Journal articles: 'Nucleoid Organization'

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Chen, Inês. "Nucleoid organization." Nature Structural & Molecular Biology 18, no. 10 (October 2011): 1085. http://dx.doi.org/10.1038/nsmb.2156.

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Farge, Géraldine, and Maria Falkenberg. "Organization of DNA in Mammalian Mitochondria." International Journal of Molecular Sciences 20, no. 11 (June 5, 2019): 2770. http://dx.doi.org/10.3390/ijms20112770.

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As with all organisms that must organize and condense their DNA to fit within the limited volume of a cell or a nucleus, mammalian mitochondrial DNA (mtDNA) is packaged into nucleoprotein structures called nucleoids. In this study, we first introduce the general modes of DNA compaction, especially the role of the nucleoid-associated proteins (NAPs) that structure the bacterial chromosome. We then present the mitochondrial nucleoid and the main factors responsible for packaging of mtDNA: ARS- (autonomously replicating sequence-) binding factor 2 protein (Abf2p) in yeast and mitochondrial transcription factor A (TFAM) in mammals. We summarize the single-molecule manipulation experiments on mtDNA compaction and visualization of mitochondrial nucleoids that have led to our current knowledge on mtDNA compaction. Lastly, we discuss the possible regulatory role of DNA packaging by TFAM in DNA transactions such as mtDNA replication and transcription.

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Bogenhagen, Daniel F. "Does mtDNA nucleoid organization impact aging?" Experimental Gerontology 45, no. 7-8 (August 2010): 473–77. http://dx.doi.org/10.1016/j.exger.2009.12.002.

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Macvanin, Mirjana, and Sankar Adhya. "Architectural organization in E. coli nucleoid." Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 1819, no. 7 (July 2012): 830–35. http://dx.doi.org/10.1016/j.bbagrm.2012.02.012.

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Castellana, Michele, Sophia Hsin-Jung Li, and Ned S. Wingreen. "Spatial organization of bacterial transcription and translation." Proceedings of the National Academy of Sciences 113, no. 33 (August 2, 2016): 9286–91. http://dx.doi.org/10.1073/pnas.1604995113.

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In bacteria such as Escherichia coli, DNA is compacted into a nucleoid near the cell center, whereas ribosomes—molecular complexes that translate mRNAs into proteins—are mainly localized to the poles. We study the impact of this spatial organization using a minimal reaction–diffusion model for the cellular transcriptional–translational machinery. Although genome-wide mRNA-nucleoid segregation still lacks experimental validation, our model predicts that ∼90% of mRNAs are segregated to the poles. In addition, our analysis reveals a “circulation” of ribosomes driven by the flux of mRNAs, from synthesis in the nucleoid to degradation at the poles. We show that our results are robust with respect to multiple, biologically relevant factors, such as mRNA degradation by RNase enzymes, different phases of the cell division cycle and growth rates, and the existence of nonspecific, transient interactions between ribosomes and mRNAs. Finally, we confirm that the observed nucleoid size stems from a balance between the forces that the chromosome and mRNAs exert on each other. This suggests a potential global feedback circuit in which gene expression feeds back on itself via nucleoid compaction.

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Passot, Fanny Marie, Hong Ha Nguyen, Cloelia Dard-Dascot, Claude Thermes, Pascale Servant, Olivier Espéli, and Suzanne Sommer. "Nucleoid organization in the radioresistant bacteriumDeinococcus radiodurans." Molecular Microbiology 97, no. 4 (June 25, 2015): 759–74. http://dx.doi.org/10.1111/mmi.13064.

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Rebelo, Adriana P., Lloye M. Dillon, and Carlos T. Moraes. "Mitochondrial DNA transcription regulation and nucleoid organization." Journal of Inherited Metabolic Disease 34, no. 4 (May 4, 2011): 941–51. http://dx.doi.org/10.1007/s10545-011-9330-8.

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Hsu, Y. H. "Distribution of gyrase and topoisomerase IV on bacterial nucleoid: implications for nucleoid organization." Nucleic Acids Research 34, no. 10 (May 31, 2006): 3128–38. http://dx.doi.org/10.1093/nar/gkl392.

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Eltsov, Mikhail, and Jacques Dubochet. "Fine Structure of the Deinococcus radiodurans Nucleoid Revealed by Cryoelectron Microscopy of Vitreous Sections." Journal of Bacteriology 187, no. 23 (December 1, 2005): 8047–54. http://dx.doi.org/10.1128/jb.187.23.8047-8054.2005.

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ABSTRACT Transmission electron microscopy revealed that the nucleoid of the extremely radioresistant bacteria Deinococcus radiodurans may adopt an unusual ring shape. This led to the hypothesis that the tight toroidal package of the D. radiodurans genome might contribute to radioresistance by preventing diffusion of ends of double-stranded DNA breaks. The molecular arrangement of DNA in the nucleoid, which must be determined to test this hypothesis, is not discernible by conventional methods of electron microscopy. We have applied cryoelectron microscopy of vitreous sections and found that the DNA arrangement in D. radiodurans differs from toroidal spooling. Diffuse coralline nucleoids of exponentially growing D. radiodurans do not reveal any particular molecular order. Electron-dense granules are generally observed in the centers of nucleoids. In stationary-phase cells, the nucleoid segregates from cytoplasm and DNA filaments show locally parallel arrangements, with increasing aspects of cholesteric liquid crystalline phase upon prolonged starvation. The relevance of the observed nucleoid organization to the radiation resistance of D. radiodurans is discussed.

