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Khanna N, Zhang Y, Lucas JS, Dudko OK, Murre C. Chromosome dynamics near the sol-gel phase transition dictate the timing of remote genomic interactions. Nat Commun 2019; 10:2771. [PMID: 31235807 PMCID: PMC6591236 DOI: 10.1038/s41467-019-10628-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 05/20/2019] [Indexed: 11/08/2022] Open
Abstract
Diverse antibody repertoires are generated through remote genomic interactions involving immunoglobulin variable (VH), diversity (DH) and joining (JH) gene segments. How such interactions are orchestrated remains unknown. Here we develop a strategy to track VH-DHJH motion in B-lymphocytes. We find that VH and DHJH segments are trapped in configurations that allow only local motion, such that spatially proximal segments remain in proximity, while spatially remote segments remain remote. Within a subset of cells, however, abrupt changes in VH-DHJH motion are observed, plausibly caused by temporal alterations in chromatin configurations. Comparison of experimental and simulated data suggests that constrained motion is imposed by a network of cross-linked chromatin chains characteristic of a gel phase, yet poised near the sol phase, a solution of independent chromatin chains. These results suggest that chromosome organization near the sol-gel phase transition dictates the timing of genomic interactions to orchestrate gene expression and somatic recombination.
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Affiliation(s)
- Nimish Khanna
- Division of Biological Sciences, 0377, Department of Molecular Biology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Yaojun Zhang
- Princeton Center for Theoretical Science, Princeton University, Princeton, NJ, 08544, USA
| | - Joseph S Lucas
- Division of Biological Sciences, 0377, Department of Molecular Biology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Olga K Dudko
- Department of Physics, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Cornelis Murre
- Division of Biological Sciences, 0377, Department of Molecular Biology, University of California, San Diego, La Jolla, CA, 92093, USA.
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Guérin TM, Béneut C, Barinova N, López V, Lazar-Stefanita L, Deshayes A, Thierry A, Koszul R, Dubrana K, Marcand S. Condensin-Mediated Chromosome Folding and Internal Telomeres Drive Dicentric Severing by Cytokinesis. Mol Cell 2019; 75:131-144.e3. [PMID: 31204167 DOI: 10.1016/j.molcel.2019.05.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 02/12/2019] [Accepted: 05/13/2019] [Indexed: 12/13/2022]
Abstract
In Saccharomyces cerevisiae, dicentric chromosomes stemming from telomere fusions preferentially break at the fusion. This process restores a normal karyotype and protects chromosomes from the detrimental consequences of accidental fusions. Here, we address the molecular basis of this rescue pathway. We observe that tandem arrays tightly bound by the telomere factor Rap1 or a heterologous high-affinity DNA binding factor are sufficient to establish breakage hotspots, mimicking telomere fusions within dicentrics. We also show that condensins generate forces sufficient to rapidly refold dicentrics prior to breakage by cytokinesis and are essential to the preferential breakage at telomere fusions. Thus, the rescue of fused telomeres results from a condensin- and Rap1-driven chromosome folding that favors fusion entrapment where abscission takes place. Because a close spacing between the DNA-bound Rap1 molecules is essential to this process, Rap1 may act by stalling condensins.
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Affiliation(s)
- Thomas M Guérin
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France
| | - Claire Béneut
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France
| | - Natalja Barinova
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France
| | - Virginia López
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France
| | - Luciana Lazar-Stefanita
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS UMR 3525, Sorbonne Université, Paris, France
| | - Alice Deshayes
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France
| | - Agnès Thierry
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS UMR 3525, Sorbonne Université, Paris, France
| | - Romain Koszul
- Institut Pasteur, Unité Régulation Spatiale des Génomes, CNRS UMR 3525, Sorbonne Université, Paris, France
| | - Karine Dubrana
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France
| | - Stéphane Marcand
- CEA Paris-Saclay, Unité Stabilité Génétique Cellules Souches et Radiations, INSERM U1274, Université de Paris, Université Paris-Saclay, Fontenay-aux-roses, France.
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Transient Replication in Specialized Cells Favors Transfer of an Integrative and Conjugative Element. mBio 2019; 10:mBio.01133-19. [PMID: 31186329 PMCID: PMC6561031 DOI: 10.1128/mbio.01133-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial evolution is driven to a large extent by horizontal gene transfer (HGT)—the processes that distribute genetic material between species rather than by vertical descent. The different elements and processes mediating HGT have been characterized in great molecular detail. In contrast, very little is known on adaptive features selecting HGT evolvability and fitness optimization. By studying the molecular behavior of an integrated mobile DNA of the class of integrative and conjugative elements in individual Pseudomonas putida donor bacteria, we report here how transient replication of the element after its excision from the chromosome is favorable for its transfer success. Since successful transfer into a new recipient is a measure of the element’s fitness, transient replication may have been selected as an adaptive benefit for more-optimal transfer. Integrative and conjugative elements (ICEs) are widespread mobile DNA within bacterial genomes, whose lifestyle is relatively poorly understood. ICEs transmit vertically through donor cell chromosome replication, but in order to transfer, they have to excise from the chromosome. The excision step makes ICEs prone to loss, in case the donor cell divides and the ICE is not replicated. By adapting the system of LacI-cyan fluorescent protein (CFP) binding to lacO operator arrays, we analyze here the process of excision and transfer of the ICE for 3-chlorobenzoate degradation (ICEclc) in individual cells of the bacterium Pseudomonas putida. We provide evidence that ICEclc excises exclusively in a subset of specialized transfer-competent cells. ICEclc copy numbers in transfer-competent cells were higher than in regular nontransferring cells but were reduced in mutants lacking the ICE oriT1 origin of transfer, the ICE DNA relaxase, or the excision recombination sites. Consistently, transfer-competent cells showed a higher proportion without any observable LacI-CFP foci, suggesting ICEclc loss, but this proportion was independent of the ICE relaxase or the ICE origins of transfer. Our results thus indicated that the excised ICE becomes transiently replicated in transfer-competent cells, with up to six observable copies from LacI-CFP fluorescent focus measurements. Most of the observed ICEclc transfer to ICE-free P. putida recipients occurred from donors displaying 3 to 4 ICE copies, which constitute a minority among all transfer-competent cells. This finding suggests, therefore, that replication of the excised ICEclc in donors is beneficial for transfer fitness to recipient cells.
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Characterisation of ParB encoded on multipartite genome in Deinococcus radiodurans and their roles in radioresistance. Microbiol Res 2019; 223-225:22-32. [DOI: 10.1016/j.micres.2019.03.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 02/27/2019] [Accepted: 03/16/2019] [Indexed: 01/05/2023]
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Eykelenboom JK, Gierliński M, Yue Z, Hegarat N, Pollard H, Fukagawa T, Hochegger H, Tanaka TU. Live imaging of marked chromosome regions reveals their dynamic resolution and compaction in mitosis. J Cell Biol 2019; 218:1531-1552. [PMID: 30858191 PMCID: PMC6504890 DOI: 10.1083/jcb.201807125] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 12/19/2018] [Accepted: 02/05/2019] [Indexed: 01/27/2023] Open
Abstract
When human cells enter mitosis, chromosomes undergo substantial changes in their organization to resolve sister chromatids and compact chromosomes. To comprehend the timing and coordination of these events, we need to evaluate the progression of both sister chromatid resolution and chromosome compaction in one assay. Here we achieved this by analyzing changes in configuration of marked chromosome regions over time, with high spatial and temporal resolution. This assay showed that sister chromatids cycle between nonresolved and partially resolved states with an interval of a few minutes during G2 phase before completing full resolution in prophase. Cohesins and WAPL antagonistically regulate sister chromatid resolution in late G2 and prophase while local enrichment of cohesin on chromosomes prevents precocious sister chromatid resolution. Moreover, our assay allowed quantitative evaluation of condensin II and I activities, which differentially promote sister chromatid resolution and chromosome compaction, respectively. Our assay reveals novel aspects of dynamics in mitotic chromosome resolution and compaction that were previously obscure in global chromosome assays.
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Affiliation(s)
- John K Eykelenboom
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Marek Gierliński
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
- Data Analysis Group, School of Life Sciences, University of Dundee, Dundee, UK
| | - Zuojun Yue
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Nadia Hegarat
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | - Hilary Pollard
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | - Tatsuo Fukagawa
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Helfrid Hochegger
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | - Tomoyuki U Tanaka
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
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56
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Kim J, Goñi‐Moreno A, Calles B, de Lorenzo V. Spatial organization of the gene expression hardware in
Pseudomonas putida. Environ Microbiol 2019; 21:1645-1658. [DOI: 10.1111/1462-2920.14544] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 12/09/2018] [Accepted: 01/23/2019] [Indexed: 12/11/2022]
Affiliation(s)
| | | | - Belén Calles
- Systems Biology ProgramCentro Nacional de Biotecnología‐CSIC, Campus de Cantoblanco Madrid, 28049 Spain
| | - Víctor de Lorenzo
- Systems Biology ProgramCentro Nacional de Biotecnología‐CSIC, Campus de Cantoblanco Madrid, 28049 Spain
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57
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Romero H, Rösch TC, Hernández-Tamayo R, Lucena D, Ayora S, Alonso JC, Graumann PL. Single molecule tracking reveals functions for RarA at replication forks but also independently from replication during DNA repair in Bacillus subtilis. Sci Rep 2019; 9:1997. [PMID: 30760776 PMCID: PMC6374455 DOI: 10.1038/s41598-018-38289-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 12/18/2018] [Indexed: 12/19/2022] Open
Abstract
RarA is a widely conserved protein proposed to be involved in recombination-dependent replication. We present a cell biological approach to identify functional connections between RarA and other proteins using single molecule tracking. We found that 50% of RarA molecules were static, mostly close to replication forks and likely DNA-bound, while the remaining fraction was highly dynamic throughout the cells. RarA alternated between static and dynamic states. Exposure to H2O2 increased the fraction of dynamic molecules, but not treatment with mitomycin C or with methyl methanesulfonate, which was exacerbated by the absence of RecJ, RecD2, RecS and RecU proteins. The ratio between static and dynamic RarA also changed in replication temperature-sensitive mutants, but in opposite manners, dependent upon inhibition of DnaB or of DnaC (pre)primosomal proteins, revealing an intricate function related to DNA replication restart. RarA likely acts in the context of collapsed replication forks, as well as in conjunction with a network of proteins that affect the activity of the RecA recombinase. Our novel approach reveals intricate interactions of RarA, and is widely applicable for in vivo protein studies, to underpin genetic or biochemical connections, and is especially helpful for investigating proteins whose absence does not lead to any detectable phenotype.
