METHODS AND RESULTS We augmented the PCR with further primers, and tested 76 isolates of C. fetus and 16 isolates of other Campylobacter spp. PCR failed to correlate well with phenotyping, especially for CFV. We characterized the amplicon of the CFV-specific primers (reported as plasmid derived, but unavailable on the public databases); and predicted a parA gene sequence, anticipated to be plasmid-associated. However, although plasmid isolations from selected CFV isolates demonstrated the presence of several plasmids, there was no correlation between plasmid profile and PCR result. Further, the parA sequence was not detected by PCR in any of the plasmid bands. CONCLUSIONS This PCR is not suitable for subspeciation of C. fetus in the UK. The results suggest that this is a reflection of the presence of an unusual clone of CFV currently present in cattle in this country. SIGNIFICANCE AND IMPACT OF THE STUDY PCR cannot substitute for phenotyping of C. fetus isolates in the UK. The reasons for failure of PCR genotyping may reflect local strains and/or plasmid profiles. Further study is required to better elucidate molecular sub-speciation of C. fetus.
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Affiliation(s)
- K Willoughby
- Moredun Research Institute, Bush Loan, Penicuik, Midlothian, UK.
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30
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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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31
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Wang X, Possoz C, Sherratt DJ. Dancing around the divisome: asymmetric chromosome segregation in Escherichia coli. Genes Dev 2005; 19:2367-77. [PMID: 16204186 PMCID: PMC1240045 DOI: 10.1101/gad.345305] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
By simultaneously tracking pairs of specific genetic regions and divisome proteins in live Escherichia coli, we develop a new scheme for the relationship between DNA replication-segregation, chromosome organization, and cell division. A remarkable asymmetric pattern of segregation of different loci in the replication termination region (ter) suggests that individual replichores segregate to distinct nucleoid positions, consistent with an asymmetric segregation of leading and lagging strand templates after replication. Cells growing with a generation time of 100 min are born with a nonreplicating chromosome and have their origin region close to mid-cell and their ter polar. After replication initiation, the two newly replicated origin regions move away from mid-cell to opposite cell halves. By mid-S phase, FtsZ forms a ring at mid-cell at the time of initiation of nucleoid separation; ter remains polar. In the latter half of S phase, ter moves quickly toward mid-cell. FtsK, which coordinates the late stages of chromosome segregation with cell division, forms a ring coincident with the FtsZ ring as S phase completes, approximately 50 min after its initiation. As ter duplicates at mid-cell, sister nucleoid separation appears complete. After initiation of invagination, the FtsZ ring disassembles, leaving FtsK to complete chromosome segregation and cytokinesis.
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Affiliation(s)
- Xindan Wang
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
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32
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Lim GE, Derman AI, Pogliano J. Bacterial DNA segregation by dynamic SopA polymers. Proc Natl Acad Sci U S A 2005; 102:17658-63. [PMID: 16306264 PMCID: PMC1308903 DOI: 10.1073/pnas.0507222102] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many bacterial plasmids and chromosomes rely on ParA ATPases for proper positioning within the cell and for efficient segregation to daughter cells. Here we demonstrate that the F-plasmid-partitioning protein SopA polymerizes into filaments in an ATP-dependent manner in vitro, and that the filaments elongate at a rate that is similar to that of plasmid separation in vivo. We show that SopA is a dynamic protein within the cell, undergoing cycles of polymerization and depolymerization, and shuttling back and forth between nucleoprotein complexes that are composed of the SopB protein bound to sopC-containing plasmids (SopB/sopC). The dynamic behavior of SopA is critical for Sop-mediated plasmid DNA segregation; mutations that lock SopA into a static polymer in the cell inhibit plasmid segregation. We show that SopA colocalizes with SopB/sopC in the cell and that SopB/sopC nucleates the assembly of SopA and is required for its dynamic behavior. When SopA is polymerized in vitro in the presence of SopB and sopC-containing DNA, SopA filaments emanate from the plasmid DNA in radial asters. We propose a mechanism in which plasmid separation is driven by the polymerization of SopA, and we speculate that the radial assembly of SopA polymers is responsible for positioning plasmids both before and after segregation.