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Sun, Qin, and William Margolin. "Effects of Perturbing Nucleoid Structure on Nucleoid Occlusion-Mediated Toporegulation of FtsZ Ring Assembly." Journal of Bacteriology 186, no. 12 (June 15, 2004): 3951–59. http://dx.doi.org/10.1128/jb.186.12.3951-3959.2004.

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ABSTRACT In Escherichia coli, assembly of the FtsZ ring (Z ring) at the cell division site is negatively regulated by the nucleoid in a phenomenon called nucleoid occlusion (NO). Previous studies have indicated that chromosome packing plays a role in NO, as mukB mutants grown in rich medium often exhibit FtsZ rings on top of diffuse, unsegregated nucleoids. To address the potential role of overall nucleoid structure on NO, we investigated the effects of disrupting chromosome structure on Z-ring positioning. We found that NO was mostly normal in cells with inactivated DNA gyrase or in mukB-null mutants lacking topA, although some suppression of NO was evident in the latter case. Previous reports suggesting that transcription, translation, and membrane insertion of proteins (“transertion”) influence nucleoid structure prompted us to investigate whether disruption of these activities had effects on NO. Blocking transcription caused nucleoids to become diffuse, and FtsZ relocalized to multiple bands on top of these nucleoids, biased towards midcell. This suggested that these diffuse nucleoids were defective in NO. Blocking translation with chloramphenicol caused characteristic nucleoid compaction, but FtsZ rarely assembled on top of these centrally positioned nucleoids. This suggested that NO remained active upon translation inhibition. Blocking protein secretion by thermoinduction of a secA(Ts) strain caused a chromosome segregation defect similar to that in parC mutants, and NO was active. Although indirect effects are certainly possible with these experiments, the above data suggest that optimum NO activity may require specific organization and structure of the nucleoid.

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Stracy, Mathew, Christian Lesterlin, Federico Garza de Leon, Stephan Uphoff, Pawel Zawadzki, and Achillefs N. Kapanidis. "Live-cell superresolution microscopy reveals the organization of RNA polymerase in the bacterial nucleoid." Proceedings of the National Academy of Sciences 112, no. 32 (July 29, 2015): E4390—E4399. http://dx.doi.org/10.1073/pnas.1507592112.

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Despite the fundamental importance of transcription, a comprehensive analysis of RNA polymerase (RNAP) behavior and its role in the nucleoid organization in vivo is lacking. Here, we used superresolution microscopy to study the localization and dynamics of the transcription machinery and DNA in live bacterial cells, at both the single-molecule and the population level. We used photoactivated single-molecule tracking to discriminate between mobile RNAPs and RNAPs specifically bound to DNA, either on promoters or transcribed genes. Mobile RNAPs can explore the whole nucleoid while searching for promoters, and spend 85% of their search time in nonspecific interactions with DNA. On the other hand, the distribution of specifically bound RNAPs shows that low levels of transcription can occur throughout the nucleoid. Further, clustering analysis and 3D structured illumination microscopy (SIM) show that dense clusters of transcribing RNAPs form almost exclusively at the nucleoid periphery. Treatment with rifampicin shows that active transcription is necessary for maintaining this spatial organization. In faster growth conditions, the fraction of transcribing RNAPs increases, as well as their clustering. Under these conditions, we observed dramatic phase separation between the densest clusters of RNAPs and the densest regions of the nucleoid. These findings show that transcription can cause spatial reorganization of the nucleoid, with movement of gene loci out of the bulk of DNA as levels of transcription increase. This work provides a global view of the organization of RNA polymerase and transcription in living cells.

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Miyakawa, I., N. Sando, S. Kawano, S. Nakamura, and T. Kuroiwa. "Isolation of morphologically intact mitochondrial nucleoids from the yeast, Saccharomyces cerevisiae." Journal of Cell Science 88, no. 4 (November 1, 1987): 431–39. http://dx.doi.org/10.1242/jcs.88.4.431.

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Mitochondrial nucleoids (mt-nucleoids) of the yeast, Saccharomyces cerevisiae, were isolated from spheroplasts of stationary phase cells and their structure and organization were investigated by fluorescence microscopy, electron microscopy, and biochemical techniques. Isolated mt-nucleoids were spherical or ovoid and 0.3-0.6 micron in diameter, and were about the same size and shape as those observed in the cell by the DAPI staining technique. Measurement of DNA content of mt-nucleoids, using a video-intensified microscope system, after DAPI staining revealed that a mt-nucleoid in spheroplasts from stationary phase cells contains, on average, 3.9 mtDNA molecules and an isolated mt-nucleoid contains, on average, 3.1. Negatively stained electron micrographs showed that mt-nucleoids consist of particles 20–50 nm in diameter. SDS-polyacrylamide gel electrophoresis of mt-nucleoids detected 20 species of polypeptides in the molecular weight range from 10 X 10(3) to 70 X 10(3). Acid-urea/SDS two-dimensional electrophoresis of acid extract from mt-nucleoids indicated that a polypeptide of 20 X 10(3) is the only major polypeptide with basic property like histones.