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Affiliation(s)
- Hector Romero
- SYNMIKRO, LOEWE-Zentrum für Synthetische Mikrobiologie, Philipps-Universität Marburg, Hans-Meerwein-Straße, Mehrzweckgebäude, 35043, Marburg, Germany
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032, Marburg, Germany
- Department Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin St., 28049, Cantoblanco, Madrid, Spain
| | - Thomas C Rösch
- SYNMIKRO, LOEWE-Zentrum für Synthetische Mikrobiologie, Philipps-Universität Marburg, Hans-Meerwein-Straße, Mehrzweckgebäude, 35043, Marburg, Germany
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032, Marburg, Germany
| | - Rogelio Hernández-Tamayo
- SYNMIKRO, LOEWE-Zentrum für Synthetische Mikrobiologie, Philipps-Universität Marburg, Hans-Meerwein-Straße, Mehrzweckgebäude, 35043, Marburg, Germany
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032, Marburg, Germany
| | - Daniella Lucena
- SYNMIKRO, LOEWE-Zentrum für Synthetische Mikrobiologie, Philipps-Universität Marburg, Hans-Meerwein-Straße, Mehrzweckgebäude, 35043, Marburg, Germany
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032, Marburg, Germany
| | - Silvia Ayora
- Department Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin St., 28049, Cantoblanco, Madrid, Spain
| | - Juan C Alonso
- Department Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin St., 28049, Cantoblanco, Madrid, Spain.
| | - Peter L Graumann
- SYNMIKRO, LOEWE-Zentrum für Synthetische Mikrobiologie, Philipps-Universität Marburg, Hans-Meerwein-Straße, Mehrzweckgebäude, 35043, Marburg, Germany.
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032, Marburg, Germany.
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58
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Trojanowski D, Hołówka J, Zakrzewska-Czerwińska J. Where and When Bacterial Chromosome Replication Starts: A Single Cell Perspective. Front Microbiol 2018; 9:2819. [PMID: 30534115 PMCID: PMC6275241 DOI: 10.3389/fmicb.2018.02819] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 11/02/2018] [Indexed: 12/18/2022] Open
Abstract
Bacterial chromosomes have a single, unique replication origin (named oriC), from which DNA synthesis starts. This study describes methods of visualizing oriC regions and the chromosome replication in single living bacterial cells in real-time. This review also discusses the impact of live cell imaging techniques on understanding of chromosome replication dynamics, particularly at the initiation step, in different species of bacteria.
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Affiliation(s)
- Damian Trojanowski
- Department of Molecular Microbiology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Joanna Hołówka
- Department of Molecular Microbiology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
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59
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Mediati DG, Burke CM, Ansari S, Harry EJ, Duggin IG. High-throughput sequencing of sorted expression libraries reveals inhibitors of bacterial cell division. BMC Genomics 2018; 19:781. [PMID: 30373517 PMCID: PMC6206680 DOI: 10.1186/s12864-018-5187-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 10/19/2018] [Indexed: 11/24/2022] Open
Abstract
Background Bacterial filamentation occurs when rod-shaped bacteria grow without dividing. To identify genetically encoded inhibitors of division that promote filamentation, we used cell sorting flow cytometry to enrich filamentous clones from an inducible expression library, and then identified the cloned DNA with high-throughput DNA sequencing. We applied the method to an expression library made from fragmented genomic DNA of uropathogenic E. coli UTI89, which undergoes extensive reversible filamentation in urinary tract infections and might encode additional regulators of division. Results We identified 55 genomic regions that reproducibly caused filamentation when expressed from the plasmid vector, and then further localized the cause of filamentation in several of these to specific genes or sub-fragments. Many of the identified genomic fragments encode genes that are known to participate in cell division or its regulation, and others may play previously-unknown roles. Some of the prophage genes identified were previously implicated in cell division arrest. A number of the other fragments encoded potential short transcripts or peptides. Conclusions The results provided evidence of potential new links between cell division and distinct cellular processes including central carbon metabolism and gene regulation. Candidate regulators of the UTI-associated filamentation response or others were identified amongst the results. In addition, some genomic fragments that caused filamentation may not have evolved to control cell division, but may have applications as artificial inhibitors. Our approach offers the opportunity to carry out in depth surveys of diverse DNA libraries to identify new genes or sequences encoding the capacity to inhibit division and cause filamentation. Electronic supplementary material The online version of this article (10.1186/s12864-018-5187-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel G Mediati
- The ithree institute, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Catherine M Burke
- The ithree institute, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Shirin Ansari
- The ithree institute, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Elizabeth J Harry
- The ithree institute, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Iain G Duggin
- The ithree institute, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
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60
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Abstract
Coordination between chromosome replication and segregation is essential for equal partitioning of genetic material between daughter cells. In bacteria, this is achieved through the proximity of the origin of replication, oriC, and the chromosome partitioning site, parS We report here that in Pseudomonas aeruginosa, segregation but not replication is also controlled at the terminus region of the chromosome. Using the fluorescent repressor operator system (FROS), we investigated chromosome segregation in P. aeruginosa strain PAO1-UW, wherein the chromosome dimer resolution site, dif, is asymmetrically positioned relative to oriC In these cells, segregation proceeded sequentially along the two chromosomal arms and terminated at dif In contrast, chromosome replication terminated elsewhere, opposite from oriC We further found two large domains on the longer arm of the chromosome, wherein DNA segregated simultaneously. Notably, GC-skew, which reflects a bias in nucleotide usage between the leading and lagging strands of the chromosome, switches polarity at the dif locus but not necessarily at the terminus of replication. These data demonstrate that termination of chromosome replication and segregation can be physically separated without adverse effects on bacterial fitness. They also reveal the critical role of the dif region in defining the global layout of the chromosome and the progression of chromosome segregation and suggest that chromosome packing adapts to its subcellular layout.IMPORTANCE Segregation of genetic information is a central event in cellular life. In bacteria, chromosome segregation occurs concurrently with replication, sequentially along the two arms from oriC to dif How the two processes are coordinated is unknown. We explored here chromosome segregation in an opportunistic human pathogen, Pseudomonas aeruginosa, using its strain with markedly unequal chromosomal arms. We found that replication and segregation diverge in this strain and terminate at very different locations, whereas the longer chromosomal arm folds into large domains to align itself with the shorter arm. The significance of this research is in establishing that segregation and replication of bacterial chromosomes are largely uncoupled from each other and that the large-scale structure of the chromosome adapts to its subcellular layout.
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61
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Maurya GK, Misra HS. Plasmids for making multiple knockouts in a radioresistant bacterium Deinococcus radiodurans. Plasmid 2018; 100:6-13. [PMID: 30261215 DOI: 10.1016/j.plasmid.2018.09.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Revised: 08/28/2018] [Accepted: 09/07/2018] [Indexed: 11/26/2022]
Abstract
The gene knockouts are mostly created using homologous recombination-based replacement of target gene(s) with the expressing cassette of selection marker gene(s). Here, we constructed a series of plasmids bearing the expressing cassettes of genes encoding different antibiotics markers like nptII (KanR), aadA (SpecR), cat (CmR) and aac(3) (GenR). D. radiodurans is a radioresistant Gram positive bacterium that does not support the independent maintenance of colE1 origin-based plasmids. Using these constructs, the disruption mutants of both single and multiple genes involved in segregation of secondary genome elements have been generated in this bacterium. Unlike single mutants, the double and triple mutants showed growth retardation under normal growth conditions and the synergistic effects with Topoisomerase II inhibitor on the growth of this bacterium. Thus, these plasmids could be useful in creating multiple deletions/disruptions in bacteria that do not support independent maintenance of colE1 origin-based plasmid.
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Affiliation(s)
- Ganesh K Maurya
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Mumbai 400094, India
| | - Hari S Misra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Mumbai 400094, India.
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62
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Carrasco B, Seco EM, López-Sanz M, Alonso JC, Ayora S. Bacillus subtilis RarA modulates replication restart. Nucleic Acids Res 2018; 46:7206-7220. [PMID: 29947798 PMCID: PMC6101539 DOI: 10.1093/nar/gky541] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 06/05/2018] [Indexed: 02/01/2023] Open
Abstract
The ubiquitous RarA/Mgs1/WRNIP protein plays a crucial, but poorly understood role in genome maintenance. We show that Bacillus subtilis RarA, in the apo form, preferentially binds single-stranded (ss) over double-stranded (ds) DNA. SsbA bound to ssDNA loads RarA, and for such recruitment the amphipathic C-terminal domain of SsbA is required. RarA is a DNA-dependent ATPase strongly stimulated by ssDNA–dsDNA junctions and SsbA, or by dsDNA ends. RarA, which may interact with PriA, does not stimulate PriA DNA unwinding. In a reconstituted PriA-dependent DNA replication system, RarA inhibited initiation, but not chain elongation. The RarA effect was not observed in the absence of SsbA, or when the host-encoded preprimosome and the DNA helicase are replaced by proteins from the SPP1 phage with similar function. We propose that RarA assembles at blocked forks to maintain genome integrity. Through its interaction with SsbA and with a preprimosomal component, RarA might impede the assembly of the replicative helicase, to prevent that recombination intermediates contribute to pathological DNA replication restart.
