51
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Oligomerization and ATP stimulate condensin-mediated DNA compaction. Sci Rep 2017; 7:14279. [PMID: 29079757 PMCID: PMC5660149 DOI: 10.1038/s41598-017-14701-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 10/16/2017] [Indexed: 11/09/2022] Open
Abstract
Large-scale chromatin remodeling during mitosis is catalyzed by a heteropentameric enzyme known as condensin. The DNA-organizing mechanism of condensin depends on the energy of ATP hydrolysis but how this activity specifically promotes proper compaction and segregation of chromosomes during mitosis remains poorly understood. Purification of budding yeast condensin reveals that it occurs not only in the classical heteropentameric "monomer" form, but that it also adopts much larger configurations consistent with oligomerization. We use a single-DNA magnetic tweezers assay to study compaction of DNA by yeast condensin, with the result that only the multimer shows ATP-enhanced DNA-compaction. The compaction reaction involves step-like events of 200 nm (600 bp) size and is strongly suppressed by forces above 1 pN, consistent with a loop-capture mechanism for initial binding and compaction. The compaction reactions are largely insensitive to DNA torsional stress. Our results suggest a physiological role for oligomerized condensin in driving gradual chromatin compaction by step-like and slow "creeping" dynamics consistent with a loop-extrusion mechanism.
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52
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Wang X, Brandão HB, Le TBK, Laub MT, Rudner DZ. Bacillus subtilis SMC complexes juxtapose chromosome arms as they travel from origin to terminus. Science 2017; 355:524-527. [PMID: 28154080 DOI: 10.1126/science.aai8982] [Citation(s) in RCA: 196] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 01/05/2017] [Indexed: 01/18/2023]
Abstract
Structural maintenance of chromosomes (SMC) complexes play critical roles in chromosome dynamics in virtually all organisms, but how they function remains poorly understood. In the bacterium Bacillus subtilis, SMC-condensin complexes are topologically loaded at centromeric sites adjacent to the replication origin. Here we provide evidence that these ring-shaped assemblies tether the left and right chromosome arms together while traveling from the origin to the terminus (>2 megabases) at rates >50 kilobases per minute. Condensin movement scales linearly with time, providing evidence for an active transport mechanism. These data support a model in which SMC complexes function by processively enlarging DNA loops. Loop formation followed by processive enlargement provides a mechanism by which condensin complexes compact and resolve sister chromatids in mitosis and by which cohesin generates topologically associating domains during interphase.
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Affiliation(s)
- Xindan Wang
- Department of Microbiology and Immunobiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
| | - Hugo B Brandão
- Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138, USA
| | - Tung B K Le
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael T Laub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David Z Rudner
- Department of Microbiology and Immunobiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
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53
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Diebold-Durand ML, Lee H, Ruiz Avila LB, Noh H, Shin HC, Im H, Bock FP, Bürmann F, Durand A, Basfeld A, Ham S, Basquin J, Oh BH, Gruber S. Structure of Full-Length SMC and Rearrangements Required for Chromosome Organization. Mol Cell 2017; 67:334-347.e5. [PMID: 28689660 PMCID: PMC5526789 DOI: 10.1016/j.molcel.2017.06.010] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 05/03/2017] [Accepted: 06/09/2017] [Indexed: 01/09/2023]
Abstract
Multi-subunit SMC complexes control chromosome superstructure and promote chromosome disjunction, conceivably by actively translocating along DNA double helices. SMC subunits comprise an ABC ATPase "head" and a "hinge" dimerization domain connected by a 49 nm coiled-coil "arm." The heads undergo ATP-dependent engagement and disengagement to drive SMC action on the chromosome. Here, we elucidate the architecture of prokaryotic Smc dimers by high-throughput cysteine cross-linking and crystallography. Co-alignment of the Smc arms tightly closes the interarm space and misaligns the Smc head domains at the end of the rod by close apposition of their ABC signature motifs. Sandwiching of ATP molecules between Smc heads requires them to substantially tilt and translate relative to each other, thereby opening up the Smc arms. We show that this mechanochemical gating reaction regulates chromosome targeting and propose a mechanism for DNA translocation based on the merging of DNA loops upon closure of Smc arms.
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Affiliation(s)
- Marie-Laure Diebold-Durand
- Chromosome Organisation and Dynamics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany; Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, 1015 Lausanne, Switzerland
| | - Hansol Lee
- Department of Biological Sciences, KAIST Institute for the Biocentury, Cancer Metastasis Control Center, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea
| | - Laura B Ruiz Avila
- Chromosome Organisation and Dynamics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Haemin Noh
- Department of Biological Sciences, KAIST Institute for the Biocentury, Cancer Metastasis Control Center, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea
| | - Ho-Chul Shin
- Department of Biological Sciences, KAIST Institute for the Biocentury, Cancer Metastasis Control Center, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea
| | - Haeri Im
- Department of Chemistry, Sookmyung Women's University, Cheongpa-ro-47-gil 100, Yongsan-ku, Seoul 04310, Korea
| | - Florian P Bock
- Chromosome Organisation and Dynamics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany; Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, 1015 Lausanne, Switzerland
| | - Frank Bürmann
- Chromosome Organisation and Dynamics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Alexandre Durand
- Chromosome Organisation and Dynamics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany; Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, 1015 Lausanne, Switzerland
| | - Alrun Basfeld
- Chromosome Organisation and Dynamics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Sihyun Ham
- Department of Chemistry, Sookmyung Women's University, Cheongpa-ro-47-gil 100, Yongsan-ku, Seoul 04310, Korea
| | - Jérôme Basquin
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Byung-Ha Oh
- Department of Biological Sciences, KAIST Institute for the Biocentury, Cancer Metastasis Control Center, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea.
| | - Stephan Gruber
- Chromosome Organisation and Dynamics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany; Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, 1015 Lausanne, Switzerland.
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54
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Chromosome segregation drives division site selection in Streptococcus pneumoniae. Proc Natl Acad Sci U S A 2017; 114:E5959-E5968. [PMID: 28674002 DOI: 10.1073/pnas.1620608114] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Accurate spatial and temporal positioning of the tubulin-like protein FtsZ is key for proper bacterial cell division. Streptococcus pneumoniae (pneumococcus) is an oval-shaped, symmetrically dividing opportunistic human pathogen lacking the canonical systems for division site control (nucleoid occlusion and the Min-system). Recently, the early division protein MapZ was identified and implicated in pneumococcal division site selection. We show that MapZ is important for proper division plane selection; thus, the question remains as to what drives pneumococcal division site selection. By mapping the cell cycle in detail, we show that directly after replication both chromosomal origin regions localize to the future cell division sites, before FtsZ. Interestingly, Z-ring formation occurs coincidently with initiation of DNA replication. Perturbing the longitudinal chromosomal organization by mutating the condensin SMC, by CRISPR/Cas9-mediated chromosome cutting, or by poisoning DNA decatenation resulted in mistiming of MapZ and FtsZ positioning and subsequent cell elongation. Together, we demonstrate an intimate relationship between DNA replication, chromosome segregation, and division site selection in the pneumococcus, providing a simple way to ensure equally sized daughter cells.