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Affiliation(s)
- Grace E Lim
- Division of Biological Sciences, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0377, USA
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33
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Bannikova S, Zorov DB, Shoeman RL, Tolstonog GV, Traub P. Stability and Association with the Cytomatrix of Mitochondrial DNA in Spontaneously Immortalized Mouse Embryo Fibroblasts Containing or Lacking the Intermediate Filament Protein Vimentin. DNA Cell Biol 2005; 24:710-35. [PMID: 16274293 DOI: 10.1089/dna.2005.24.710] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To extend previous observations demonstrating differences in number, morphology, and activity of mitochondria in spontaneously immortalized vim(+) and vim(-) fibroblasts derived from wild-type and vimentin knockout mice, some structural and functional aspects of mitochondrial genome performance and integrity in both types of cells were investigated. Primary Vim(+/+) and Vim(-/-) fibroblasts, which escaped terminal differentiation by immortalization were characterized by an almost twofold lower mtDNA content in comparison to that of their primary precursor cells, whereby the average mtDNA copy number in two clones of vim(+) cells was lower by a factor of 0.6 than that in four clones of vim(-) cells. However, during serial subcultivation up to high passage numbers, the vim(+) and vim() fibroblasts increased their mtDNA copy number 1.5- and 2.5-fold, respectively. While early-passage cells of the vim(+) and vim(-) fibroblast clones differed only slightly in the ratio between mtDNA content and mitochondrial mass represented by mtHSP70 protein, after ca. 300 population doublings the average mtDNA/mtmass ratio in the vim(+) and vim() cells was increased by a factor of 2 and 4.5, respectively. During subcultivation, both types of cells acquired the fully transformed phenotype. These findings suggest that cytoskeletal vimentin filaments exert a strong influence on the mechanisms controlling mtDNA copy number during serial subcultivation of immortalized mouse embryo fibroblasts, and that vimentin deficiency causes a disproportionately enhanced mtDNA content in high-passage vim(-) fibroblasts. Such a role of vimentin filaments was supported by the stronger retention potential for mtDNA and mtDNA polymerase (gamma) detected in vim(+) fibroblasts by Triton X-100 extraction of mitochondria and agaroseembedded cells. Moreover, although the vim(+) and vim(-) fibroblasts were equally active in generating free radicals, the vim(-) cells exhibited higher levels of immunologically detectable 8-oxoG and mismatch repair proteins MSH2 and MLH1 in their mitochondria. Because in vim(-) fibroblasts only one point mutation was detected in the mtDNA D-loop control region, these cells are apparently able to efficiently remove oxidatively damaged nucleobases. On the other hand, a number of large-scale mtDNA deletions were found in high-passage vim(-) fibroblasts, but not in low-passage vim(-) cells and vim(+) cells of both low and high passage. Large mtDNA deletions were also induced in young vim(-) fibroblasts by treatment with the DNA intercalator ethidium bromide, whereas no such deletions were found after treatment of vim(+) cells. These results indicate that in immortalized vim(-) fibroblasts the mitochondrial genome is prone to large-scale rearrangements, probably due to insufficient control of mtDNA repair and recombination processes in the absence of vimentin.
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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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35
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Zhao J, Lambowitz AM. A bacterial group II intron-encoded reverse transcriptase localizes to cellular poles. Proc Natl Acad Sci U S A 2005; 102:16133-40. [PMID: 16186487 PMCID: PMC1283441 DOI: 10.1073/pnas.0507057102] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Lactococcus lactis Ll.LtrB group II intron encodes a reverse transcriptase (LtrA protein) that binds the intron RNA to promote RNA splicing and intron mobility. Here, we used LtrA-GFP fusions and immunofluorescence microscopy to show that LtrA localizes to cellular poles in Escherichia coli and Lactococcus lactis. This polar localization occurs with or without coexpression of Ll.LtrB intron RNA, is observed over a wide range of cellular growth rates and expression levels, and is independent of replication origin function. The same localization pattern was found for three nonoverlapping LtrA subsegments, possibly reflecting dependence on common redundant signals and/or protein physical properties. When coexpressed in E. coli, LtrA interferes with the polar localization of the Shigella IcsA protein, which mediates polarized actin tail assembly, suggesting competition for a common localization determinant. The polar localization of LtrA could account for the preferential insertion of the Ll.LtrB intron in the origin and terminus regions of the E. coli chromosome, may facilitate access to exposed DNA in these regions, and could potentially link group II intron mobility to the host DNA replication and/or cell division machinery.