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Affiliation(s)
- Begoña Carrasco
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, (CNB-CSIC), Cantoblanco 28049, Madrid, Spain
| | - Elena M Seco
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, (CNB-CSIC), Cantoblanco 28049, Madrid, Spain
| | - María López-Sanz
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, (CNB-CSIC), Cantoblanco 28049, Madrid, Spain
| | - Juan C Alonso
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, (CNB-CSIC), Cantoblanco 28049, Madrid, Spain
| | - Silvia Ayora
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, (CNB-CSIC), Cantoblanco 28049, Madrid, Spain
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63
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Brustel J, Kozik Z, Gromak N, Savic V, Sweet SMM. Large XPF-dependent deletions following misrepair of a DNA double strand break are prevented by the RNA:DNA helicase Senataxin. Sci Rep 2018; 8:3850. [PMID: 29497062 PMCID: PMC5832799 DOI: 10.1038/s41598-018-21806-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 02/09/2018] [Indexed: 01/04/2023] Open
Abstract
Deletions and chromosome re-arrangements are common features of cancer cells. We have established a new two-component system reporting on epigenetic silencing or deletion of an actively transcribed gene adjacent to a double-strand break (DSB). Unexpectedly, we find that a targeted DSB results in a minority (<10%) misrepair event of kilobase deletions encompassing the DSB site and transcribed gene. Deletions are reduced upon RNaseH1 over-expression and increased after knockdown of the DNA:RNA helicase Senataxin, implicating a role for DNA:RNA hybrids. We further demonstrate that the majority of these large deletions are dependent on the 3′ flap endonuclease XPF. DNA:RNA hybrids were detected by DNA:RNA immunoprecipitation in our system after DSB generation. These hybrids were reduced by RNaseH1 over-expression and increased by Senataxin knock-down, consistent with a role in deletions. Overall, these data are consistent with DNA:RNA hybrid generation at the site of a DSB, mis-processing of which results in genome instability in the form of large deletions.
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Affiliation(s)
- Julien Brustel
- Genome Damage and Stability Centre (GDSC), University of Sussex, Brighton, BN1 9RQ, UK
| | - Zuzanna Kozik
- Genome Damage and Stability Centre (GDSC), University of Sussex, Brighton, BN1 9RQ, UK
| | - Natalia Gromak
- Sir William Dunn School of Pathology, University of Oxford, Oxford, South Parks Road, OX1 3RE, UK
| | - Velibor Savic
- Brighton and Sussex Medical School (BSMS), University of Sussex, Brighton, BN1 9RQ, UK.,Horizon Discovery Ltd, 8100 Cambridge Research Park, Cambridge, CB25 9TL, UK
| | - Steve M M Sweet
- Genome Damage and Stability Centre (GDSC), University of Sussex, Brighton, BN1 9RQ, UK. .,NantOmics, 9600 Medical Center Drive, Rockville, MD, 20850, USA.
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Lianga N, Doré C, Kennedy EK, Yeh E, Williams EC, Fortinez CM, Wang A, Bloom KS, Rudner AD. Cdk1 phosphorylation of Esp1/Separase functions with PP2A and Slk19 to regulate pericentric Cohesin and anaphase onset. PLoS Genet 2018; 14:e1007029. [PMID: 29561844 PMCID: PMC5880407 DOI: 10.1371/journal.pgen.1007029] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 04/02/2018] [Accepted: 09/17/2017] [Indexed: 12/27/2022] Open
Abstract
Anaphase onset is an irreversible cell cycle transition that is triggered by the activation of the protease Separase. Separase cleaves the Mcd1 (also known as Scc1) subunit of Cohesin, a complex of proteins that physically links sister chromatids, triggering sister chromatid separation. Separase is regulated by the degradation of the anaphase inhibitor Securin which liberates Separase from inhibitory Securin/Separase complexes. In many organisms, Securin is not essential suggesting that Separase is regulated by additional mechanisms. In this work, we show that in budding yeast Cdk1 activates Separase (Esp1 in yeast) through phosphorylation to trigger anaphase onset. Esp1 activation is opposed by protein phosphatase 2A associated with its regulatory subunit Cdc55 (PP2ACdc55) and the spindle protein Slk19. Premature anaphase spindle elongation occurs when Securin (Pds1 in yeast) is inducibly degraded in cells that also contain phospho-mimetic mutations in ESP1, or deletion of CDC55 or SLK19. This striking phenotype is accompanied by advanced degradation of Mcd1, disruption of pericentric Cohesin organization and chromosome mis-segregation. Our findings suggest that PP2ACdc55 and Slk19 function redundantly with Pds1 to inhibit Esp1 within pericentric chromatin, and both Pds1 degradation and Cdk1-dependent phosphorylation of Esp1 act together to trigger anaphase onset.
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Affiliation(s)
- Noel Lianga
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Carole Doré
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Erin K. Kennedy
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Elaine Yeh
- University of North Carolina, Chapel Hill, Department of Biology, Chapel Hill, NC, United States of America
| | - Elizabeth C. Williams
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Camille Marie Fortinez
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Alick Wang
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Kerry S. Bloom
- University of North Carolina, Chapel Hill, Department of Biology, Chapel Hill, NC, United States of America
| | - Adam D. Rudner
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
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Thomson NM, Shirai T, Chiapello M, Kondo A, Mukherjee KJ, Sivaniah E, Numata K, Summers DK. Efficient 3-Hydroxybutyrate Production by QuiescentEscherichia coliMicrobial Cell Factories is Facilitated by Indole-Induced Proteomic and Metabolomic Changes. Biotechnol J 2018; 13:e1700571. [DOI: 10.1002/biot.201700571] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 12/09/2017] [Indexed: 01/05/2023]
Affiliation(s)
- Nicholas M. Thomson
- Enzyme Research Team; RIKEN Centre for Sustainable Resource Science; Wako-shi 351-0198 Japan
- Department of Genetics; University of Cambridge; Cambridge CB2 3EH UK
| | - Tomokazu Shirai
- Cell Factory Research Team; RIKEN Centre for Sustainable Resource Science; Yokohama 230-0045 Japan
| | - Marco Chiapello
- Cambridge Centre for Proteomics; University of Cambridge; Cambridge CB2 1QR UK
| | - Akihiko Kondo
- Cell Factory Research Team; RIKEN Centre for Sustainable Resource Science; Yokohama 230-0045 Japan
| | | | - Easan Sivaniah
- Institute for Integrated Cell-Material Sciences (iCeMS); Kyoto University; Kyoto 606-8501 Japan
| | - Keiji Numata
- Enzyme Research Team; RIKEN Centre for Sustainable Resource Science; Wako-shi 351-0198 Japan
| | - David K. Summers
- Department of Genetics; University of Cambridge; Cambridge CB2 3EH UK
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66
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Stanage TH, Page AN, Cox MM. DNA flap creation by the RarA/MgsA protein of Escherichia coli. Nucleic Acids Res 2017; 45:2724-2735. [PMID: 28053120 PMCID: PMC5389604 DOI: 10.1093/nar/gkw1322] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 12/19/2016] [Indexed: 11/24/2022] Open
Abstract
We identify a novel activity of the RarA (also MgsA) protein of Escherichia coli, demonstrating that this protein functions at DNA ends to generate flaps. A AAA+ ATPase in the clamp loader clade, RarA protein is part of a highly conserved family of DNA metabolism proteins. We demonstrate that RarA binds to double-stranded DNA in its ATP-bound state and single-stranded DNA in its apo state. RarA ATPase activity is stimulated by single-stranded DNA gaps and double-stranded DNA ends. At these double-stranded DNA ends, RarA couples the energy of ATP binding and hydrolysis to separating the strands of duplex DNA, creating flaps. We hypothesize that the creation of a flap at the site of a leading strand discontinuity could, in principle, allow DnaB and the associated replisome to continue DNA synthesis without impediment, with leading strand re-priming by DnaG. Replication forks could thus be rescued in a manner that does not involve replisome disassembly or reassembly, albeit with loss of one of the two chromosomal products of a replication cycle.
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Affiliation(s)
- Tyler H Stanage
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, USA
| | - Asher N Page
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, USA
| | - Michael M Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, USA
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68
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Sellars LE, Bryant JA, Sánchez-Romero MA, Sánchez-Morán E, Busby SJW, Lee DJ. Development of a new fluorescent reporter:operator system: location of AraC regulated genes in Escherichia coli K-12. BMC Microbiol 2017; 17:170. [PMID: 28774286 PMCID: PMC5543585 DOI: 10.1186/s12866-017-1079-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 07/18/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In bacteria, many transcription activator and repressor proteins regulate multiple transcription units that are often distally distributed on the bacterial genome. To investigate the subcellular location of DNA bound proteins in the folded bacterial nucleoid, fluorescent reporters have been developed which can be targeted to specific DNA operator sites. Such Fluorescent Reporter-Operator System (FROS) probes consist of a fluorescent protein fused to a DNA binding protein, which binds to an array of DNA operator sites located within the genome. Here we have developed a new FROS probe using the Escherichia coli MalI transcription factor, fused to mCherry fluorescent protein. We have used this in combination with a LacI repressor::GFP protein based FROS probe to assess the cellular location of commonly regulated transcription units that are distal on the Escherichia coli genome. RESULTS We developed a new DNA binding fluorescent reporter, consisting of the Escherichia coli MalI protein fused to the mCherry fluorescent protein. This was used in combination with a Lac repressor:green fluorescent protein fusion to examine the spatial positioning and possible co-localisation of target genes, regulated by the Escherichia coli AraC protein. We report that induction of gene expression with arabinose does not result in co-localisation of AraC-regulated transcription units. However, measurable repositioning was observed when gene expression was induced at the AraC-regulated promoter controlling expression of the araFGH genes, located close to the DNA replication terminus on the chromosome. Moreover, in dividing cells, arabinose-induced expression at the araFGH locus enhanced chromosome segregation after replication. CONCLUSION Regions of the chromosome regulated by AraC do not colocalise, but transcription events can induce movement of chromosome loci in bacteria and our observations suggest a role for gene expression in chromosome segregation.