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55
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Gruber S. Shaping chromosomes by DNA capture and release: gating the SMC rings. Curr Opin Cell Biol 2017; 46:87-93. [PMID: 28460277 DOI: 10.1016/j.ceb.2017.04.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 04/05/2017] [Accepted: 04/07/2017] [Indexed: 11/22/2022]
Abstract
SMC proteins organize chromosomes to coordinate essential nuclear processes such as gene expression and DNA recombination as well as to segregate chromosomes during cell division. SMC mediated DNA bridging keeps sister chromatids aligned for much of the cell cycle, while the active extrusion of DNA loops by SMC presumably compacts chromosomes. Chromosome superstructure is thus given by the number of DNA linkages and the size of chromosomal DNA loops, which in turn depend on the dynamics of SMC loading and unloading. The latter is regulated by the intrinsic SMC ATPase activity, multiple external factors and post-translational modification. Here, I highlight recent advances in our understanding of DNA capture and release by SMC-with a focus on cohesin.
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Affiliation(s)
- Stephan Gruber
- Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, 1015 Lausanne, Switzerland.
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56
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Wuchty S, Rajagopala SV, Blazie SM, Parrish JR, Khuri S, Finley RL, Uetz P. The Protein Interactome of Streptococcus pneumoniae and Bacterial Meta-interactomes Improve Function Predictions. mSystems 2017; 2:e00019-17. [PMID: 28744484 PMCID: PMC5513735 DOI: 10.1128/msystems.00019-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 05/11/2017] [Indexed: 01/01/2023] Open
Abstract
The functions of roughly a third of all proteins in Streptococcus pneumoniae, a significant human-pathogenic bacterium, are unknown. Using a yeast two-hybrid approach, we have determined more than 2,000 novel protein interactions in this organism. We augmented this network with meta-interactome data that we defined as the pool of all interactions between evolutionarily conserved proteins in other bacteria. We found that such interactions significantly improved our ability to predict a protein's function, allowing us to provide functional predictions for 299 S. pneumoniae proteins with previously unknown functions. IMPORTANCE Identification of protein interactions in bacterial species can help define the individual roles that proteins play in cellular pathways and pathogenesis. Very few protein interactions have been identified for the important human pathogen S. pneumoniae. We used an experimental approach to identify over 2,000 new protein interactions for S. pneumoniae, the most extensive interactome data for this bacterium to date. To predict protein function, we used our interactome data augmented with interactions from other closely related bacteria. The combination of the experimental data and meta-interactome data significantly improved the prediction results, allowing us to assign possible functions to a large number of poorly characterized proteins.
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Affiliation(s)
- S. Wuchty
- Department of Computer Science, University of Miami, Coral Gables, Florida, USA
- Center for Computational Science, University of Miami, Coral Gables, Florida, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida, USA
- Department of Biology, University of Miami, Coral Gables, Florida, USA
| | | | - S. M. Blazie
- J Craig Venter Institute, Rockville, Maryland, USA
| | - J. R. Parrish
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - S. Khuri
- Department of Computer Science, University of Miami, Coral Gables, Florida, USA
- Center for Computational Science, University of Miami, Coral Gables, Florida, USA
| | - R. L. Finley
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - P. Uetz
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia, USA
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57
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Fisher GLM, Pastrana CL, Higman VA, Koh A, Taylor JA, Butterer A, Craggs T, Sobott F, Murray H, Crump MP, Moreno-Herrero F, Dillingham MS. The structural basis for dynamic DNA binding and bridging interactions which condense the bacterial centromere. eLife 2017; 6:e28086. [PMID: 29244022 PMCID: PMC5731820 DOI: 10.7554/elife.28086] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 12/02/2017] [Indexed: 01/20/2023] Open
Abstract
The ParB protein forms DNA bridging interactions around parS to condense DNA and earmark the bacterial chromosome for segregation. The molecular mechanism underlying the formation of these ParB networks is unclear. We show here that while the central DNA binding domain is essential for anchoring at parS, this interaction is not required for DNA condensation. Structural analysis of the C-terminal domain reveals a dimer with a lysine-rich surface that binds DNA non-specifically and is essential for DNA condensation in vitro. Mutation of either the dimerisation or the DNA binding interface eliminates ParB-GFP foci formation in vivo. Moreover, the free C-terminal domain can rapidly decondense ParB networks independently of its ability to bind DNA. Our work reveals a dual role for the C-terminal domain of ParB as both a DNA binding and bridging interface, and highlights the dynamic nature of ParB networks in Bacillus subtilis.