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Affiliation(s)
- Junhua Zhao
- Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry, and Section of Molecular Genetics and Microbiology, University of Texas, Austin, TX 78712, USA
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36
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Hashimoto M, Ichimura T, Mizoguchi H, Tanaka K, Fujimitsu K, Keyamura K, Ote T, Yamakawa T, Yamazaki Y, Mori H, Katayama T, Kato JI. Cell size and nucleoid organization of engineered Escherichia coli cells with a reduced genome. Mol Microbiol 2005; 55:137-49. [PMID: 15612923 DOI: 10.1111/j.1365-2958.2004.04386.x] [Citation(s) in RCA: 202] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The minimization of a genome is necessary to identify experimentally the minimal gene set that contains only those genes that are essential and sufficient to sustain a functioning cell. Recent developments in genetic techniques have made it possible to generate bacteria with a markedly reduced genome. We developed a simple system for formation of markerless chromosomal deletions, and constructed and characterized a series of large-scale chromosomal deletion mutants of Escherichia coli that lack between 2.4 and 29.7% of the parental chromosome. Combining deletion mutations changes cell length and width, and the mutant cells with larger deletions were even longer and wider than the parental cells. The nucleoid organization of the mutants is also changed: the nucleoids occur as multiple small nucleoids and are localized peripherally near the envelope. Inhibition of translation causes them to condense into one or two packed nucleoids, suggesting that the coupling of transcription and translation of membrane proteins peripherally localizes chromosomes. Because these phenotypes are similar to those of spherical cells, those may be a consequence of the morphological change. Based on the nucleoid localization observed with these mutants, we discuss the cellular nucleoid dynamics.
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Affiliation(s)
- Masayuki Hashimoto
- Department of Biology, Graduate School of Science, Tokyo Metropolitan University, Minamiohsawa, Hachioji, Tokyo, Japan
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37
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Abstract
The importance of the cell membrane in bacterial chromosomal replication continues to emerge. Recent advances include better definition of the biochemical interaction between membrane acidic phospholipids and the replication initiator, DnaA protein, the physiological impact that an altered membrane lipid composition has on chromosomal replication and the identification and characterization of recently identified membrane-associated proteins that regulate replication and participate in chromosomal segregation.
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Affiliation(s)
- Kelly Boeneman
- Department of Biochemistry, Georgetown University Medical Center, 3900 Reservoir Road, Basic Science Building, Washington DC, 20007, USA
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38
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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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39
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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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40
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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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41
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Abstract
The ParA family protein Soj appears to negatively regulate sporulation in Bacillus subtilis by inhibiting transcription from promoters that are activated by phosphorylated Spo0A. We tested in vitro Soj inhibition of Spo0A-independent variants of a promoter that Soj inhibited (PspoIIG). Transcription from the variants was less sensitive to Soj inhibition, suggesting that inhibition of wild-type PspoIIG was linked to transcription activation by Spo0A.
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Affiliation(s)
- Brett N McLeod
- Department of Microbiology and Immunology, University of British Columbia, 6174 University Blvd., Vancouver, British Columbia V6T 1Z3, Canada.
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42
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Egan ES, Fogel MA, Waldor MK. MicroReview: Divided genomes: negotiating the cell cycle in prokaryotes with multiple chromosomes. Mol Microbiol 2005; 56:1129-38. [PMID: 15882408 DOI: 10.1111/j.1365-2958.2005.04622.x] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Historically, the prokaryotic genome was assumed to consist of a single circular replicon. However, as more microbial genome sequencing projects are completed, it is becoming clear that multipartite genomes comprised of more than one chromosome are not unusual among prokaryotes. Chromosomes are distinguished from plasmids by the presence of essential genes as well as characteristic cell cycle-linked replication kinetics; unlike plasmids, chromosomes initiate replication once per cell cycle. The existence of multipartite prokaryotic genomes raises several questions regarding how multiple chromosomes are replicated and segregated during the cell cycle. These divided genomes also introduce questions regarding chromosome evolution and genome stability. In this review, we discuss these and other issues, with particular emphasis on the cholera pathogen Vibrio cholerae.
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Affiliation(s)
- Elizabeth S Egan
- Genetics Program, Tufts University School of Medicine and Howard Hughes Medical Institute, 136 Harrison Ave, Boston, MA 02111, USA
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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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44
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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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45
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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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Abstract
Bacterial plasmids of low copy number, P1 prophage among them, are actively partitioned to nascent daughter cells. The process is typically mediated by a pair of plasmid-encoded proteins and a cis-acting DNA site or cluster of sites, referred to as the plasmid centromere. P1 ParB protein, which binds to the P1 centromere (parS), can spread for several kilobases along flanking DNA. We argue that studies of mutant ParB that demonstrated a strong correlation between spreading capacity and the ability to engage in partitioning may be misleading, and describe here a critical test of the dependence of partitioning on the spreading of the wild-type protein. Physical constraints imposed on the spreading of P1 ParB were found to have only a minor, but reproducible, effect on partitioning. We conclude that, whereas extensive ParB spreading is not required for partitioning, spreading may have an auxiliary role in the process.