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Affiliation(s)
- Laura E. Sellars
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
| | - Jack A. Bryant
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
| | | | | | - Stephen J. W. Busby
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
| | - David J. Lee
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
- Department of Life Sciences, Birmingham City University, Edgbaston, Birmingham, B15 3TN UK
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Pankert T, Jegou T, Caudron-Herger M, Rippe K. Tethering RNA to chromatin for fluorescence microscopy based analysis of nuclear organization. Methods 2017; 123:89-101. [DOI: 10.1016/j.ymeth.2017.01.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Revised: 01/23/2017] [Accepted: 01/30/2017] [Indexed: 12/22/2022] Open
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Döhlemann J, Wagner M, Happel C, Carrillo M, Sobetzko P, Erb TJ, Thanbichler M, Becker A. A Family of Single Copy repABC-Type Shuttle Vectors Stably Maintained in the Alpha-Proteobacterium Sinorhizobium meliloti. ACS Synth Biol 2017; 6:968-984. [PMID: 28264559 PMCID: PMC7610768 DOI: 10.1021/acssynbio.6b00320] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
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A considerable
share of bacterial species maintains segmented genomes.
Plant symbiotic α-proteobacterial rhizobia contain up to six repABC-type replicons in addition to the primary chromosome.
These low or unit-copy replicons, classified as secondary chromosomes,
chromids, or megaplasmids, are exclusively found in α-proteobacteria.
Replication and faithful partitioning of these replicons to the daughter
cells is mediated by the repABC region. The importance
of α-rhizobial symbiotic nitrogen fixation for sustainable agriculture
and Agrobacterium-mediated plant transformation as
a tool in plant sciences has increasingly moved biological engineering
of these organisms into focus. Plasmids are ideal DNA-carrying vectors
for these engineering efforts. On the basis of repABC regions collected from α-rhizobial secondary replicons, and
origins of replication derived from traditional cloning vectors, we
devised the versatile family of pABC shuttle vectors propagating in Sinorhizobium meliloti, related members of the Rhizobiales, and Escherichia coli. A modular plasmid library
providing the elemental parts for pABC vector assembly was founded.
The standardized design of these vectors involves five basic modules:
(1) repABC cassette, (2) plasmid-derived origin of
replication, (3) RK2/RP4 mobilization site (optional), (4) antibiotic
resistance gene, and (5) multiple cloning site flanked by transcription
terminators. In S. meliloti, pABC vectors showed
high propagation stability and unit-copy number. We demonstrated stable
coexistence of three pABC vectors in addition to the two indigenous
megaplasmids in S. meliloti, suggesting combinability
of multiple compatible pABC plasmids. We further devised an in vivo cloning strategy involving Cre/lox-mediated translocation of large DNA fragments to an autonomously
replicating repABC-based vector, followed by conjugation-mediated
transfer either to compatible rhizobia or E. coli.
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Affiliation(s)
- Johannes Döhlemann
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
- Faculty of Biology, Philipps-Universität Marburg, Marburg, 35043, Germany
| | - Marcel Wagner
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
- Faculty of Biology, Philipps-Universität Marburg, Marburg, 35043, Germany
| | - Carina Happel
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
- Faculty of Biology, Philipps-Universität Marburg, Marburg, 35043, Germany
| | - Martina Carrillo
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
- Biochemistry and Synthetic Biology of Microbial Metabolism Group, Max Planck Institute for Terrestrial Microbiology, Marburg, 35043, Germany
| | - Patrick Sobetzko
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
| | - Tobias J. Erb
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
- Biochemistry and Synthetic Biology of Microbial Metabolism Group, Max Planck Institute for Terrestrial Microbiology, Marburg, 35043, Germany
| | - Martin Thanbichler
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
- Faculty of Biology, Philipps-Universität Marburg, Marburg, 35043, Germany
| | - Anke Becker
- LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
- Faculty of Biology, Philipps-Universität Marburg, Marburg, 35043, Germany
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71
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Cass JA, Kuwada NJ, Traxler B, Wiggins PA. Escherichia coli Chromosomal Loci Segregate from Midcell with Universal Dynamics. Biophys J 2017; 110:2597-2609. [PMID: 27332118 DOI: 10.1016/j.bpj.2016.04.046] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 03/31/2016] [Accepted: 04/28/2016] [Indexed: 12/31/2022] Open
Abstract
The structure of the Escherichia coli chromosome is inherently dynamic over the duration of the cell cycle. Genetic loci undergo both stochastic motion around their initial positions and directed motion to opposite poles of the rod-shaped cell during segregation. We developed a quantitative method to characterize cell-cycle dynamics of the E. coli chromosome to probe the chromosomal steady-state mobility and segregation process. By tracking fluorescently labeled chromosomal loci in thousands of cells throughout the entire cell cycle, our method allows for the statistical analysis of locus position and motion, the step-size distribution for movement during segregation, and the locus drift velocity. The robust statistics of our detailed analysis of the wild-type E. coli nucleoid allow us to observe loci moving toward midcell before segregation occurs, consistent with a replication factory model. Then, as segregation initiates, we perform a detailed characterization of the average segregation velocity of loci. Contrary to origin-centric models of segregation, which predict distinct dynamics for oriC-proximal versus oriC-distal loci, we find that the dynamics of loci were universal and independent of genetic position.
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Affiliation(s)
- Julie A Cass
- Departments of Physics, Bioengineering, and Microbiology, University of Washington, Seattle, Washington
| | - Nathan J Kuwada
- Departments of Physics, Bioengineering, and Microbiology, University of Washington, Seattle, Washington
| | - Beth Traxler
- Departments of Physics, Bioengineering, and Microbiology, University of Washington, Seattle, Washington
| | - Paul A Wiggins
- Departments of Physics, Bioengineering, and Microbiology, University of Washington, Seattle, Washington.
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72
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BiFCROS: A Low-Background Fluorescence Repressor Operator System for Labeling of Genomic Loci. G3-GENES GENOMES GENETICS 2017; 7:1969-1977. [PMID: 28450375 PMCID: PMC5473772 DOI: 10.1534/g3.117.040782] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Fluorescence-based methods are widely used to analyze elementary cell processes such as DNA replication or chromosomal folding and segregation. Labeling DNA with a fluorescent protein allows the visualization of its temporal and spatial organization. One popular approach is FROS (fluorescence repressor operator system). This method specifically labels DNA in vivo through binding of a fusion of a fluorescent protein and a repressor protein to an operator array, which contains numerous copies of the repressor binding site integrated into the genomic site of interest. Bound fluorescent proteins are then visible as foci in microscopic analyses and can be distinguished from the background fluorescence caused by unbound fusion proteins. Even though this method is widely used, no attempt has been made so far to decrease the background fluorescence to facilitate analysis of the actual signal of interest. Here, we present a new method that greatly reduces the background signal of FROS. BiFCROS (Bimolecular Fluorescence Complementation and Repressor Operator System) is based on fusions of repressor proteins to halves of a split fluorescent protein. Binding to a hybrid FROS array results in fluorescence signals due to bimolecular fluorescence complementation. Only proteins bound to the hybrid FROS array fluoresce, greatly improving the signal to noise ratio compared to conventional FROS. We present the development of BiFCROS and discuss its potential to be used as a fast and single-cell readout for copy numbers of genetic loci.
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73
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Garza de Leon F, Sellars L, Stracy M, Busby SJW, Kapanidis AN. Tracking Low-Copy Transcription Factors in Living Bacteria: The Case of the lac Repressor. Biophys J 2017; 112:1316-1327. [PMID: 28402875 PMCID: PMC5390046 DOI: 10.1016/j.bpj.2017.02.028] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 01/20/2017] [Accepted: 02/16/2017] [Indexed: 11/30/2022] Open
Abstract
Transcription factors control the expression of genes by binding to specific sites in DNA and repressing or activating transcription in response to stimuli. The lac repressor (LacI) is a well characterized transcription factor that regulates the ability of bacterial cells to uptake and metabolize lactose. Here, we study the intracellular mobility and spatial distribution of LacI in live bacteria using photoactivated localization microscopy combined with single-particle tracking. Since we track single LacI molecules in live cells by stochastically photoactivating and observing fluorescent proteins individually, there are no limitations on the copy number of the protein under study; as a result, we were able to study the behavior of LacI in bacterial strains containing the natural copy numbers (∼40 monomers), as well as in strains with much higher copy numbers due to LacI overexpression. Our results allowed us to determine the relative abundance of specific, near-specific, and non-specific DNA binding modes of LacI in vivo, showing that all these modes are operational inside living cells. Further, we examined the spatial distribution of LacI in live cells, confirming its specific binding to lac operator regions on the chromosome; we also showed that mobile LacI molecules explore the bacterial nucleoid in a way similar to exploration by other DNA-binding proteins. Our work also provides an example of applying tracking photoactivated localization microscopy to studies of low-copy-number proteins in living bacteria.
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Affiliation(s)
- Federico Garza de Leon
- Gene Machines Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, United Kingdom
| | - Laura Sellars
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Mathew Stracy
- Gene Machines Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, United Kingdom
| | - Stephen J W Busby
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Achillefs N Kapanidis
- Gene Machines Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, United Kingdom.
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74
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Michel B, Sinha AK. The inactivation of rfaP, rarA or sspA gene improves the viability of the Escherichia coli DNA polymerase III holD mutant. Mol Microbiol 2017; 104:1008-1026. [PMID: 28342235 DOI: 10.1111/mmi.13677] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2017] [Indexed: 12/11/2022]
Abstract
The Escherichia coli holD mutant is poorly viable because the stability of holoenzyme polymerase III (Pol III HE) on DNA is compromised. Consequently, the SOS response is induced and the SOS polymerases DinB and Pol II further hinder replication. Mutations that restore the holD mutant viability belong to two classes, those that stabilize Pol III on DNA and those that prevent the deleterious effects of DinB over-production. We identified a dnaX mutation and the inactivation of rfaP and sspA genes as belonging to the first class of holD mutant suppressors. dnaX encodes a Pol III clamp loader subunit that interacts with HolD. rfaP encodes a lipopolysaccharide kinase that acts in outer membrane biogenesis. Its inactivation improves the holD mutant growth in part by affecting potassium import, previously proposed to stabilize Pol III HE on DNA by increasing electrostatic interactions. sspA encodes a global transcriptional regulator and growth of the holD mutant in its absence suggests that SspA controls genes that affect protein-DNA interactions. The inactivation of rarA belongs to the second class of suppressor mutations. rarA inactivation has a weak effect but is additive with other suppressor mutations. Our results suggest that RarA facilitates DinB binding to abandoned forks.