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Zimmerman, Steven B. "Underlying regularity in the shapes of nucleoids of Escherichia coli: Implications for nucleoid organization and partition." Journal of Structural Biology 142, no. 2 (May 2003): 256–65. http://dx.doi.org/10.1016/s1047-8477(02)00637-8.

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14

Peeters, Eveline, Rosalie P. C. Driessen, Finn Werner, and Remus T. Dame. "The interplay between nucleoid organization and transcription in archaeal genomes." Nature Reviews Microbiology 13, no. 6 (May 6, 2015): 333–41. http://dx.doi.org/10.1038/nrmicro3467.

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15

Wang, W., G. W. Li, C. Chen, X. S. Xie, and X. Zhuang. "Chromosome Organization by a Nucleoid-Associated Protein in Live Bacteria." Science 333, no. 6048 (September 8, 2011): 1445–49. http://dx.doi.org/10.1126/science.1204697.

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Gray, William T., Sander K. Govers, Yingjie Xiang, Bradley R. Parry, Manuel Campos, Sangjin Kim, and Christine Jacobs-Wagner. "Nucleoid Size Scaling and Intracellular Organization of Translation across Bacteria." Cell 177, no. 6 (May 2019): 1632–48. http://dx.doi.org/10.1016/j.cell.2019.05.017.

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Chen, Chongyi, Wenqin Wang, Gene-Wei Li, Xiaowei Zhuang, and X. Sunney Xie. "Chromosome Organization by a Nucleoid-Associated Protein in Live Bacteria." Biophysical Journal 102, no. 3 (January 2012): 479a. http://dx.doi.org/10.1016/j.bpj.2011.11.2628.

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Driessen, Rosalie P. C., and Remus Th Dame. "Nucleoid-associated proteins in Crenarchaea." Biochemical Society Transactions 39, no. 1 (January 19, 2011): 116–21. http://dx.doi.org/10.1042/bst0390116.

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Architectural proteins play an important role in compacting and organizing the chromosomal DNA in all three kingdoms of life (Eukarya, Bacteria and Archaea). These proteins are generally not conserved at the amino acid sequence level, but the mechanisms by which they modulate the genome do seem to be functionally conserved across kingdoms. On a generic level, architectural proteins can be classified based on their structural effect as DNA benders, DNA bridgers or DNA wrappers. Although chromatin organization in archaea has not been studied extensively, quite a number of architectural proteins have been identified. In the present paper, we summarize the knowledge currently available on these proteins in Crenarchaea. By the type of architectural proteins available, the crenarchaeal nucleoid shows similarities with that of Bacteria. It relies on the action of a large set of small, abundant and generally basic proteins to compact and organize their genome and to modulate its activity.

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Thacker, Vivek V., Krystyna Bromek, Benoit Meijer, Jurij Kotar, Bianca Sclavi, Marco Cosentino Lagomarsino, Ulrich F. Keyser, and Pietro Cicuta. "Bacterial nucleoid structure probed by active drag and resistive pulse sensing." Integr. Biol. 6, no. 2 (2014): 184–91. http://dx.doi.org/10.1039/c3ib40147b.

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20

Meeusen, Shelly, and Jodi Nunnari. "Evidence for a two membrane–spanning autonomous mitochondrial DNA replisome." Journal of Cell Biology 163, no. 3 (November 3, 2003): 503–10. http://dx.doi.org/10.1083/jcb.200304040.

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The unit of inheritance for mitochondrial DNA (mtDNA) is a complex nucleoprotein structure termed the nucleoid. The organization of the nucleoid as well as its role in mtDNA replication remain largely unknown. Here, we show in Saccharomyces cerevisiae that at least two populations of nucleoids exist within the same mitochondrion and can be distinguished by their association with a discrete proteinaceous structure that spans the outer and inner mitochondrial membranes. Surprisingly, this two membrane–spanning structure (TMS) persists and self-replicates in the absence of mtDNA. We tested whether TMS functions to direct the replication of mtDNA. By monitoring BrdU incorporation, we observed that actively replicating nucleoids are associated exclusively with TMS. Consistent with TMS's role in mtDNA replication, we found that Mip1, the mtDNA polymerase, is also a stable component of TMS. Taken together, our observations reveal the existence of an autonomous two membrane–spanning mitochondrial replisome as well as provide a mechanism for how mtDNA replication and inheritance may be physically linked.

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Driessen, Rosalie P. C., and Remus Th Dame. "Structure and dynamics of the crenarchaeal nucleoid." Biochemical Society Transactions 41, no. 1 (January 29, 2013): 321–25. http://dx.doi.org/10.1042/bst20120336.

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Crenarchaeal genomes are organized into a compact nucleoid by a set of small chromatin proteins. Although there is little knowledge of chromatin structure in Archaea, similarities between crenarchaeal and bacterial chromatin proteins suggest that organization and regulation could be achieved by similar mechanisms. In the present review, we describe the molecular properties of crenarchaeal chromatin proteins and discuss the possible role of these architectural proteins in organizing the crenarchaeal chromatin and in gene regulation.