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Affiliation(s)
- Gemma LM Fisher
- DNA:protein Interactions Unit, School of BiochemistryUniversity of BristolBristolUnited Kingdom
| | - César L Pastrana
- Department of Macromolecular StructuresCentro Nacional de Biotecnologia, Consejo Superior de Investigaciones CientificasMadridSpain
| | | | - Alan Koh
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular BiosciencesNewcastle UniversityNewcastleUnited Kingdom
| | - James A Taylor
- DNA:protein Interactions Unit, School of BiochemistryUniversity of BristolBristolUnited Kingdom
| | - Annika Butterer
- Biomolecular and Analytical Mass Spectrometry Group, Department of ChemistryUniversity of AntwerpAntwerpenBelgium
| | - Timothy Craggs
- Department of ChemistryUniversity of SheffieldSheffieldUnited Kingdom
| | - Frank Sobott
- Biomolecular and Analytical Mass Spectrometry Group, Department of ChemistryUniversity of AntwerpAntwerpenBelgium,Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsUnited Kingdom,School of Molecular and Cellular BiologyUniversity of LeedsLeedsUnited Kingdom
| | - Heath Murray
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular BiosciencesNewcastle UniversityNewcastleUnited Kingdom
| | - Matthew P Crump
- School of ChemistryUniversity of BristolBristolUnited Kingdom
| | - Fernando Moreno-Herrero
- Department of Macromolecular StructuresCentro Nacional de Biotecnologia, Consejo Superior de Investigaciones CientificasMadridSpain
| | - Mark S Dillingham
- DNA:protein Interactions Unit, School of BiochemistryUniversity of BristolBristolUnited Kingdom
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58
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Lagage V, Boccard F, Vallet-Gely I. Regional Control of Chromosome Segregation in Pseudomonas aeruginosa. PLoS Genet 2016; 12:e1006428. [PMID: 27820816 PMCID: PMC5098823 DOI: 10.1371/journal.pgen.1006428] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 10/15/2016] [Indexed: 01/31/2023] Open
Abstract
Chromosome segregation in bacteria occurs concomitantly with DNA replication, and the duplicated regions containing the replication origin oriC are generally the first to separate and migrate to their final specific location inside the cell. In numerous bacterial species, a three-component partition machinery called the ParABS system is crucial for chromosome segregation. This is the case in the gammaproteobacterium Pseudomonas aeruginosa, where impairing the ParABS system is very detrimental for growth, as it increases the generation time and leads to the formation of anucleate cells and to oriC mispositioning inside the cell. In this study, we investigate in vivo the ParABS system in P. aeruginosa. Using chromatin immuno-precipitation coupled with high throughput sequencing, we show that ParB binds to four parS site located within 15 kb of oriC in vivo, and that this binding promotes the formation of a high order nucleoprotein complex. We show that one parS site is enough to prevent anucleate cell formation, therefore for correct chromosome segregation. By displacing the parS site from its native position on the chromosome, we demonstrate that parS is the first chromosomal locus to be separated upon DNA replication, which indicates that it is the site of force exertion of the segregation process. We identify a region of approximatively 650 kb surrounding oriC in which the parS site must be positioned for chromosome segregation to proceed correctly, and we called it “competence zone” of the parS site. Mutant strains that have undergone specific genetic rearrangements allow us to propose that the distance between oriC and parS defines this “competence zone”. Implications for the control of chromosome segregation in P. aeruginosa are discussed. Accurate transmission of the genetic information relies on replication and segregation, two processes essential to all living organisms. In bacteria, these processes occur concomitantly. Replication of the bacterial circular chromosome initiates at a single specific sequence called oriC, and proceed bi-directionally along the chromosome arms. A partition system called ParABS is involved in chromosome segregation in many bacteria. It involves the binding of the ParB protein to parS sequences, which are often found in the close vicinity of oriC. The importance of this system for chromosome segregation varies according to species, ranging from essential to dispensable. In Pseudomonas aeruginosa, an important opportunistic pathogen, the ParABS system plays an important role in chromosome segregation, as mutants affected in this system present a severe growth defect as well as anucleate cells formation, but is not essential. In this study, we characterize the activity of the different determinants of the ParABS system in P. aeruginosa and demonstrate that it is critical for the parS site to be located close to oriC, which suggest that the timing of separation of regions close to oriC after replication is important, and that it could be a function of the ParABS system to keep this timing.
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Affiliation(s)
- Valentine Lagage
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette cedex, France
| | - Frédéric Boccard
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette cedex, France
- * E-mail: (IVG); (FB)
| | - Isabelle Vallet-Gely
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette cedex, France
- * E-mail: (IVG); (FB)
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59
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Abstract
Bacillus subtilis is one of the best-studied organisms. Due to the broad knowledge and annotation and the well-developed genetic system, this bacterium is an excellent starting point for genome minimization with the aim of constructing a minimal cell. We have analyzed the genome of B. subtilis and selected all genes that are required to allow life in complex medium at 37°C. This selection is based on the known information on essential genes and functions as well as on gene and protein expression data and gene conservation. The list presented here includes 523 and 119 genes coding for proteins and RNAs, respectively. These proteins and RNAs are required for the basic functions of life in information processing (replication and chromosome maintenance, transcription, translation, protein folding, and secretion), metabolism, cell division, and the integrity of the minimal cell. The completeness of the selected metabolic pathways, reactions, and enzymes was verified by the development of a model of metabolism of the minimal cell. A comparison of the MiniBacillus genome to the recently reported designed minimal genome of Mycoplasma mycoides JCVI-syn3.0 indicates excellent agreement in the information-processing pathways, whereas each species has a metabolism that reflects specific evolution and adaptation. The blueprint of MiniBacillus presented here serves as the starting point for a successive reduction of the B. subtilis genome.
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60
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Abstract
If fully stretched out, a typical bacterial chromosome would be nearly 1 mm long, approximately 1,000 times the length of a cell. Not only must cells massively compact their genetic material, but they must also organize their DNA in a manner that is compatible with a range of cellular processes, including DNA replication, DNA repair, homologous recombination, and horizontal gene transfer. Recent work, driven in part by technological advances, has begun to reveal the general principles of chromosome organization in bacteria. Here, drawing on studies of many different organisms, we review the emerging picture of how bacterial chromosomes are structured at multiple length scales, highlighting the functions of various DNA-binding proteins and the impact of physical forces. Additionally, we discuss the spatial dynamics of chromosomes, particularly during their segregation to daughter cells. Although there has been tremendous progress, we also highlight gaps that remain in understanding chromosome organization and segregation.
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61
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Duan Y, Huey JD, Herman JK. The DnaA inhibitor SirA acts in the same pathway as Soj (ParA) to facilitateoriCsegregation duringBacillus subtilissporulation. Mol Microbiol 2016; 102:530-544. [DOI: 10.1111/mmi.13477] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2016] [Indexed: 01/18/2023]
Affiliation(s)
- Yi Duan
- Department of Biochemistry and Biophysics; Texas A&M University; College Station TX USA
| | - Jack D. Huey
- Department of Biochemistry and Biophysics; Texas A&M University; College Station TX USA
| | - Jennifer K. Herman
- Department of Biochemistry and Biophysics; Texas A&M University; College Station TX USA
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62
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Shao Q, Trinh JT, McIntosh CS, Christenson B, Balázsi G, Zeng L. Lysis-lysogeny coexistence: prophage integration during lytic development. Microbiologyopen 2016; 6. [PMID: 27530202 PMCID: PMC5300877 DOI: 10.1002/mbo3.395] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 06/30/2016] [Indexed: 11/11/2022] Open
Abstract
The infection of Escherichia coli cells by bacteriophage lambda results in bifurcated means of propagation, where the phage decides between the lytic and lysogenic pathways. Although traditionally thought to be mutually exclusive, increasing evidence suggests that this lysis-lysogeny decision is more complex than once believed, but exploring its intricacies requires an improved resolution of study. Here, with a newly developed fluorescent reporter system labeling single phage and E. coli DNAs, these two distinct pathways can be visualized by following the DNA movements in vivo. Surprisingly, we frequently observed an interesting "lyso-lysis" phenomenon in lytic cells, where phage integrates its DNA into the host, a characteristic event of the lysogenic pathway, followed by cell lysis. Furthermore, the frequency of lyso-lysis increases with the number of infecting phages, and specifically, with CII activity. Moreover, in lytic cells, the integration site attB on the E. coli genome migrates toward the polar region over time, leading to more spatial overlap with the phage DNA and frequent colocalization/collision of attB and phage DNA, possibly contributing to a higher chance for DNA integration.