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Affiliation(s)
- Bénédicte Michel
- Genome Biology Department, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, 91198, France
| | - Anurag Kumar Sinha
- Genome Biology Department, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, 91198, France
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75
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McLeod BN, Allison-Gamble GE, Barge MT, Tonthat NK, Schumacher MA, Hayes F, Barillà D. A three-dimensional ParF meshwork assembles through the nucleoid to mediate plasmid segregation. Nucleic Acids Res 2017; 45:3158-3171. [PMID: 28034957 PMCID: PMC5389482 DOI: 10.1093/nar/gkw1302] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 12/12/2016] [Accepted: 12/16/2016] [Indexed: 12/23/2022] Open
Abstract
Genome segregation is a fundamental step in the life cycle of every cell. Most bacteria rely on dedicated DNA partition proteins to actively segregate chromosomes and low copy-number plasmids. Here, by employing super resolution microscopy, we establish that the ParF DNA partition protein of the ParA family assembles into a three-dimensional meshwork that uses the nucleoid as a scaffold and periodically shuttles between its poles. Whereas ParF specifies the territory for plasmid trafficking, the ParG partner protein dictates the tempo of ParF assembly cycles and plasmid segregation events by stimulating ParF adenosine triphosphate hydrolysis. Mutants in which this ParG temporal regulation is ablated show partition deficient phenotypes as a result of either altered ParF structure or dynamics and indicate that ParF nucleoid localization and dynamic relocation, although necessary, are not sufficient per se to ensure plasmid segregation. We propose a Venus flytrap model that merges the concepts of ParA polymerization and gradient formation and speculate that a transient, dynamic network of intersecting polymers that branches into the nucleoid interior is a widespread mechanism to distribute sizeable cargos within prokaryotic cells.
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Affiliation(s)
- Brett N. McLeod
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | | | - Madhuri T. Barge
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Nam K. Tonthat
- Department of Biochemistry, Duke University Medical Center, Duke University, Durham, NC 27710, USA
| | - Maria A. Schumacher
- Department of Biochemistry, Duke University Medical Center, Duke University, Durham, NC 27710, USA
| | - Finbarr Hayes
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PL, UK
| | - Daniela Barillà
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
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76
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Mangiameli SM, Merrikh CN, Wiggins PA, Merrikh H. Transcription leads to pervasive replisome instability in bacteria. eLife 2017; 6. [PMID: 28092263 PMCID: PMC5305214 DOI: 10.7554/elife.19848] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 01/15/2017] [Indexed: 12/19/2022] Open
Abstract
The canonical model of DNA replication describes a highly-processive and largely continuous process by which the genome is duplicated. This continuous model is based upon in vitro reconstitution and in vivo ensemble experiments. Here, we characterize the replisome-complex stoichiometry and dynamics with single-molecule resolution in bacterial cells. Strikingly, the stoichiometries of the replicative helicase, DNA polymerase, and clamp loader complexes are consistent with the presence of only one active replisome in a significant fraction of cells (>40%). Furthermore, many of the observed complexes have short lifetimes (<8 min), suggesting that replisome disassembly is quite prevalent, possibly occurring several times per cell cycle. The instability of the replisome complex is conflict-induced: transcription inhibition stabilizes these complexes, restoring the second replisome in many of the cells. Our results suggest that, in contrast to the canonical model, DNA replication is a largely discontinuous process in vivo due to pervasive replication-transcription conflicts. DOI:http://dx.doi.org/10.7554/eLife.19848.001
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Affiliation(s)
| | | | - Paul A Wiggins
- Department of Physics, University of Washington, Seattle, United States.,Department of Microbiology, University of Washington, Seattle, United States.,Department of Bioengineering, University of Washington, Seattle, United States
| | - Houra Merrikh
- Department of Microbiology, University of Washington, Seattle, United States.,Department of Genome Sciences, University of Washington, Seattle, United States
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77
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Mangiameli SM, Merrikh CN, Wiggins PA, Merrikh H. Transcription leads to pervasive replisome instability in bacteria. eLife 2017; 6. [PMID: 28092263 DOI: 10.7554/elife.19848.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 01/15/2017] [Indexed: 05/21/2023] Open
Abstract
The canonical model of DNA replication describes a highly-processive and largely continuous process by which the genome is duplicated. This continuous model is based upon in vitro reconstitution and in vivo ensemble experiments. Here, we characterize the replisome-complex stoichiometry and dynamics with single-molecule resolution in bacterial cells. Strikingly, the stoichiometries of the replicative helicase, DNA polymerase, and clamp loader complexes are consistent with the presence of only one active replisome in a significant fraction of cells (>40%). Furthermore, many of the observed complexes have short lifetimes (<8 min), suggesting that replisome disassembly is quite prevalent, possibly occurring several times per cell cycle. The instability of the replisome complex is conflict-induced: transcription inhibition stabilizes these complexes, restoring the second replisome in many of the cells. Our results suggest that, in contrast to the canonical model, DNA replication is a largely discontinuous process in vivo due to pervasive replication-transcription conflicts.
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Affiliation(s)
| | | | - Paul A Wiggins
- Department of Physics, University of Washington, Seattle, United States
- Department of Microbiology, University of Washington, Seattle, United States
- Department of Bioengineering, University of Washington, Seattle, United States
| | - Houra Merrikh
- Department of Microbiology, University of Washington, Seattle, United States
- Department of Genome Sciences, University of Washington, Seattle, United States
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78
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Demarre G, Prudent V, Espéli O. Imaging the Cell Cycle of Pathogen E. coli During Growth in Macrophage. Methods Mol Biol 2017; 1624:227-236. [PMID: 28842887 DOI: 10.1007/978-1-4939-7098-8_17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The study of the bacterial cell cycle at the single cell level can not only give insights on the fitness of the bacterial population but also reveal heterogeneous behavior. Typically, the DNA replication, the cell division, and the nucleoid conformation are appropriate representatives of the bacterial cell cycle. Because bacteria rapidly adapt their growth rate to environmental changes, the measure of cell cycle parameters gives valuable insights for the study of bacterial stress response or host-pathogen interactions. Here we describe methods to first introduce fluorescent fusion proteins and fluorescent tag within the chromosome of pathogenic bacteria to study these cell cycle steps; then to follow them within macrophages using a confocal spinning disk microscope.
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Affiliation(s)
- Gaëlle Demarre
- CIRB, Collège de France, UMR CNRS 7241 INSERM U1050, 11 Place Marcelin Berthelot, 75005, Paris, France.
| | - Victoria Prudent
- CIRB, Collège de France, UMR CNRS 7241 INSERM U1050, 11 Place Marcelin Berthelot, 75005, Paris, France
| | - Olivier Espéli
- CIRB, Collège de France, UMR CNRS 7241 INSERM U1050, 11 Place Marcelin Berthelot, 75005, Paris, France.
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79
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Rademacher A, Erdel F, Trojanowski J, Schumacher S, Rippe K. Real-time observation of light-controlled transcription in living cells. J Cell Sci 2017. [DOI: 10.1242/jcs.205534] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023] Open
Abstract
Gene expression is tightly regulated in space and time. To dissect this process with high temporal resolution, we introduce an optogenetic tool termed BLInCR (Blue Light-Induced Chromatin Recruitment) that combines rapid and reversible light-dependent recruitment of effector proteins with a real-time readout for transcription. We used BLInCR to control the activity of a reporter gene cluster in the human osteosarcoma cell line U2OS by reversibly recruiting the viral transactivator VP16. RNA production was detectable ∼2 minutes after VP16 recruitment and readily decreased when VP16 dissociated from the cluster in the absence of light. Quantitative assessment of the activation process revealed biphasic activation kinetics with a pronounced early phase in cells treated with the histone deacetylase inhibitor SAHA. Comparison with kinetic models for transcription activation suggests that the gene cluster undergoes a maturation process when activated. We anticipate that BLInCR will facilitate the study of transcription dynamics in living cells.
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Affiliation(s)
- Anne Rademacher
- German Cancer Research Center (DKFZ) and Bioquant, Division of Chromatin Networks, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Fabian Erdel
- German Cancer Research Center (DKFZ) and Bioquant, Division of Chromatin Networks, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Jorge Trojanowski
- German Cancer Research Center (DKFZ) and Bioquant, Division of Chromatin Networks, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Sabrina Schumacher
- German Cancer Research Center (DKFZ) and Bioquant, Division of Chromatin Networks, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Karsten Rippe
- German Cancer Research Center (DKFZ) and Bioquant, Division of Chromatin Networks, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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80
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Schindler D, Milbredt S, Sperlea T, Waldminghaus T. Design and Assembly of DNA Sequence Libraries for Chromosomal Insertion in Bacteria Based on a Set of Modified MoClo Vectors. ACS Synth Biol 2016; 5:1362-1368. [PMID: 27306697 DOI: 10.1021/acssynbio.6b00089] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Efficient assembly of large DNA constructs is a key technology in synthetic biology. One of the most popular assembly systems is the MoClo standard in which restriction and ligation of multiple fragments occurs in a one-pot reaction. The system is based on a smart vector design and type IIs restriction enzymes, which cut outside their recognition site. While the initial MoClo vectors had been developed for the assembly of multiple transcription units of plants, some derivatives of the vectors have been developed over the last years. Here we present a new set of MoClo vectors for the assembly of fragment libraries and insertion of constructs into bacterial chromosomes. The vectors are accompanied by a computer program that generates a degenerate synthetic DNA sequence that excludes "forbidden" DNA motifs. We demonstrate the usability of the new approach by construction of a stable fluorescence repressor operator system (FROS).