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Amit, Roee, Amos B. Oppenheim, and Joel Stavans. "Single Molecule Elasticity Measurements: A Biophysical Approach to Bacterial Nucleoid Organization." Biophysical Journal 87, no. 2 (August 2004): 1392–93. http://dx.doi.org/10.1529/biophysj.104.039503.

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Ghatak, Payel, Kajari Karmakar, Sanjay Kasetty, and Dipankar Chatterji. "Unveiling the Role of Dps in the Organization of Mycobacterial Nucleoid." PLoS ONE 6, no. 1 (January 24, 2011): e16019. http://dx.doi.org/10.1371/journal.pone.0016019.

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Kobayashi, Yusuke, Mari Takusagawa, Naomi Harada, Yoichiro Fukao, Shohei Yamaoka, Takayuki Kohchi, Koichi Hori, Hiroyuki Ohta, Toshiharu Shikanai, and Yoshiki Nishimura. "Eukaryotic Components Remodeled Chloroplast Nucleoid Organization during the Green Plant Evolution." Genome Biology and Evolution 8, no. 1 (November 25, 2015): 1–16. http://dx.doi.org/10.1093/gbe/evv233.

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Scolari, V. F., M. Zarei, M. Osella, and M. Cosentino Lagomarsino. "NuST: analysis of the interplay between nucleoid organization and gene expression." Bioinformatics 28, no. 12 (April 23, 2012): 1643–44. http://dx.doi.org/10.1093/bioinformatics/bts201.

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Mayer, Frank, and Cornelius G. Friedrich. "Higher order structural organization of the nucleoid in the thiobacteriumThiosphaera pantotropha." FEMS Microbiology Letters 37, no. 1 (October 1986): 109–12. http://dx.doi.org/10.1111/j.1574-6968.1986.tb01776.x.

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Woldringh, Conrad L. "The Bacterial Nucleoid: From Electron Microscopy to Polymer Physics—A Personal Recollection." Life 13, no. 4 (March 28, 2023): 895. http://dx.doi.org/10.3390/life13040895.

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In the 1960s, electron microscopy did not provide a clear answer regarding the compact or dispersed organization of the bacterial nucleoid. This was due to the necessary preparation steps of fixation and dehydration (for embedding) and freezing (for freeze-fracturing). Nevertheless, it was possible to measure the lengths of nucleoids in thin sections of slow-growing Escherichia coli cells, showing their gradual increase along with cell elongation. Later, through application of the so-called agar filtration method for electron microscopy, we were able to perform accurate measurements of cell size and shape. The introduction of confocal and fluorescence light microscopy enabled measurements of size and position of the bacterial nucleoid in living cells, inducing the concepts of “nucleoid occlusion” for localizing cell division and of “transertion” for the final step of nucleoid segregation. The question of why the DNA does not spread throughout the cytoplasm was approached by applying polymer-physical concepts of interactions between DNA and proteins. This gave a mechanistic insight in the depletion of proteins from the nucleoid, in accordance with its low refractive index observed by phase-contrast microscopy. Although in most bacterial species, the widely conserved proteins of the ParABS-system play a role in directing the segregation of newly replicated DNA strands, the basis for the separation and opposing movement of the chromosome arms was proposed to lie in preventing intermingling of nascent daughter strands already in the early replication bubble. E. coli, lacking the ParABS system, may be suitable for investigating this basic mechanism of DNA strand separation and segregation.

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Hammel, Michal, Dhar Amlanjyoti, Francis E. Reyes, Jian-Hua Chen, Rochelle Parpana, Henry Y. H. Tang, Carolyn A. Larabell, John A. Tainer, and Sankar Adhya. "HU multimerization shift controls nucleoid compaction." Science Advances 2, no. 7 (July 2016): e1600650. http://dx.doi.org/10.1126/sciadv.1600650.

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Molecular mechanisms controlling functional bacterial chromosome (nucleoid) compaction and organization are surprisingly enigmatic but partly depend on conserved, histone-like proteins HUαα and HUαβ and their interactions that span the nanoscale and mesoscale from protein-DNA complexes to the bacterial chromosome and nucleoid structure. We determined the crystal structures of these chromosome-associated proteins in complex with native duplex DNA. Distinct DNA binding modes of HUαα and HUαβ elucidate fundamental features of bacterial chromosome packing that regulate gene transcription. By combining crystal structures with solution x-ray scattering results, we determined architectures of HU-DNA nucleoproteins in solution under near-physiological conditions. These macromolecular conformations and interactions result in contraction at the cellular level based on in vivo imaging of native unlabeled nucleoid by soft x-ray tomography upon HUβ and ectopic HUα38 expression. Structural characterization of charge-altered HUαα-DNA complexes reveals an HU molecular switch that is suitable for condensing nucleoid and reprogramming noninvasiveEscherichia coliinto an invasive form. Collective findings suggest that shifts between networking and cooperative and noncooperative DNA-dependent HU multimerization control DNA compaction and supercoiling independently of cellular topoisomerase activity. By integrating x-ray crystal structures, x-ray scattering, mutational tests, and x-ray imaging that span from protein-DNA complexes to the bacterial chromosome and nucleoid structure, we show that defined dynamic HU interaction networks can promote nucleoid reorganization and transcriptional regulation as efficient general microbial mechanisms to help synchronize genetic responses to cell cycle, changing environments, and pathogenesis.