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Affiliation(s)
- Qiuyan Shao
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA.,Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - Jimmy T Trinh
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA.,Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - Colby S McIntosh
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Brita Christenson
- Department of Biology and Biochemistry, University of Northwestern - St. Paul, St. Paul, Minnesota, USA
| | - Gábor Balázsi
- Laufer Center for Physical & Quantitative Biology, Stony Brook University, Stony Brook, New York, USA.,Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York, USA
| | - Lanying Zeng
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA.,Center for Phage Technology, Texas A&M University, College Station, Texas, USA
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63
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Comparative Genomics of Interreplichore Translocations in Bacteria: A Measure of Chromosome Topology? G3-GENES GENOMES GENETICS 2016; 6:1597-606. [PMID: 27172194 PMCID: PMC4889656 DOI: 10.1534/g3.116.028274] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Genomes evolve not only in base sequence but also in terms of their architecture, defined by gene organization and chromosome topology. Whereas genome sequence data inform us about the changes in base sequences for a large variety of organisms, the study of chromosome topology is restricted to a few model organisms studied using microscopy and chromosome conformation capture techniques. Here, we exploit whole genome sequence data to study the link between gene organization and chromosome topology in bacteria. Using comparative genomics across ∼250 pairs of closely related bacteria we show that: (a) many organisms show a high degree of interreplichore translocations throughout the chromosome and not limited to the inversion-prone terminus (ter) or the origin of replication (oriC); (b) translocation maps may reflect chromosome topologies; and (c) symmetric interreplichore translocations do not disrupt the distance of a gene from oriC or affect gene expression states or strand biases in gene densities. In summary, we suggest that translocation maps might be a first line in defining a gross chromosome topology given a pair of closely related genome sequences.
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64
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65
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Connecting the dots of the bacterial cell cycle: Coordinating chromosome replication and segregation with cell division. Semin Cell Dev Biol 2016; 53:2-9. [DOI: 10.1016/j.semcdb.2015.11.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 11/26/2015] [Indexed: 12/20/2022]
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66
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Tsabar M, Haase J, Harrison B, Snider CE, Eldridge B, Kaminsky L, Hine RM, Haber JE, Bloom K. A Cohesin-Based Partitioning Mechanism Revealed upon Transcriptional Inactivation of Centromere. PLoS Genet 2016; 12:e1006021. [PMID: 27128635 PMCID: PMC4851351 DOI: 10.1371/journal.pgen.1006021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 04/08/2016] [Indexed: 12/24/2022] Open
Abstract
Transcriptional inactivation of the budding yeast centromere has been a widely used tool in studies of chromosome segregation and aneuploidy. In haploid cells when an essential chromosome contains a single conditionally inactivated centromere (GAL-CEN), cell growth rate is slowed and segregation fidelity is reduced; but colony formation is nearly 100%. Pedigree analysis revealed that only 30% of the time both mother and daughter cell inherit the GAL-CEN chromosome. The reduced segregation capacity of the GAL-CEN chromosome is further compromised upon reduction of pericentric cohesin (mcm21∆), as reflected in a further diminishment of the Mif2 kinetochore protein at GAL-CEN. By redistributing cohesin from the nucleolus to the pericentromere (by deleting SIR2), there is increased presence of the kinetochore protein Mif2 at GAL-CEN and restoration of cell viability. These studies identify the ability of cohesin to promote chromosome segregation via kinetochore assembly, in a situation where the centromere has been severely compromised.
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Affiliation(s)
- Michael Tsabar
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Julian Haase
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Benjamin Harrison
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Chloe E. Snider
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Brittany Eldridge
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Lila Kaminsky
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Rebecca M. Hine
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - James E. Haber
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Kerry Bloom
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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67
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Abstract
Condensins are large protein complexes that play a central role in chromosome organization and segregation in the three domains of life. They display highly characteristic, rod-shaped structures with SMC (structural maintenance of chromosomes) ATPases as their core subunits and organize large-scale chromosome structure through active mechanisms. Most eukaryotic species have two distinct condensin complexes whose balanced usage is adapted flexibly to different organisms and cell types. Studies of bacterial condensins provide deep insights into the fundamental mechanisms of chromosome segregation. This Review surveys both conserved features and rich variations of condensin-based chromosome organization and discusses their evolutionary implications.
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Affiliation(s)
- Tatsuya Hirano
- Chromosome Dynamics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
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68
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Minnen A, Bürmann F, Wilhelm L, Anchimiuk A, Diebold-Durand ML, Gruber S. Control of Smc Coiled Coil Architecture by the ATPase Heads Facilitates Targeting to Chromosomal ParB/parS and Release onto Flanking DNA. Cell Rep 2016; 14:2003-16. [PMID: 26904953 PMCID: PMC4785775 DOI: 10.1016/j.celrep.2016.01.066] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 12/22/2015] [Accepted: 01/21/2016] [Indexed: 11/01/2022] Open
Abstract
Smc/ScpAB promotes chromosome segregation in prokaryotes, presumably by compacting and resolving nascent sister chromosomes. The underlying mechanisms, however, are poorly understood. Here, we investigate the role of the Smc ATPase activity in the recruitment of Smc/ScpAB to the Bacillus subtilis chromosome. We demonstrate that targeting of Smc/ScpAB to ParB/parS loading sites is strictly dependent on engagement of Smc head domains and relies on an open organization of the Smc coiled coils. We find that dimerization of the Smc hinge domain stabilizes closed Smc rods and hinders head engagement as well as chromosomal targeting. Conversely, the ScpAB sub-complex promotes head engagement and Smc rod opening and thereby facilitates recruitment of Smc to parS sites. Upon ATP hydrolysis, Smc/ScpAB is released from loading sites and relocates within the chromosome-presumably through translocation along DNA double helices. Our findings define an intermediate state in the process of chromosome organization by Smc.