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Affiliation(s)
- Daniel Schindler
- Chromosome Biology Group,
LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-Universität Marburg, Hans-Meerwein-Str. 6, D-35043 Marburg, Germany
| | - Sarah Milbredt
- Chromosome Biology Group,
LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-Universität Marburg, Hans-Meerwein-Str. 6, D-35043 Marburg, Germany
| | - Theodor Sperlea
- Chromosome Biology Group,
LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-Universität Marburg, Hans-Meerwein-Str. 6, D-35043 Marburg, Germany
| | - Torsten Waldminghaus
- Chromosome Biology Group,
LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-Universität Marburg, Hans-Meerwein-Str. 6, D-35043 Marburg, Germany
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81
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Kois-Ostrowska A, Strzałka A, Lipietta N, Tilley E, Zakrzewska-Czerwińska J, Herron P, Jakimowicz D. Unique Function of the Bacterial Chromosome Segregation Machinery in Apically Growing Streptomyces - Targeting the Chromosome to New Hyphal Tubes and its Anchorage at the Tips. PLoS Genet 2016; 12:e1006488. [PMID: 27977672 PMCID: PMC5157956 DOI: 10.1371/journal.pgen.1006488] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 11/16/2016] [Indexed: 01/26/2023] Open
Abstract
The coordination of chromosome segregation with cell growth is fundamental to the proliferation of any organism. In most unicellular bacteria, chromosome segregation is strictly coordinated with cell division and involves ParA that moves the ParB nucleoprotein complexes bi- or unidirectionally toward the cell pole(s). However, the chromosome organization in multiploid, apically extending and branching Streptomyces hyphae challenges the known mechanisms of bacterial chromosome segregation. The complex Streptomyces life cycle involves two stages: vegetative growth and sporulation. In the latter stage, multiple cell divisions accompanied by chromosome compaction and ParAB assisted segregation turn multigenomic hyphal cell into a chain of unigenomic spores. However, the requirement for active chromosome segregation is unclear in the absence of canonical cell division during vegetative growth except in the process of branch formation. The mechanism by which chromosomes are targeted to new hyphae in streptomycete vegetative growth has remained unknown until now. Here, we address the question of whether active chromosome segregation occurs at this stage. Applied for the first time in Streptomyces, labelling of the chromosomal replication initiation region (oriC) and time-lapse microscopy, revealed that in vegetative hyphae every copy of the chromosome is complexed with ParB, whereas ParA, through interaction with the apical protein complex (polarisome), tightly anchors only one chromosome at the hyphal tip. The anchor is maintained during replication, when ParA captures one of the daughter oriCs. During spore germination and branching, ParA targets one of the multiple chromosomal copies to the new hyphal tip, enabling efficient elongation of hyphal tube. Thus, our studies reveal a novel role for ParAB proteins during hyphal tip establishment and extension. To proliferate, cells synchronize growth and division with chromosome segregation. In unicellular bacteria, chromosomes segregate during replication by active movement of nucleoprotein complexes toward the cell pole(s). Here, we asked the question how active chromosome segregation occurs in the absence of cell division, during hyphal growth and branching of the filamentous bacterium, Streptomyces coelicolor. We show that in multigenomic Streptomyces hyphae, the bacterial segregation machinery anchors a single chromosome at the hyphal tip. Through chromosomal anchorage, segregation proteins facilitate chromosome targeting to the newly formed germ tubes or branches. Thus, being adapted for apical growth, in Streptomyces hyphae the bacterial segregation machinery imposes a chromosome distribution that is reminiscent of nuclear distribution in apically growing eukaryotic cells such as filamentous fungi.
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Affiliation(s)
| | | | | | - Emma Tilley
- Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Jolanta Zakrzewska-Czerwińska
- Faculty of Biotechnology, University of Wroclaw, Poland
- Institute of Immunology and Experimental Therapy, Wroclaw, Poland
| | - Paul Herron
- Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Dagmara Jakimowicz
- Faculty of Biotechnology, University of Wroclaw, Poland
- Institute of Immunology and Experimental Therapy, Wroclaw, Poland
- * E-mail:
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82
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Affiliation(s)
- Tao Jin
- Iowa State University; Department of Chemical and Biological Engineering; 2114 Sweeney Hall, 618 Bissell Rd. Ames, IA 50011 USA
| | - Jieni Lian
- Iowa State University; Department of Chemical and Biological Engineering; 2114 Sweeney Hall, 618 Bissell Rd. Ames, IA 50011 USA
| | - Laura R. Jarboe
- Iowa State University; Department of Chemical and Biological Engineering; 2114 Sweeney Hall, 618 Bissell Rd. Ames, IA 50011 USA
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83
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Surovtsev IV, Campos M, Jacobs-Wagner C. DNA-relay mechanism is sufficient to explain ParA-dependent intracellular transport and patterning of single and multiple cargos. Proc Natl Acad Sci U S A 2016; 113:E7268-E7276. [PMID: 27799522 PMCID: PMC5135302 DOI: 10.1073/pnas.1616118113] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Spatial ordering of macromolecular components inside cells is important for cellular physiology and replication. In bacteria, ParA/B systems are known to generate various intracellular patterns that underlie the transport and partitioning of low-copy-number cargos such as plasmids. ParA/B systems consist of ParA, an ATPase that dimerizes and binds DNA upon ATP binding, and ParB, a protein that binds the cargo and stimulates ParA ATPase activity. Inside cells, ParA is asymmetrically distributed, forming a propagating wave that is followed by the ParB-rich cargo. These correlated dynamics lead to cargo oscillation or equidistant spacing over the nucleoid depending on whether the cargo is in single or multiple copies. Currently, there is no model that explains how these different spatial patterns arise and relate to each other. Here, we test a simple DNA-relay model that has no imposed asymmetry and that only considers the ParA/ParB biochemistry and the known fluctuating and elastic dynamics of chromosomal loci. Stochastic simulations with experimentally derived parameters demonstrate that this model is sufficient to reproduce the signature patterns of ParA/B systems: the propagating ParA gradient correlated with the cargo dynamics, the single-cargo oscillatory motion, and the multicargo equidistant patterning. Stochasticity of ATP hydrolysis breaks the initial symmetry in ParA distribution, resulting in imbalance of elastic force acting on the cargo. Our results may apply beyond ParA/B systems as they reveal how a minimal system of two players, one binding to DNA and the other modulating this binding, can transform directionally random DNA fluctuations into directed motion and intracellular patterning.
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Affiliation(s)
- Ivan V Surovtsev
- Microbial Sciences Institute, Yale University, West Haven, CT 06517
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06516
- Howard Hughes Medical Institute, Yale University, New Haven, CT 06516
| | - Manuel Campos
- Microbial Sciences Institute, Yale University, West Haven, CT 06517
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06516
- Howard Hughes Medical Institute, Yale University, New Haven, CT 06516
| | - Christine Jacobs-Wagner
- Microbial Sciences Institute, Yale University, West Haven, CT 06517;
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06516
- Howard Hughes Medical Institute, Yale University, New Haven, CT 06516
- Department of Microbial Pathogenesis, Yale Medical School, New Haven, CT 06516
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84
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Affiliation(s)
- Ido Golding
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030;
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
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85
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Lavatine L, He S, Caumont-Sarcos A, Guynet C, Marty B, Chandler M, Ton-Hoang B. Single strand transposition at the host replication fork. Nucleic Acids Res 2016; 44:7866-83. [PMID: 27466393 PMCID: PMC5027513 DOI: 10.1093/nar/gkw661] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 07/12/2016] [Accepted: 07/13/2016] [Indexed: 11/21/2022] Open
Abstract
Members of the IS200/IS605 insertion sequence family differ fundamentally from classical IS essentially by their specific single-strand (ss) transposition mechanism, orchestrated by the Y1 transposase, TnpA, a small HuH enzyme which recognizes and processes ss DNA substrates. Transposition occurs by the 'peel and paste' pathway composed of two steps: precise excision of the top strand as a circular ss DNA intermediate; and subsequent integration into a specific ssDNA target. Transposition of family members was experimentally shown or suggested by in silico high-throughput analysis to be intimately coupled to the lagging strand template of the replication fork. In this study, we investigated factors involved in replication fork targeting and analysed DNA-binding properties of the transposase which can assist localization of ss DNA substrates on the replication fork. We showed that TnpA interacts with the β sliding clamp, DnaN and recognizes DNA which mimics replication fork structures. We also showed that dsDNA can facilitate TnpA targeting ssDNA substrates. We analysed the effect of Ssb and RecA proteins on TnpA activity in vitro and showed that while RecA does not show a notable effect, Ssb inhibits integration. Finally we discuss the way(s) in which integration may be directed into ssDNA at the replication fork.