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Japaridze, Aleksandre, Sylvain Renevey, Patrick Sobetzko, Liubov Stoliar, William Nasser, Giovanni Dietler, and Georgi Muskhelishvili. "Spatial organization of DNA sequences directs the assembly of bacterial chromatin by a nucleoid-associated protein." Journal of Biological Chemistry 292, no. 18 (March 18, 2017): 7607–18. http://dx.doi.org/10.1074/jbc.m117.780239.

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Structural differentiation of bacterial chromatin depends on cooperative binding of abundant nucleoid-associated proteins at numerous genomic DNA sites and stabilization of distinct long-range nucleoprotein structures. Histone-like nucleoid-structuring protein (H-NS) is an abundant DNA-bridging, nucleoid-associated protein that binds to an AT-rich conserved DNA sequence motif and regulates both the shape and the genetic expression of the bacterial chromosome. Although there is ample evidence that the mode of H-NS binding depends on environmental conditions, the role of the spatial organization of H-NS-binding sequences in the assembly of long-range nucleoprotein structures remains unknown. In this study, by using high-resolution atomic force microscopy combined with biochemical assays, we explored the formation of H-NS nucleoprotein complexes on circular DNA molecules having different arrangements of identical sequences containing high-affinity H-NS-binding sites. We provide the first experimental evidence that variable sequence arrangements result in various three-dimensional nucleoprotein structures that differ in their shape and the capacity to constrain supercoils and compact the DNA. We believe that the DNA sequence-directed versatile assembly of periodic higher-order structures reveals a general organizational principle that can be exploited for knowledge-based design of long-range nucleoprotein complexes and purposeful manipulation of the bacterial chromatin architecture.

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Burlibaşa, L. "Analysis of DNA looped domains organization during Triturus cristatus spermatogenesis." Zygote 20, no. 4 (May 18, 2011): 339–45. http://dx.doi.org/10.1017/s0967199411000293.

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SummaryChromatin from eukaryotes is organized in DNA loops with sequential attachments to a nucleoskeleton named nuclear matrix. This organization plays major roles in replication, transcription, recombination, DNA repair, chromosome condensation and segregation. During spermatogenesis, chromatin undergoes several dynamic transitions, which are often associated with important changes not only in its physical conformation but even in its compositions and structure. To understand the periodical change in the functional organization of chromatin during spermatogenesis, the higher order organization of chromatin in different testicular cell types (pachytene spermatocytes, round spermatids) and the epididymal sperm of Triturus cristatus have been investigated. The expansion and the contraction of nucleoid DNA were measured with a fluorescence microscope following exposure of nucleoids to increasing concentrations of ethidium bromide (EtBr) (2.5–200 μg/ml) as an intercalating dye to induce DNA-positive supercoils. Nucleoids from all studied cell types exhibited a biphasic change (condensed–relaxed–condensed) in size as a consequence of exposure to increasing concentrations of EtBr, indicating that they contained negatively supercoiled DNA. At higher EtBr concentrations, maximum positive supercoiling occurred in pachytene DNA loops. Our data suggest that pachytene DNA is the most open chromatin conformation in terms of EtBr intercalation.

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Lieber, Arnon, Andrew Leis, Ariel Kushmaro, Abraham Minsky, and Ohad Medalia. "Chromatin Organization and Radio Resistance in the Bacterium Gemmata obscuriglobus." Journal of Bacteriology 191, no. 5 (December 12, 2008): 1439–45. http://dx.doi.org/10.1128/jb.01513-08.

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ABSTRACT The organization of chromatin has a major impact on cellular activities, such as gene expression. For bacteria, it was suggested that the spatial organization of the genetic material correlates with transcriptional levels, implying a specific architecture of the chromosome within the cytoplasm. Accordingly, recent technological advances have emphasized the organization of the genetic material within nucleoid structures. Gemmata obscuriglobus, a member of the phylum Planctomycetes, exhibits a distinctive nucleoid structure in which chromatin is encapsulated within a discrete membrane-bound compartment. Here, we show that this soil and freshwater bacterium tolerates high doses of UV and ionizing radiation. Cryoelectron tomography of frozen hydrated sections and electron microscopy of freeze-substituted cells have indicated a more highly ordered condensed-chromatin organization in actively dividing and stationary-phase G. obscuriglobus cells. These three-dimensional analyses revealed a complex network of double membranes that engulf the condensed DNA. Bioinformatics analysis has revealed the existence of a putative component involved in nonhomologous DNA end joining that presumably plays a role in maintaining chromatin integrity within the bacterium. Thus, our observations further support the notion that packed chromatin organization enhances radiation tolerance.

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Dame, Remus T., Niels Laurens, Maarten C. Noom, Felix J. H. Hol, Malcolm F. White, and Gijs J. L. Wuite. "Unravelling the Role of Alba in the Organization of the Archaeal Nucleoid." Biophysical Journal 98, no. 3 (January 2010): 206a. http://dx.doi.org/10.1016/j.bpj.2009.12.1103.