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Affiliation(s)
- Anita Minnen
- Research Group 'Chromosome Organization and Dynamics', Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Frank Bürmann
- Research Group 'Chromosome Organization and Dynamics', Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Larissa Wilhelm
- Research Group 'Chromosome Organization and Dynamics', Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Anna Anchimiuk
- Research Group 'Chromosome Organization and Dynamics', Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Marie-Laure Diebold-Durand
- Research Group 'Chromosome Organization and Dynamics', Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Stephan Gruber
- Research Group 'Chromosome Organization and Dynamics', Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
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69
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Kim H, Loparo JJ. Multistep assembly of DNA condensation clusters by SMC. Nat Commun 2016; 7:10200. [PMID: 26725510 PMCID: PMC4725763 DOI: 10.1038/ncomms10200] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 11/13/2015] [Indexed: 11/09/2022] Open
Abstract
SMC (structural maintenance of chromosomes) family members play essential roles in chromosome condensation, sister chromatid cohesion and DNA repair. It remains unclear how SMCs structure chromosomes and how their mechanochemical cycle regulates their interactions with DNA. Here we used single-molecule fluorescence microscopy to visualize how Bacillus subtilis SMC (BsSMC) interacts with flow-stretched DNAs. We report that BsSMC can slide on DNA, switching between static binding and diffusion. At higher concentrations, BsSMCs form clusters that condense DNA in a weakly ATP-dependent manner. ATP increases the apparent cooperativity of DNA condensation, demonstrating that BsSMC can interact cooperatively through their ATPase head domains. Consistent with these results, ATPase mutants compact DNA more slowly than wild-type BsSMC in the presence of ATP. Our results suggest that transiently static BsSMC molecules can nucleate the formation of clusters that act to locally condense the chromosome while forming long-range DNA bridges. The Structural Maintenance of Chromosomes (SMC) proteins are essential for chromosome condensation, cohesion and DNA repair. Here the authors use single molecule imaging to visualise how Bacillus subtilis SMC interacts with and condenses DNA.
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Affiliation(s)
- HyeongJun Kim
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Joseph J Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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70
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Palecek JJ, Gruber S. Kite Proteins: a Superfamily of SMC/Kleisin Partners Conserved Across Bacteria, Archaea, and Eukaryotes. Structure 2015; 23:2183-2190. [DOI: 10.1016/j.str.2015.10.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 09/23/2015] [Accepted: 10/01/2015] [Indexed: 10/22/2022]
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71
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Benoist C, Guérin C, Noirot P, Dervyn E. Constitutive Stringent Response Restores Viability of Bacillus subtilis Lacking Structural Maintenance of Chromosome Protein. PLoS One 2015; 10:e0142308. [PMID: 26539825 PMCID: PMC4634966 DOI: 10.1371/journal.pone.0142308] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 10/19/2015] [Indexed: 11/18/2022] Open
Abstract
Bacillus subtilis mutants lacking the SMC-ScpAB complex are severely impaired for chromosome condensation and partitioning, DNA repair, and cells are not viable under standard laboratory conditions. We isolated suppressor mutations that restored the capacity of a smc deletion mutant (Δsmc) to grow under standard conditions. These suppressor mutations reduced chromosome segregation defects and abrogated hypersensitivity to gyrase inhibitors of Δsmc. Three suppressor mutations were mapped in genes involved in tRNA aminoacylation and maturation pathways. A transcriptomic survey of isolated suppressor mutations pointed to a potential link between suppression of Δsmc and induction of the stringent response. This link was confirmed by (p)ppGpp quantification which indicated a constitutive induction of the stringent response in multiple suppressor strains. Furthermore, sublethal concentrations of arginine hydroxamate (RHX), a potent inducer of stringent response, restored growth of Δsmc under non permissive conditions. We showed that production of (p)ppGpp alone was sufficient to suppress the thermosensitivity exhibited by the Δsmc mutant. Our findings shed new light on the coordination between chromosome dynamics mediated by SMC-ScpAB and other cellular processes during rapid bacterial growth.
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Affiliation(s)
- Camille Benoist
- INRA, UMR1319 Micalis, 78350, Jouy-en-Josas, France
- AgroParisTech, UMR Micalis 1319, 78350, Jouy-en-Josas, France
| | - Cyprien Guérin
- Mathématiques et Informatique Appliquées du Génome à l’Environnement, UR1404, INRA, Domaine de Vilvert, 78350, Jouy-en-Josas, France
| | - Philippe Noirot
- INRA, UMR1319 Micalis, 78350, Jouy-en-Josas, France
- AgroParisTech, UMR Micalis 1319, 78350, Jouy-en-Josas, France
| | - Etienne Dervyn
- INRA, UMR1319 Micalis, 78350, Jouy-en-Josas, France
- AgroParisTech, UMR Micalis 1319, 78350, Jouy-en-Josas, France
- * E-mail:
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72
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Wang X, Le TBK, Lajoie BR, Dekker J, Laub MT, Rudner DZ. Condensin promotes the juxtaposition of DNA flanking its loading site in Bacillus subtilis. Genes Dev 2015; 29:1661-75. [PMID: 26253537 PMCID: PMC4536313 DOI: 10.1101/gad.265876.115] [Citation(s) in RCA: 164] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
SMC condensin complexes play a central role in compacting and resolving replicated chromosomes in virtually all organisms, yet how they accomplish this remains elusive. In Bacillus subtilis, condensin is loaded at centromeric parS sites, where it encircles DNA and individualizes newly replicated origins. Using chromosome conformation capture and cytological assays, we show that condensin recruitment to origin-proximal parS sites is required for the juxtaposition of the two chromosome arms. Recruitment to ectopic parS sites promotes alignment of large tracks of DNA flanking these sites. Importantly, insertion of parS sites on opposing arms indicates that these "zip-up" interactions only occur between adjacent DNA segments. Collectively, our data suggest that condensin resolves replicated origins by promoting the juxtaposition of DNA flanking parS sites, drawing sister origins in on themselves and away from each other. These results are consistent with a model in which condensin encircles the DNA flanking its loading site and then slides down, tethering the two arms together. Lengthwise condensation via loop extrusion could provide a generalizable mechanism by which condensin complexes act dynamically to individualize origins in B. subtilis and, when loaded along eukaryotic chromosomes, resolve them during mitosis.
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Affiliation(s)
- Xindan Wang
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Tung B K Le
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Bryan R Lajoie
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Michael T Laub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - David Z Rudner
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115, USA
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73
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Wang X, Rudner DZ. Spatial organization of bacterial chromosomes. Curr Opin Microbiol 2015; 22:66-72. [PMID: 25460798 DOI: 10.1016/j.mib.2014.09.016] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 09/24/2014] [Accepted: 09/25/2014] [Indexed: 10/24/2022]
Abstract
Bacterial chromosomes are organized in stereotypical patterns that are faithfully and robustly regenerated in daughter cells. Two distinct spatial patterns were described almost a decade ago in our most tractable model organisms. In recent years, analysis of chromosome organization in a larger and more diverse set of bacteria and a deeper characterization of chromosome dynamics in the original model systems have provided a broader and more complete picture of both chromosome organization and the activities that generate the observed spatial patterns. Here, we summarize these different patterns highlighting similarities and differences and discuss the protein factors that help establish and maintain them.