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Affiliation(s)
- Laure Lavatine
- Laboratoire de Microbiologie et Génétique Moléculaires, CBI, CNRS, 118 Route de Narbonne, F-31062 Toulouse Cedex, France
| | - Susu He
- Laboratoire de Microbiologie et Génétique Moléculaires, CBI, CNRS, 118 Route de Narbonne, F-31062 Toulouse Cedex, France
| | - Anne Caumont-Sarcos
- Laboratoire de Microbiologie et Génétique Moléculaires, CBI, CNRS, 118 Route de Narbonne, F-31062 Toulouse Cedex, France
| | - Catherine Guynet
- Laboratoire de Microbiologie et Génétique Moléculaires, CBI, CNRS, 118 Route de Narbonne, F-31062 Toulouse Cedex, France
| | - Brigitte Marty
- Laboratoire de Microbiologie et Génétique Moléculaires, CBI, CNRS, 118 Route de Narbonne, F-31062 Toulouse Cedex, France
| | - Mick Chandler
- Laboratoire de Microbiologie et Génétique Moléculaires, CBI, CNRS, 118 Route de Narbonne, F-31062 Toulouse Cedex, France
| | - Bao Ton-Hoang
- Laboratoire de Microbiologie et Génétique Moléculaires, CBI, CNRS, 118 Route de Narbonne, F-31062 Toulouse Cedex, France
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86
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Dickerson D, Gierliński M, Singh V, Kitamura E, Ball G, Tanaka TU, Owen-Hughes T. High resolution imaging reveals heterogeneity in chromatin states between cells that is not inherited through cell division. BMC Cell Biol 2016; 17:33. [PMID: 27609610 PMCID: PMC5016949 DOI: 10.1186/s12860-016-0111-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 08/25/2016] [Indexed: 01/23/2023] Open
Abstract
Background Genomes of eukaryotes exist as chromatin, and it is known that different chromatin states can influence gene regulation. Chromatin is not a static structure, but is known to be dynamic and vary between cells. In order to monitor the organisation of chromatin in live cells we have engineered fluorescent fusion proteins which recognize specific operator sequences to tag pairs of syntenic gene loci. The separation of these loci was then tracked in three dimensions over time using fluorescence microscopy. Results We established a work flow for measuring the distance between two fluorescently tagged, syntenic gene loci with a mean measurement error of 63 nm. In general, physical separation was observed to increase with increasing genomic separations. However, the extent to which chromatin is compressed varies for different genomic regions. No correlation was observed between compaction and the distribution of chromatin markers from genomic datasets or with contacts identified using capture based approaches. Variation in spatial separation was also observed within cells over time and between cells. Differences in the conformation of individual loci can persist for minutes in individual cells. Separation of reporter loci was found to be similar in related and unrelated daughter cell pairs. Conclusions The directly observed physical separation of reporter loci in live cells is highly dynamic both over time and from cell to cell. However, consistent differences in separation are observed over some chromosomal regions that do not correlate with factors known to influence chromatin states. We conclude that as yet unidentified parameters influence chromatin configuration. We also find that while heterogeneity in chromatin states can be maintained for minutes between cells, it is not inherited through cell division. This may contribute to cell-to-cell transcriptional heterogeneity. Electronic supplementary material The online version of this article (doi:10.1186/s12860-016-0111-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- David Dickerson
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Marek Gierliński
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Vijender Singh
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Etsushi Kitamura
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Graeme Ball
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Tomoyuki U Tanaka
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Tom Owen-Hughes
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK. .,Wellcome Trust Building, University of Dundee, Dow Street, Dundee, DD1 5EH, UK.
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87
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Mettrick KA, Lawrence N, Mason C, Weaver GM, Corocher TA, Grainge I. Inducing a Site Specific Replication Blockage in E. coli Using a Fluorescent Repressor Operator System. J Vis Exp 2016. [PMID: 27583408 DOI: 10.3791/54434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Obstacles present on DNA, including tightly-bound proteins and various lesions, can severely inhibit the progression of the cell's replication machinery. The stalling of a replisome can lead to its dissociation from the chromosome, either in part or its entirety, leading to the collapse of the replication fork. The recovery from this collapse is a necessity for the cell to accurately complete chromosomal duplication and subsequently divide. Therefore, when the collapse occurs, the cell has evolved diverse mechanisms that take place to restore the DNA fork and allow replication to be completed with high fidelity. Previously, these replication repair pathways in bacteria have been studied using UV damage, which has the disadvantage of not being localized to a known site. This manuscript describes a system utilizing a Fluorescence Repressor Operator System (FROS) to create a site-specific protein block that can induce the stalling and collapse of replication forks in Escherichia coli. Protocols detail how the status of replication can be visualized in single living cells using fluorescence microscopy and DNA replication intermediates can be analyzed by 2-dimensional agarose gel electrophoresis. Temperature sensitive mutants of replisome components (e.g. DnaBts) can be incorporated into the system to induce a synchronous collapse of the replication forks. Furthermore, the roles of the recombination proteins and helicases that are involved in these processes can be studied using genetic knockouts within this system.
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Affiliation(s)
- Karla A Mettrick
- School of Environmental and Life Sciences, University of Newcastle
| | - Nikki Lawrence
- School of Environmental and Life Sciences, University of Newcastle
| | - Claire Mason
- School of Environmental and Life Sciences, University of Newcastle
| | - Georgia M Weaver
- School of Environmental and Life Sciences, University of Newcastle
| | | | - Ian Grainge
- School of Environmental and Life Sciences, University of Newcastle;
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88
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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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89
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The Synchronization of Replication and Division Cycles in Individual E. coli Cells. Cell 2016; 166:729-739. [DOI: 10.1016/j.cell.2016.06.052] [Citation(s) in RCA: 245] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 03/25/2016] [Accepted: 06/28/2016] [Indexed: 01/20/2023]
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90
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Hayes S, Wang W, Rajamanickam K, Chu A, Banerjee A, Hayes C. Lambda gpP-DnaB Helicase Sequestration and gpP-RpoB Associated Effects: On Screens for Auxotrophs, Selection for Rif(R), Toxicity, Mutagenicity, Plasmid Curing. Viruses 2016; 8:E172. [PMID: 27338450 PMCID: PMC4926192 DOI: 10.3390/v8060172] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 05/25/2016] [Accepted: 06/09/2016] [Indexed: 12/03/2022] Open
Abstract
The bacteriophage lambda replication initiation protein P exhibits a toxic effect on its Escherichia coli (E. coli) host, likely due to the formation of a dead-end P-DnaB complex, sequestering the replicative DnaB helicase from further activity. Intracellular expression of P triggers SOS-independent cellular filamentation and rapidly cures resident ColE1 plasmids. The toxicity of P is suppressed by alleles of P or dnaB. We asked whether P buildup within a cell can influence E. coli replication fidelity. The influence of P expression from a defective prophage, or when cloned and expressed from a plasmid was examined by screening for auxotrophic mutants, or by selection for rifampicin resistant (Rif(R)) cells acquiring mutations within the rpoB gene encoding the β-subunit of RNA polymerase (RNAP), nine of which proved unique. Using fluctuation assays, we show that the intracellular expression of P evokes a mutator effect. Most of the Rif(R) mutants remained P(S) and localized to the Rif binding pocket in RNAP, but a subset acquired a P(R) phenotype, lost sensitivity to ColE1 plasmid curing, and localized outside of the pocket. One P(R) mutation was identical to rpo*Q148P, which alleviates the UV-sensitivity of ruv strains defective in the migration and resolution of Holliday junctions and destabilizes stalled RNAP elongation complexes. The results suggest that P-DnaB sequestration is mutagenic and supports an earlier observation that P can interact with RNAP.
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Affiliation(s)
- Sidney Hayes
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada.
| | - Wen Wang
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada.
| | - Karthic Rajamanickam
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada.
| | - Audrey Chu
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada.
| | - Anirban Banerjee
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada.
| | - Connie Hayes
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada.
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91
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Probing Chromosome Dynamics in Bacillus subtilis. Methods Mol Biol 2016. [PMID: 27283304 DOI: 10.1007/978-1-4939-3631-1_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Research over the last two decades has revealed that bacterial genomes are, in fact, highly organized. The goal of future research is to understand the molecular mechanisms underlying bacterial chromosome architecture and dynamics during the cell cycle. Here we discuss techniques that can be used with live cells to analyze chromosome structure and segregation in the gram-positive model organism Bacillus subtilis.
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92
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Wiktor J, Lesterlin C, Sherratt DJ, Dekker C. CRISPR-mediated control of the bacterial initiation of replication. Nucleic Acids Res 2016; 44:3801-10. [PMID: 27036863 PMCID: PMC4857001 DOI: 10.1093/nar/gkw214] [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: 01/27/2016] [Revised: 03/16/2016] [Accepted: 03/18/2016] [Indexed: 12/20/2022] Open
Abstract
Programmable control of the cell cycle has been shown to be a powerful tool in cell-biology studies. Here, we develop a novel system for controlling the bacterial cell cycle, based on binding of CRISPR/dCas9 to the origin-of-replication locus. Initiation of replication of bacterial chromosomes is accurately regulated by the DnaA protein, which promotes the unwinding of DNA at oriC We demonstrate that the binding of CRISPR/dCas9 to any position within origin or replication blocks the initiation of replication. Serial-dilution plating, single-cell fluorescence microscopy, and flow-cytometry experiments show that ongoing rounds of chromosome replication are finished upon CRISPR/dCas9 binding, but no new rounds are initiated. Upon arrest, cells stay metabolically active and accumulate cell mass. We find that elevating the temperature from 37 to 42°C releases the CRISR/dCas9 replication inhibition, and we use this feature to recover cells from the arrest. Our simple and robust method of controlling the bacterial cell cycle is a useful asset for synthetic biology and DNA-replication studies in particular. The inactivation of CRISPR/dCas9 binding at elevated temperatures may furthermore be of wide interest for CRISPR/Cas9 applications in genomic engineering.