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Noom, Maarten C., Felix J. H. Hol, Niels Laurens, Malcolm F. White, Remus T. Dame, and Gijs J. L. Wuite. "Unravelling The Role Of Alba In The Organization Of The Archaeal Nucleoid." Biophysical Journal 96, no. 3 (February 2009): 61a. http://dx.doi.org/10.1016/j.bpj.2008.12.214.

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Zhang, Le, Joost Willemse, Dennis Claessen, and Gilles P. van Wezel. "SepG coordinates sporulation-specific cell division and nucleoid organization in Streptomyces coelicolor." Open Biology 6, no. 4 (April 2016): 150164. http://dx.doi.org/10.1098/rsob.150164.

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Bacterial cell division is a highly complex process that requires tight coordination between septum formation and chromosome replication and segregation. In bacteria that divide by binary fission a single septum is formed at mid-cell, a process that is coordinated by the conserved cell division scaffold protein FtsZ. In contrast, during sporulation-specific cell division in streptomycetes, up to a hundred rings of FtsZ (Z rings) are produced almost simultaneously, dividing the multinucleoid aerial hyphae into long chains of unigenomic spores. This involves the active recruitment of FtsZ by the SsgB protein, and at the same time requires sophisticated systems to regulate chromosome dynamics. Here, we show that SepG is required for the onset of sporulation and acts by ensuring that SsgB is localized to future septum sites. Förster resonance energy transfer imaging suggests direct interaction between SepG and SsgB. The beta-lactamase reporter system showed that SepG is a transmembrane protein with its central domain oriented towards the cytoplasm. Without SepG, SsgB fails to localize properly, consistent with a crucial role for SepG in the membrane localization of the SsgB–FtsZ complex. While SsgB remains associated with FtsZ, SepG re-localizes to the (pre)spore periphery. Expanded doughnut-shaped nucleoids are formed in sepG null mutants, suggesting that SepG is required for nucleoid compaction. Taken together, our work shows that SepG, encoded by one of the last genes in the conserved dcw cluster of cell division and cell-wall-related genes in Gram-positive bacteria whose function was still largely unresolved , coordinates septum synthesis and chromosome organization in Streptomyces .

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Weng, Xiaoli, Christopher H. Bohrer, Kelsey Bettridge, Arvin Cesar Lagda, Cedric Cagliero, Ding Jun Jin, and Jie Xiao. "Spatial organization of RNA polymerase and its relationship with transcription in Escherichia coli." Proceedings of the National Academy of Sciences 116, no. 40 (September 16, 2019): 20115–23. http://dx.doi.org/10.1073/pnas.1903968116.

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Recent studies have shown that RNA polymerase (RNAP) is organized into distinct clusters in Escherichia coli and Bacillus subtilis cells. Spatially organized molecular components in prokaryotic systems imply compartmentalization without the use of membranes, which may offer insights into unique functions and regulations. It has been proposed that the formation of RNAP clusters is driven by active ribosomal RNA (rRNA) transcription and that RNAP clusters function as factories for highly efficient transcription. In this work, we examined these hypotheses by investigating the spatial organization and transcription activity of RNAP in E. coli cells using quantitative superresolution imaging coupled with genetic and biochemical assays. We observed that RNAP formed distinct clusters that were engaged in active rRNA synthesis under a rich medium growth condition. Surprisingly, a large fraction of RNAP clusters persisted in the absence of high rRNA transcription activities or when the housekeeping σ70 was sequestered, and was only significantly diminished when all RNA transcription was inhibited globally. In contrast, the cellular distribution of RNAP closely followed the morphology of the underlying nucleoid under all conditions tested irrespective of the corresponding transcription activity, and RNAP redistributed into dispersed, smaller clusters when the supercoiling state of the nucleoid was perturbed. These results suggest that RNAP was organized into active transcription centers under the rich medium growth condition; its spatial arrangement at the cellular level, however, was not dependent on rRNA synthesis activity and was likely organized by the underlying nucleoid.

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Puvion-Dutilleul, F., E. Pichard, M. Laithier, and E. H. Leduc. "Effect of dehydrating agents on DNA organization in herpes viruses." Journal of Histochemistry & Cytochemistry 35, no. 6 (June 1987): 635–45. http://dx.doi.org/10.1177/35.6.3033063.

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With routine procedures of Epon- or GMA-embedding and a stain specific for DNA, the nucleoid of mature herpes simplex virus-type 1 (HSV-1) assumes the well-known form of a short, compact, hollow cylinder or torus. A new, more complex organization of DNA filaments in encapsidated HSV-1 was found in infected cells after aldehyde fixation, methanol dehydration, and Lowicryl embedment. We have determined that it is the use of methanol as dehydrating agent that permits visualization of this internal structure. The same new spatial organization of DNA can be seen in Epon and GMA sections when methanol dehydration is used. This organization is lost in a methanol-ethanol sequence of dehydration but can be restored in an ethanol-methanol sequence. Dimethylsulfoxide (DMSO) is the only other agent among several reviewed here which resembles methanol in its effect on HSV-1 DNA. Methanol had the same effect on five subfamilies of the herpes group (HSV-1, HSV-2, CCV, CMV, CTHV) but did not alter the nucleoid ultrastructure in simian virus 40 (SV40) and adenovirus type 5 (Ad 5). Therefore, it may sometimes, but not always, provide additional information about the organization of biological structures.