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Affiliation(s)
- Xindan Wang
- Department of Microbiology and Immunobiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
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74
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Gruber S. Multilayer chromosome organization through DNA bending, bridging and extrusion. Curr Opin Microbiol 2015; 22:102-10. [PMID: 25460803 DOI: 10.1016/j.mib.2014.09.018] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 09/24/2014] [Accepted: 09/25/2014] [Indexed: 11/25/2022]
Abstract
All living cells have to master the extraordinarily extended and tangly nature of genomic DNA molecules — in particular during cell division when sister chromosomes are resolved from one another and confined to opposite halves of a cell. Bacteria have evolved diverse sets of proteins, which collectively ensure the formation of compact and yet highly dynamic nucleoids. Some of these players act locally by changing the path of DNA through the bending of its double helical backbone. Other proteins have wider or even global impact on chromosome organization, for example by interconnecting two distant segments of chromosomal DNA or by actively relocating DNA within a cell. Here, I highlight different modes of chromosome organization in bacteria and on this basis consider models for the function of SMC protein complexes, whose mechanism of action is only poorly understood so far.
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Affiliation(s)
- Stephan Gruber
- Chromosome Organization and Dynamics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
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75
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Marbouty M, Le Gall A, Cattoni D, Cournac A, Koh A, Fiche JB, Mozziconacci J, Murray H, Koszul R, Nollmann M. Condensin- and Replication-Mediated Bacterial Chromosome Folding and Origin Condensation Revealed by Hi-C and Super-resolution Imaging. Mol Cell 2015; 59:588-602. [DOI: 10.1016/j.molcel.2015.07.020] [Citation(s) in RCA: 205] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Revised: 06/10/2015] [Accepted: 07/21/2015] [Indexed: 12/01/2022]
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76
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Frosi Y, Haering CH. Control of chromosome interactions by condensin complexes. Curr Opin Cell Biol 2015; 34:94-100. [PMID: 26093128 DOI: 10.1016/j.ceb.2015.05.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 05/21/2015] [Accepted: 05/22/2015] [Indexed: 10/23/2022]
Abstract
Although condensin protein complexes have long been known for their central role during the formation of mitotic chromosomes, new evidence suggests they also act as global regulators of genome topology during all phases of the cell cycle. By controlling intra-chromosomal and inter-chromosomal DNA interactions, condensins function in various contexts of chromosome biology, from the regulation of transcription to the unpairing of homologous chromosomes. This review highlights recent advances in understanding how these global functions might be intimately linked to the molecular architecture of condensins and their extraordinary mode of binding to DNA.
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Affiliation(s)
- Yuri Frosi
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Christian H Haering
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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77
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Insights into ParB spreading from the complex structure of Spo0J and parS. Proc Natl Acad Sci U S A 2015; 112:6613-8. [PMID: 25964325 DOI: 10.1073/pnas.1421927112] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Spo0J (stage 0 sporulation protein J, a member of the ParB superfamily) is an essential component of the ParABS (partition system of ParA, ParB, and parS)-related bacterial chromosome segregation system. ParB (partition protein B) and its regulatory protein, ParA, act cooperatively through parS (partition S) DNA to facilitate chromosome segregation. ParB binds to chromosomal DNA at specific parS sites as well as the neighboring nonspecific DNA sites. Various ParB molecules can associate together and spread along the chromosomal DNA. ParB oligomer and parS DNA interact together to form a high-order nucleoprotein that is required for the loading of the structural maintenance of chromosomes proteins onto the chromosome for chromosomal DNA condensation. In this report, we characterized the binding of parS and Spo0J from Helicobacter pylori (HpSpo0J) and solved the crystal structure of the C-terminal domain truncated protein (Ct-HpSpo0J)-parS complex. Ct-HpSpo0J folds into an elongated structure that includes a flexible N-terminal domain for protein-protein interaction and a conserved DNA-binding domain for parS binding. Two Ct-HpSpo0J molecules bind with one parS. Ct-HpSpo0J interacts vertically and horizontally with its neighbors through the N-terminal domain to form an oligomer. These adjacent and transverse interactions are accomplished via a highly conserved arginine patch: RRLR. These interactions might be needed for molecular assembly of a high-order nucleoprotein complex and for ParB spreading. A structural model for ParB spreading and chromosomal DNA condensation that lead to chromosome segregation is proposed.
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78
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Wilhelm L, Bürmann F, Minnen A, Shin HC, Toseland CP, Oh BH, Gruber S. SMC condensin entraps chromosomal DNA by an ATP hydrolysis dependent loading mechanism in Bacillus subtilis. eLife 2015; 4. [PMID: 25951515 PMCID: PMC4442127 DOI: 10.7554/elife.06659] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Accepted: 05/06/2015] [Indexed: 12/18/2022] Open
Abstract
Smc–ScpAB forms elongated, annular structures that promote chromosome segregation, presumably by compacting and resolving sister DNA molecules. The mechanistic basis for its action, however, is only poorly understood. Here, we have established a physical assay to determine whether the binding of condensin to native chromosomes in Bacillus subtilis involves entrapment of DNA by the Smc–ScpAB ring. To do so, we have chemically cross-linked the three ring interfaces in Smc–ScpAB and thereafter isolated intact chromosomes under protein denaturing conditions. Exclusively species of Smc–ScpA, which were previously cross-linked into covalent rings, remained associated with chromosomal DNA. DNA entrapment is abolished by mutations that interfere with the Smc ATPase cycle and strongly reduced when the recruitment factor ParB is deleted, implying that most Smc–ScpAB is loaded onto the chromosome at parS sites near the replication origin. We furthermore report a physical interaction between native Smc–ScpAB and chromosomal DNA fragments. DOI:http://dx.doi.org/10.7554/eLife.06659.001 The genome of any living organism holds all the genetic information that the organism needs to live and grow. This information is written in the sequence of the organism's DNA, and is often divided into sub-structures called chromosomes. Different species have different sized genomes, but even bacteria with some of the smallest genomes still contain DNA molecules that are thousand times longer than the length of their cells. DNA molecules must thus be highly compacted in order to fit inside the cells. DNA compaction is particularly important during cell division, when the DNA is being equally distributed to the newly formed cells. In plants, animals and all other eukaryotes, large protein complexes known as condensin and cohesin play a major role in compacting, and then separating, the cell's chromosomes. Many bacteria also have condensin-like complexes. At the core of all these complexes are pairs of so-called SMC proteins. However, it is not clear how these SMC proteins direct chromosomes to become highly compacted when cells are dividing. Wilhelm et al. have now developed two new approaches to investigate how SMC proteins associate with bacterial DNA. These approaches were then used to study how SMC proteins coordinate the compaction of chromosomes in a bacterium called Bacillus subtilis. The experiments revealed that SMC proteins are in direct physical contact with the bacterial chromosome, and that bacterial DNA fibers are physically captured within a ring structure formed by the SMC proteins. Wilhelm et al. suggest that these new findings, and recent technological advances, have now set the stage for future studies to gain mechanistic insight into these protein complexes that organize and segregate chromosomes. DOI:http://dx.doi.org/10.7554/eLife.06659.002
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Affiliation(s)
- Larissa Wilhelm
- Chromosome Organization and Dynamics, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Frank Bürmann
- Chromosome Organization and Dynamics, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Anita Minnen
- Chromosome Organization and Dynamics, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ho-Chul Shin
- Department of Biological Sciences, KAIST Institute for the Biocentury, Cancer Metastasis Control Center, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Christopher P Toseland
- Chromosome Organization and Dynamics, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Byung-Ha Oh
- Department of Biological Sciences, KAIST Institute for the Biocentury, Cancer Metastasis Control Center, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Stephan Gruber
- Chromosome Organization and Dynamics, Max Planck Institute of Biochemistry, Martinsried, Germany
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79
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Building bridges within the bacterial chromosome. Trends Genet 2015; 31:164-73. [DOI: 10.1016/j.tig.2015.01.003] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 01/15/2015] [Accepted: 01/16/2015] [Indexed: 11/22/2022]
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80
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Ramachandran R, Jha J, Chattoraj DK. Chromosome segregation in Vibrio cholerae. J Mol Microbiol Biotechnol 2015; 24:360-70. [PMID: 25732338 DOI: 10.1159/000368853] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The study of chromosome segregation is currently one of the most exciting research frontiers in cell biology. In this review, we discuss our current knowledge of the chromosome segregation process in Vibrio cholerae, based primarily on findings from fluorescence microscopy experiments. This bacterium is of special interest because of its eukaryotic feature of having a divided genome, a feature shared with 10% of known bacteria. We also discuss how the segregation mechanisms of V. cholerae compare with those in other bacteria, and highlight some of the remaining questions regarding the process of bacterial chromosome segregation.