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Affiliation(s)
- Jakub Wiktor
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2628CJ Delft, The Netherlands
| | | | - David J Sherratt
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2628CJ Delft, The Netherlands
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93
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Frage B, Döhlemann J, Robledo M, Lucena D, Sobetzko P, Graumann PL, Becker A. Spatiotemporal choreography of chromosome and megaplasmids in theSinorhizobium meliloticell cycle. Mol Microbiol 2016; 100:808-23. [DOI: 10.1111/mmi.13351] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/05/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Benjamin Frage
- LOEWE Center for Synthetic Microbiology and Faculty of Biology; Philipps-Universität Marburg; 35032 Marburg Germany
| | - Johannes Döhlemann
- LOEWE Center for Synthetic Microbiology and Faculty of Biology; Philipps-Universität Marburg; 35032 Marburg Germany
| | - Marta Robledo
- LOEWE Center for Synthetic Microbiology and Faculty of Biology; Philipps-Universität Marburg; 35032 Marburg Germany
| | - Daniella Lucena
- LOEWE Center for Synthetic Microbiology and Faculty of Chemistry, Philipps-Universität Marburg, 35032; Marburg Germany
| | - Patrick Sobetzko
- LOEWE Center for Synthetic Microbiology and Faculty of Biology; Philipps-Universität Marburg; 35032 Marburg Germany
| | - Peter L. Graumann
- LOEWE Center for Synthetic Microbiology and Faculty of Chemistry, Philipps-Universität Marburg, 35032; Marburg Germany
| | - Anke Becker
- LOEWE Center for Synthetic Microbiology and Faculty of Biology; Philipps-Universität Marburg; 35032 Marburg Germany
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94
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Abstract
This chapter presents an analysis of the organization and distribution of the IS200/IS605 family of insertion sequences (IS). Members of this family are widespread in both bacteria and archaea. They are unusual because they use obligatory single-strand DNA intermediates, which distinguishes them from classical IS. We summarize studies of the experimental model systems IS608 (from Helicobacter pylori) and ISDra2 (from Deinococcus radiodurans) and present biochemical, genetic, and structural data that describe their transposition pathway and the way in which their transposase (an HuH rather than a DDE enzyme) catalyzes this process. The transposition of IS200/IS605 family members can be described as a "Peel-and-Paste" mechanism. We also address the probable domestication of IS200/IS605 family transposases as enzymes involved in multiplication of repeated extragenic palindromes and as potential homing endonucleases in intron-IS chimeras.
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95
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Lack of the H-NS Protein Results in Extended and Aberrantly Positioned DNA during Chromosome Replication and Segregation in Escherichia coli. J Bacteriol 2016; 198:1305-16. [PMID: 26858102 DOI: 10.1128/jb.00919-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 02/02/2016] [Indexed: 01/08/2023] Open
Abstract
UNLABELLED The architectural protein H-NS binds nonspecifically to hundreds of sites throughout the chromosome and can multimerize to stiffen segments of DNA as well as to form DNA-protein-DNA bridges. H-NS has been suggested to contribute to the orderly folding of the Escherichia coli chromosome in the highly compacted nucleoid. In this study, we investigated the positioning and dynamics of the origins, the replisomes, and the SeqA structures trailing the replication forks in cells lacking the H-NS protein. In H-NS mutant cells, foci of SeqA, replisomes, and origins were irregularly positioned in the cell. Further analysis showed that the average distance between the SeqA structures and the replisome was increased by ∼100 nm compared to that in wild-type cells, whereas the colocalization of SeqA-bound sister DNA behind replication forks was not affected. This result may suggest that H-NS contributes to the folding of DNA along adjacent segments. H-NS mutant cells were found to be incapable of adopting the distinct and condensed nucleoid structures characteristic of E. coli cells growing rapidly in rich medium. It appears as if H-NS mutant cells adopt a “slow-growth” type of chromosome organization under nutrient-rich conditions, which leads to a decreased cellular DNA content. IMPORTANCE It is not fully understood how and to what extent nucleoid-associated proteins contribute to chromosome folding and organization during replication and segregation in Escherichia coli. In this work, we find in vivo indications that cells lacking the nucleoid-associated protein H-NS have a lower degree of DNA condensation than wild-type cells. Our work suggests that H-NS is involved in condensing the DNA along adjacent segments on the chromosome and is not likely to tether newly replicated strands of sister DNA. We also find indications that H-NS is required for rapid growth with high DNA content and for the formation of a highly condensed nucleoid structure under such conditions.
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96
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Mettrick KA, Grainge I. Stability of blocked replication forks in vivo. Nucleic Acids Res 2016; 44:657-68. [PMID: 26490956 PMCID: PMC4737137 DOI: 10.1093/nar/gkv1079] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 10/06/2015] [Accepted: 10/07/2015] [Indexed: 11/17/2022] Open
Abstract
Replication of chromosomal DNA must be carried out to completion in order for a cell to proliferate. However, replication forks can stall during this process for a variety of reasons, including nucleoprotein 'roadblocks' and DNA lesions. In these circumstances the replisome copying the DNA may disengage from the chromosome to allow various repair processes to restore DNA integrity and enable replication to continue. Here, we report the in vivo stability of the replication fork when it encounters a nucleoprotein blockage in Escherichia coli. Using a site-specific and reversible protein block system in conjunction with the temperature sensitive DnaC helicase loader and DnaB replicative helicase, we monitored the disappearance of the Y-shaped DNA replication fork structures using neutral-neutral 2D agarose gels. We show the replication fork collapses within 5 min of encountering the roadblock. Therefore, the stalled replication fork does not pause at a block in a stable confirmation for an extended period of time as previously postulated.
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Affiliation(s)
- Karla A Mettrick
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Ian Grainge
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
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97
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Shao Q, Hawkins A, Zeng L. Phage DNA dynamics in cells with different fates. Biophys J 2016; 108:2048-60. [PMID: 25902444 DOI: 10.1016/j.bpj.2015.03.027] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 02/24/2015] [Accepted: 03/17/2015] [Indexed: 11/27/2022] Open
Abstract
Bacteriophage λ begins its infection cycle by ejecting its DNA into its host Escherichia coli cell, after which either a lytic or a lysogenic pathway is followed, resulting in different cell fates. In this study, using a new technique to monitor the spatiotemporal dynamics of the phage DNA in vivo, we found that the phage DNA moves via two distinct modes, localized motion and motion spanning the whole cell. One or the other motion is preferred, depending on where the phage DNA is ejected into the cell. By examining the phage DNA trajectories, we found the motion to be subdiffusive. Moreover, phage DNA motion is the same in the early phase of the infection cycle, irrespective of whether the lytic or lysogenic pathway is followed; hence, cell-fate decision-making appears not to be correlated with the phage DNA motion. However, after the cell commits to one pathway or the other, phage DNA movement slows during the late phase of the lytic cycle, whereas it remains the same during the entire lysogenic cycle. Throughout the infection cycle, phage DNA prefers the regions around the quarter positions of the cell.
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Affiliation(s)
- Qiuyan Shao
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas; Center for Phage Technology, Texas A&M University, College Station, Texas
| | - Alexander Hawkins
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas; Center for Phage Technology, Texas A&M University, College Station, Texas
| | - Lanying Zeng
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas; Center for Phage Technology, Texas A&M University, College Station, Texas.
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98
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Abstract
How is the bacterial chromosome organized within the bacterial cell? Over the last 60 years, a variety of approaches have been used to investigate this question. More recently, the parallel development of epifluorescence microscopy and genetic tools has enabled the direct visualization of the intracellular positioning of DNA sequences in live cells and has consequently revolutionized our view of the architecture of the nucleoid in vivo. In this chapter I present a comprehensive methodology designed to characterize the architecture of the nucleoid DNA and the positioning of specific DNA sequences in live Escherichia coli cells. DNA localization systems, preparation of stable agarose-mounted microscopy slides, and basic image analysis tools are mentioned.
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Affiliation(s)
- Christian Lesterlin
- MMSB - Molecular Microbiology and Structural Biochemistry, Université Lyon 1, CNRS, UMR 5086, 7 Passage du Vercors, 69 367, Lyon Cedex 07, France.
| | - Nelly Duabrry
- MMSB - Molecular Microbiology and Structural Biochemistry, Université Lyon 1, CNRS, UMR 5086, 7 Passage du Vercors, 69 367, Lyon Cedex 07, France.
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99
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A model for chromosome organization during the cell cycle in live E. coli. Sci Rep 2015; 5:17133. [PMID: 26597953 PMCID: PMC4657085 DOI: 10.1038/srep17133] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 09/22/2015] [Indexed: 11/09/2022] Open
Abstract
Bacterial chromosomal DNA is a highly compact nucleoid. The organization of this nucleoid is poorly understood due to limitations in the methods used to monitor the complexities of DNA organization in live bacteria. Here, we report that circular plasmid DNA is auto-packaged into a uniform dual-toroidal-spool conformation in response to mechanical stress stemming from sharp bending and un-winding by atomic force microscopic analysis. The mechanism underlying this phenomenon was deduced with basic physical principles to explain the auto-packaging behaviour of circular DNA. Based on our observations and previous studies, we propose a dynamic model of how chromosomal DNA in E. coli may be organized during a cell division cycle. Next, we test the model by monitoring the development of HNS clusters in live E. coli during a cell cycle. The results were in close agreement with the model. Furthermore, the model accommodates a majority of the thus-far-discovered remarkable features of nucleoids in vivo.
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100
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Tas H, Nguyen CT, Patel R, Kim NH, Kuhlman TE. An Integrated System for Precise Genome Modification in Escherichia coli. PLoS One 2015; 10:e0136963. [PMID: 26332675 PMCID: PMC4558010 DOI: 10.1371/journal.pone.0136963] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 08/10/2015] [Indexed: 11/18/2022] Open
Abstract
We describe an optimized system for the easy, effective, and precise modification of the Escherichia coli genome. Genome changes are introduced first through the integration of a 1.3 kbp Landing Pad consisting of a gene conferring resistance to tetracycline (tetA) or the ability to metabolize the sugar galactose (galK). The Landing Pad is then excised as a result of double-strand breaks by the homing endonuclease I-SceI, and replaced with DNA fragments bearing the desired change via λ-Red mediated homologous recombination. Repair of the double strand breaks and counterselection against the Landing Pad (using NiCl2 for tetA or 2-deoxy-galactose for galK) allows the isolation of modified bacteria without the use of additional antibiotic selection. We demonstrate the power of this method to make a variety of genome modifications: the exact integration, without any extraneous sequence, of the lac operon (~6.5 kbp) to any desired location in the genome and without the integration of antibiotic markers; the scarless deletion of ribosomal rrn operons (~6 kbp) through either intrachromosomal or oligonucleotide recombination; and the in situ fusion of native genes to fluorescent reporter genes without additional perturbation.
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Affiliation(s)
- Huseyin Tas
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Cac T. Nguyen
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Ravish Patel
- Department of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Neil H. Kim
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Thomas E. Kuhlman
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
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