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Dame, Remus T., Martijn S. Luijsterburg, Evelyne Krin, Philippe N. Bertin, Rolf Wagner, and Gijs J. L. Wuite. "DNA Bridging: a Property Shared among H-NS-Like Proteins." Journal of Bacteriology 187, no. 5 (March 1, 2005): 1845–48. http://dx.doi.org/10.1128/jb.187.5.1845-1848.2005.

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ABSTRACT The nucleoid-associated protein H-NS is thought to play an essential role in the organization of bacterial chromatin in Escherichia coli. Homologues, often with very low sequence identity, are found in most gram-negative bacteria. Microscopic analysis reveals that, despite limited sequence identity, their structural organization results in similar DNA binding properties.

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38

Sasaki, Narie, Haruko Kuroiwa, Chikako Nishitani, Hiroyoshi Takano, Tetsuya Higashiyama, Tamaki Kobayashi, Yuki Shirai, et al. "Glom Is a Novel Mitochondrial DNA Packaging Protein inPhysarum polycephalumand Causes Intense Chromatin Condensation without Suppressing DNA Functions." Molecular Biology of the Cell 14, no. 12 (December 2003): 4758–69. http://dx.doi.org/10.1091/mbc.e03-02-0099.

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Mitochondrial DNA (mtDNA) is packed into highly organized structures called mitochondrial nucleoids (mt-nucleoids). To understand the organization of mtDNA and the overall regulation of its genetic activity within the mt-nucleoids, we identified and characterized a novel mtDNA packaging protein, termed Glom (a protein inducing agglomeration of mitochondrial chromosome), from highly condensed mt-nucleoids of the true slime mold, Physarum polycephalum. This protein could bind to the entire mtDNA and package mtDNA into a highly condensed state in vitro. Immunostaining analysis showed that Glom specifically localized throughout the mt-nucleoid. Deduced amino acid sequence revealed that Glom has a lysine-rich region with proline-rich domain in the N-terminal half and two HMG boxes in C-terminal half. Deletion analysis of Glom revealed that the lysine-rich region was sufficient for the intense mtDNA condensation in vitro. When the recombinant Glom proteins containing the lysine-rich region were expressed in Escherichia coli, the condensed nucleoid structures were observed in E. coli. Such in vivo condensation did not interfere with transcription or replication of E. coli chromosome and the proline-rich domain was essential to keep those genetic activities. The expression of Glom also complemented the E. coli mutant lacking the bacterial histone-like protein HU and the HMG-boxes region of Glom was important for the complementation. Our results suggest that Glom is a new mitochondrial histone-like protein having a property to cause intense DNA condensation without suppressing DNA functions.

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Li, H., Y. Ruan, K. Zhang, F. Jian, C. Hu, L. Miao, L. Gong, et al. "Mic60/Mitofilin determines MICOS assembly essential for mitochondrial dynamics and mtDNA nucleoid organization." Cell Death & Differentiation 23, no. 3 (August 7, 2015): 380–92. http://dx.doi.org/10.1038/cdd.2015.102.

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Jin, Ding Jun, Cedric Cagliero, and Yan Ning Zhou. "Role of RNA Polymerase and Transcription in the Organization of the Bacterial Nucleoid." Chemical Reviews 113, no. 11 (August 13, 2013): 8662–82. http://dx.doi.org/10.1021/cr4001429.

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Dorman, Charles J., Jay C. D. Hinton, and Andrew Free. "Domain organization and oligomerization among H-NS-like nucleoid-associated proteins in bacteria." Trends in Microbiology 7, no. 3 (March 1999): 124–28. http://dx.doi.org/10.1016/s0966-842x(99)01455-9.

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Karcher, Daniel, Dietrich Köster, Anne Schadach, Anja Klevesath, and Ralph Bock. "The Chlamydomonas Chloroplast HLP Protein Is Required for Nucleoid Organization and Genome Maintenance." Molecular Plant 2, no. 6 (November 2009): 1223–32. http://dx.doi.org/10.1093/mp/ssp083.

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Badrinarayanan, A., C. Lesterlin, R. Reyes-Lamothe, and D. Sherratt. "The Escherichia coli SMC Complex, MukBEF, Shapes Nucleoid Organization Independently of DNA Replication." Journal of Bacteriology 194, no. 17 (June 29, 2012): 4669–76. http://dx.doi.org/10.1128/jb.00957-12.

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Fisher, Jay K., Aude Bourniquel, Guillaume Witz, Beth Weiner, Mara Prentiss, and Nancy Kleckner. "Four-Dimensional Imaging of E. coli Nucleoid Organization and Dynamics in Living Cells." Cell 153, no. 4 (May 2013): 882–95. http://dx.doi.org/10.1016/j.cell.2013.04.006.

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45

Dedrick, Rebekah M., Hans Wildschutte, and Joseph R. McCormick. "Genetic Interactions of smc, ftsK, and parB Genes in Streptomyces coelicolor and Their Developmental Genome Segregation Phenotypes." Journal of Bacteriology 191, no. 1 (October 31, 2008): 320–32. http://dx.doi.org/10.1128/jb.00858-08.