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Affiliation(s)
- Revathy Ramachandran
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Md., USA
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81
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Kleine Borgmann LAK, Graumann PL. Structural maintenance of chromosome complex in bacteria. J Mol Microbiol Biotechnol 2015; 24:384-95. [PMID: 25732340 DOI: 10.1159/000368931] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In all organisms, from eukaryotes to prokaryotes, the chromosome is highly compacted and organized. Chromosome condensation is essential in all cells and ranges from 1,000- to more than 10,000-fold between bacterial and eukaryotic cells. Replication and transcription occur in parallel with chromosome segregation in bacteria. Structural maintenance of chromosome proteins play a key role in chromosome compaction and segregation, their coordination with the cell cycle, and in various other chromosome dynamics, including DNA repair. In spite of their essential nature in almost all organisms, their function at a molecular level is only slowly beginning to emerge.
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Affiliation(s)
- Luise A K Kleine Borgmann
- Division of Biological Sciences and Section of Molecular Biology, University of California, San Diego, La Jolla, Calif., USA
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82
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Abstract
UNLABELLED Subcellular organization of the bacterial nucleoid and spatiotemporal dynamics of DNA replication and segregation have been studied intensively, but the functional link between these processes remains poorly understood. Here we use quantitative time-lapse fluorescence microscopy for single-cell analysis of chromosome organization and DNA replisome dynamics in Mycobacterium smegmatis. We report that DNA replication takes place near midcell, where, following assembly of the replisome on the replication origin, the left and right replication forks colocalize throughout the replication cycle. From its initial position near the cell pole, a fluorescently tagged chromosomal locus (attB, 245° from the origin) moves rapidly to the replisome complex just before it is replicated. The newly duplicated attB loci then segregate to mirror-symmetric positions relative to midcell. Genetic ablation of ParB, a component of the ParABS chromosome segregation system, causes marked defects in chromosome organization, condensation, and segregation. ParB deficiency also results in mislocalization of the DNA replication machinery and SMC (structural maintenance of chromosome) protein. These observations suggest that ParB and SMC play important and overlapping roles in chromosome organization and replisome dynamics in mycobacteria. IMPORTANCE We studied the spatiotemporal organization of the chromosome and DNA replication machinery in Mycobacterium smegmatis, a fast-growing relative of the human pathogen Mycobacterium tuberculosis. We show that genetic ablation of the DNA-binding proteins ParB and SMC disturbs the organization of the chromosome and causes a severe defect in subcellular localization and movement of the DNA replication complexes. These observations suggest that ParB and SMC provide a functional link between chromosome organization and DNA replication dynamics. This work also reveals important differences in the biological roles of the ParABS and SMC systems in mycobacteria versus better-characterized model organisms, such as Escherichia coli and Bacillus subtilis.
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83
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Bouet JY, Stouf M, Lebailly E, Cornet F. Mechanisms for chromosome segregation. Curr Opin Microbiol 2014; 22:60-5. [DOI: 10.1016/j.mib.2014.09.013] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 09/15/2014] [Indexed: 11/25/2022]
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84
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Murray H, Koh A. Multiple regulatory systems coordinate DNA replication with cell growth in Bacillus subtilis. PLoS Genet 2014; 10:e1004731. [PMID: 25340815 PMCID: PMC4207641 DOI: 10.1371/journal.pgen.1004731] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 09/03/2014] [Indexed: 11/18/2022] Open
Abstract
In many bacteria the rate of DNA replication is linked with cellular physiology to ensure that genome duplication is coordinated with growth. Nutrient-mediated growth rate control of DNA replication initiation has been appreciated for decades, however the mechanism(s) that connects these cell cycle activities has eluded understanding. In order to help address this fundamental question we have investigated regulation of DNA replication in the model organism Bacillus subtilis. Contrary to the prevailing view we find that changes in DnaA protein level are not sufficient to account for nutrient-mediated growth rate control of DNA replication initiation, although this regulation does require both DnaA and the endogenous replication origin. We go on to report connections between DNA replication and several essential cellular activities required for rapid bacterial growth, including respiration, central carbon metabolism, fatty acid synthesis, phospholipid synthesis, and protein synthesis. Unexpectedly, the results indicate that multiple regulatory systems are involved in coordinating DNA replication with cell physiology, with some of the regulatory systems targeting oriC while others act in a oriC-independent manner. We propose that distinct regulatory systems are utilized to control DNA replication in response to diverse physiological and chemical changes.