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Affiliation(s)
- Oleg Rodionov
- Laboratory of Biochemistry, National Cancer Institute, NIH, Bldg 37, Room 6044C, 37 Convent Drive, Bethesda, MD 20892-4255, USA
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Viollier PH, Thanbichler M, McGrath PT, West L, Meewan M, McAdams HH, Shapiro L. Rapid and sequential movement of individual chromosomal loci to specific subcellular locations during bacterial DNA replication. Proc Natl Acad Sci U S A 2004; 101:9257-62. [PMID: 15178755 PMCID: PMC438963 DOI: 10.1073/pnas.0402606101] [Citation(s) in RCA: 318] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The chromosomal origin and terminus of replication are precisely localized in bacterial cells. We examined the cellular position of 112 individual loci that are dispersed over the circular Caulobacter crescentus chromosome and found that in living cells each locus has a specific subcellular address and that these loci are arrayed in linear order along the long axis of the cell. Time-lapse microscopy of the location of the chromosomal origin and 10 selected loci in the origin-proximal half of the chromosome showed that during DNA replication, as the replisome sequentially copies each locus, the newly replicated DNA segments are moved in chronological order to their final subcellular destination in the nascent half of the predivisional cell. Thus, the remarkable organization of the chromosome is being established while DNA replication is still in progress. The fact that the movement of these 10 loci is, like that of the origin, directed and rapid, and occurs at a similar rate, suggests that the same molecular machinery serves to partition and place many, if not most, chromosomal loci at defined subcellular sites.
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Affiliation(s)
- Patrick H Viollier
- Department of Developmental Biology, Beckman Center, Stanford University School of Medicine, Stanford, CA 94305, USA
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Lai EM, Nair U, Phadke ND, Maddock JR. Proteomic screening and identification of differentially distributed membrane proteins in Escherichia coli. Mol Microbiol 2004; 52:1029-44. [PMID: 15130122 DOI: 10.1111/j.1365-2958.2004.04040.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacteria show asymmetric subcellular distribution of many proteins involved in diverse cellular processes such as chemotaxis, motility, actin polymerization, chromosome partitioning and cell division. In many cases, the specific subcellular localization of these proteins is critical for proper regulation and function. Although cellular organization of the bacterial cell clearly plays an important role in cell physiology, systematic studies to uncover asymmetrically distributed proteins have not been reported previously. In this study, we undertook a proteomics approach to uncover polar membrane proteins in Escherichia coli. We identified membrane proteins enriched in E. coli minicells using a combination of two-dimensional electrophoresis and mass spectrometry. Among a total of 173 membrane protein spots that were consistently detected, 36 spots were enriched in minicell membranes, whereas 15 spots were more abundant in rod cell membranes. The minicell-enriched proteins included the inner membrane proteins MCPs, AtpA, AtpB, YiaF and AcrA, the membrane-associated FtsZ protein and the outer membrane proteins YbhC, OmpW, Tsx, Pal, FadL, OmpT and BtuB. We immunolocalized two of the minicell-enriched proteins, OmpW and YiaF, and showed that OmpW is a bona fide polar protein whereas YiaF displays a patchy membrane distribution with a polar and septal bias.
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Affiliation(s)
- Erh-Min Lai
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 North University, Ann Arbor, MI 48109, USA
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Abstract
In bacteria, chromosome segregation and DNA replication occur concurrently and there is no clear equivalent of a eukaryote mitotic spindle. Chromosome segregation can be viewed as a two-step process. As the first step, the origin of replication regions are segregated actively, probably by a mechanism involving an as yet unidentified motor protein or proteins, and held in position. The second step is the separation and migration of the rest of the chromosome probably driven by forces generated from various cellular processes such as DNA replication, transcription and transertion.
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Affiliation(s)
- Ling Juan Wu
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
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Abstract
It is now clear that bacterial chromosomes rapidly separate in a manner independent of cell elongation, suggesting the existence of a mitotic apparatus in bacteria. Recent studies of bacterial cells reveal filamentous structures similar to the eukaryotic cytoskeleton, proteins that mediate polar chromosome anchoring during Bacillus subtilis sporulation, and SMC interacting proteins that are involved in chromosome condensation. A picture is thereby developing of how bacterial chromosomes are organized within the cell, how they are separated following duplication, and how these processes are coordinated with the cell cycle.
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Affiliation(s)
- Kit Pogliano
- Division of Biological Sciences, 9500 Gilman Drive, University of California-San Diego, La Jolla, CA 92093-0349, USA.
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