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ABSTRACT The mechanisms by which chromosomes condense and segregate during developmentally regulated cell division are of interest for Streptomyces coelicolor, a sporulating, filamentous bacterium with a large, linear genome. These processes coordinately occur as many septa synchronously form in syncytial aerial hyphae such that prespore compartments accurately receive chromosome copies. Our genetic approach analyzed mutants for ftsK, smc, and parB. DNA motor protein FtsK/SpoIIIE coordinates chromosome segregation with septum closure in rod-shaped bacteria. SMC (structural maintenance of chromosomes) participates in condensation and organization of the nucleoid. ParB/Spo0J partitions the origin of replication using a nucleoprotein complex, assembled at a centromere-like sequence. Consistent with previous work, we show that an ftsK-null mutant produces anucleate spores at the same frequency as the wild-type strain (0.8%). We report that the smc and ftsK deletion-insertion mutants (ftsK′ truncation allele) have developmental segregation defects (7% and 15% anucleate spores, respectively). By use of these latter mutants, viable double and triple mutants were isolated in all combinations with a previously described parB-null mutant (12% anucleate spores). parB and smc were in separate segregation pathways; the loss of both exacerbates the segregation defect (24% anucleate spores). For a triple mutant, deletion of the region encoding the FtsK motor domain and one transmembrane segment partially alleviates the segregation defect of the smc parB mutant (10% anucleate spores). Considerable redundancy must exist in this filamentous organism because segregation of some genomic material occurs 90% of the time during development in the absence of three functions with only a fourfold loss of spore viability. Furthermore, we report that scpA and scpAB mutants (encoding SMC-associated proteins) have spore nucleoid organization defects. Finally, FtsK-enhanced green fluorescent protein (EGFP) localized as bands or foci between incipient nucleoids, while SMC-EGFP foci were not uniformly positioned along aerial hyphae, nor were they associated with every condensing nucleoid.

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Helgesen, Emily, Solveig Fossum-Raunehaug, and Kirsten Skarstad. "Lack of the H-NS Protein Results in Extended and Aberrantly Positioned DNA during Chromosome Replication and Segregation in Escherichia coli." Journal of Bacteriology 198, no. 8 (February 8, 2016): 1305–16. http://dx.doi.org/10.1128/jb.00919-15.

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ABSTRACTThe 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 theEscherichia colichromosome 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 ofE. colicells 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.IMPORTANCEIt is not fully understood how and to what extent nucleoid-associated proteins contribute to chromosome folding and organization during replication and segregation inEscherichia coli. In this work, we findin vivoindications 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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Molan, Katja, and Darja Žgur Bertok. "Small Prokaryotic DNA-Binding Proteins Protect Genome Integrity throughout the Life Cycle." International Journal of Molecular Sciences 23, no. 7 (April 4, 2022): 4008. http://dx.doi.org/10.3390/ijms23074008.

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Genomes of all organisms are persistently threatened by endogenous and exogenous assaults. Bacterial mechanisms of genome maintenance must provide protection throughout the physiologically distinct phases of the life cycle. Spore-forming bacteria must also maintain genome integrity within the dormant endospore. The nucleoid-associated proteins (NAPs) influence nucleoid organization and may alter DNA topology to protect DNA or to alter gene expression patterns. NAPs are characteristically multifunctional; nevertheless, Dps, HU and CbpA are most strongly associated with DNA protection. Archaea display great variety in genome organization and many inhabit extreme environments. As of yet, only MC1, an archaeal NAP, has been shown to protect DNA against thermal denaturation and radiolysis. ssDNA are intermediates in vital cellular processes, such as DNA replication and recombination. Single-stranded binding proteins (SSBs) prevent the formation of secondary structures but also protect the hypersensitive ssDNA against chemical and nuclease degradation. Ionizing radiation upregulates SSBs in the extremophile Deinococcus radiodurans.

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Munoz-Espin, D., I. Holguera, D. Ballesteros-Plaza, R. Carballido-Lopez, and M. Salas. "Viral terminal protein directs early organization of phage DNA replication at the bacterial nucleoid." Proceedings of the National Academy of Sciences 107, no. 38 (September 7, 2010): 16548–53. http://dx.doi.org/10.1073/pnas.1010530107.

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Hashimoto, Masayuki, Toshiharu Ichimura, Hiroshi Mizoguchi, Kimie Tanaka, Kazuyuki Fujimitsu, Kenji Keyamura, Tomotake Ote, et al. "Cell size and nucleoid organization of engineered Escherichia coli cells with a reduced genome." Molecular Microbiology 55, no. 1 (November 25, 2004): 137–49. http://dx.doi.org/10.1111/j.1365-2958.2004.04386.x.

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Dame, Remus T. "The role of nucleoid-associated proteins in the organization and compaction of bacterial chromatin." Molecular Microbiology 56, no. 4 (March 24, 2005): 858–70. http://dx.doi.org/10.1111/j.1365-2958.2005.04598.x.

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Journal articles on the topic 'Nucleoid Organization'

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