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Affiliation(s)
- Heath Murray
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne, United Kingdom
- * E-mail:
| | - Alan Koh
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne, United Kingdom
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85
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Abstract
Centromeres are specialized domains of heterochromatin that provide the foundation for the kinetochore. Centromeric heterochromatin is characterized by specific histone modifications, a centromere-specific histone H3 variant (CENP-A), and the enrichment of cohesin, condensin, and topoisomerase II. Centromere DNA varies orders of magnitude in size from 125 bp (budding yeast) to several megabases (human). In metaphase, sister kinetochores on the surface of replicated chromosomes face away from each other, where they establish microtubule attachment and bi-orientation. Despite the disparity in centromere size, the distance between separated sister kinetochores is remarkably conserved (approximately 1 μm) throughout phylogeny. The centromere functions as a molecular spring that resists microtubule-based extensional forces in mitosis. This review explores the physical properties of DNA in order to understand how the molecular spring is built and how it contributes to the fidelity of chromosome segregation.
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Affiliation(s)
- Kerry S Bloom
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599-3280;
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86
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Switching modes of chromosome dynamics in the bacterial cell cycle. Proc Natl Acad Sci U S A 2014; 111:12580-1. [PMID: 25157151 DOI: 10.1073/pnas.1413657111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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87
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Abstract
Two new studies reveal the main actors involved in the resolution and segregation of newly replicated origins in bacteria. These results have important implications for our understanding of the mechanisms involved in precisely coordinating chromosome organization, segregation and replication.
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Affiliation(s)
- Diego I Cattoni
- Department of Single-Molecule Biophysics, Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Universités Montpellier I et II, 29 rue de Navacelles, 34090 Montpellier, France
| | - Antoine Le Gall
- Department of Single-Molecule Biophysics, Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Universités Montpellier I et II, 29 rue de Navacelles, 34090 Montpellier, France
| | - Marcelo Nöllmann
- Department of Single-Molecule Biophysics, Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Universités Montpellier I et II, 29 rue de Navacelles, 34090 Montpellier, France.
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88
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Bacillus subtilis chromosome organization oscillates between two distinct patterns. Proc Natl Acad Sci U S A 2014; 111:12877-82. [PMID: 25071173 DOI: 10.1073/pnas.1407461111] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial chromosomes have been found to possess one of two distinct patterns of spatial organization. In the first, called "ori-ter" and exemplified by Caulobacter crescentus, the chromosome arms lie side-by-side, with the replication origin and terminus at opposite cell poles. In the second, observed in slow-growing Escherichia coli ("left-ori-right"), the two chromosome arms reside in separate cell halves, on either side of a centrally located origin. These two patterns, rotated 90° relative to each other, appear to result from different segregation mechanisms. Here, we show that the Bacillus subtilis chromosome alternates between them. For most of the cell cycle, newly replicated origins are maintained at opposite poles with chromosome arms adjacent to each other, in an ori-ter configuration. Shortly after replication initiation, the duplicated origins move as a unit to midcell and the two unreplicated arms resolve into opposite cell halves, generating a left-ori-right pattern. The origins are then actively segregated toward opposite poles, resetting the cycle. Our data suggest that the condensin complex and the parABS partitioning system are the principal driving forces underlying this oscillatory cycle. We propose that the distinct organization patterns observed for bacterial chromosomes reflect a common organization-segregation mechanism, and that simple modifications to it underlie the unique patterns observed in different species.
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89
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Condensation and localization of the partitioning protein ParB on the bacterial chromosome. Proc Natl Acad Sci U S A 2014; 111:8809-14. [PMID: 24927534 DOI: 10.1073/pnas.1402529111] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ParABS system mediates chromosome segregation and plasmid partitioning in many bacteria. As part of the partitioning mechanism, ParB proteins form a nucleoprotein complex at parS sites. The biophysical basis underlying ParB-DNA complex formation and localization remains elusive. Specifically, it is unclear whether ParB spreads in 1D along DNA or assembles into a 3D protein-DNA complex. We show that a combination of 1D spreading bonds and a single 3D bridging bond between ParB proteins constitutes a minimal model for a condensed ParB-DNA complex. This model implies a scaling behavior for ParB-mediated silencing of parS-flanking genes, which we confirm to be satisfied by experimental data from P1 plasmids. Furthermore, this model is consistent with experiments on the effects of DNA roadblocks on ParB localization. Finally, we show experimentally that a single parS site is necessary and sufficient for ParB-DNA complex formation in vivo. Together with our model, this suggests that ParB binding to parS triggers a conformational switch in ParB that overcomes a nucleation barrier. Conceptually, the combination of spreading and bridging bonds in our model provides a surface tension ensuring the condensation of the ParB-DNA complex, with analogies to liquid-like compartments such as nucleoli in eukaryotes.
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90
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Gruber S, Veening JW, Bach J, Blettinger M, Bramkamp M, Errington J. Interlinked sister chromosomes arise in the absence of condensin during fast replication in B. subtilis. Curr Biol 2014; 24:293-8. [PMID: 24440399 PMCID: PMC3919155 DOI: 10.1016/j.cub.2013.12.049] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 11/28/2013] [Accepted: 12/17/2013] [Indexed: 01/05/2023]
Abstract
Condensin-an SMC-kleisin complex-is essential for efficient segregation of sister chromatids in eukaryotes [1-4]. In Escherichia coli and Bacillus subtilis, deletion of condensin subunits results in severe growth phenotypes and the accumulation of cells lacking nucleoids [5, 6]. In many other bacteria and under slow growth conditions, however, the reported phenotypes are much milder or virtually absent [7-10]. This raises the question of what role prokaryotic condensin might play during chromosome segregation under various growth conditions. In B. subtilis and Streptococcus pneumoniae, condensin complexes are enriched on the circular chromosome near the single origin of replication by ParB proteins bound to parS sequences [11, 12]. Using conditional alleles of condensin in B. subtilis, we demonstrate that depletion of its activity results in an immediate and severe defect in the partitioning of replication origins. Multiple copies of the chromosome remain unsegregated at or near the origin of replication. Surprisingly, the growth and chromosome segregation defects in rich medium are suppressed by a reduction of replication fork velocity but not by partial inhibition of translation or transcription. Prokaryotic condensin likely prevents the formation of sister DNA interconnections at the replication fork or promotes their resolution behind the fork.
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Affiliation(s)
- Stephan Gruber
- Max Planck Institute of Biochemistry, Research Group "Chromosome Organization and Dynamics," Am Klopferspitz 18, 82152 Martinsried, Germany; Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne NE2 4AX, UK.
| | - Jan-Willem Veening
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands; Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne NE2 4AX, UK
| | - Juri Bach
- Department of Biology I, Ludwig Maximilians University, Munich, Großhaderner Str. 2-4, 82152 Martinsried, Germany
| | - Martin Blettinger
- Max Planck Institute of Biochemistry, Research Group "Chromosome Organization and Dynamics," Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Marc Bramkamp
- Department of Biology I, Ludwig Maximilians University, Munich, Großhaderner Str. 2-4, 82152 Martinsried, Germany
| | - Jeff Errington
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne NE2 4AX, UK.
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