Journal articles: 'Nucleoid Proteins'

1

Hayat, M. A., and Denise A. Mancarella. "Nucleoid proteins." Micron 26, no. 5 (January 1995): 461–80. http://dx.doi.org/10.1016/0968-4328(95)00022-4.

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Oetke, Svenja, Axel J. Scheidig, and Karin Krupinska. "WHIRLY1 of Barley and Maize Share a PRAPP Motif Conferring Nucleoid Compaction." Plant and Cell Physiology 63, no. 2 (November 11, 2021): 234–47. http://dx.doi.org/10.1093/pcp/pcab164.

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Abstract WHIRLY1 in barley was shown to be a major architect of plastid nucleoids. Its accumulation in cells of Escherichia coli coincided with an induction of nucleoid compaction and growth retardation. While WHIRLY1 of maize had similar effects on E. coli cells, WHIRLY1 proteins of Arabidopsis and potato as well as WHIRLY2 proteins had no impact on nucleoid compaction in E. coli. By mutagenesis of HvWHIRLY1 the PRAPP motif at the N-terminus preceding the highly conserved WHIRLY domain was identified to be responsible for the nucleoid compacting activity of HvWHIRLY1 in bacteria. This motif is found in WHIRLY1 proteins of most members of the Poaceae family, but neither in the WHIRLY2 proteins of the family nor in any WHIRLY protein of eudicot species such as Arabidopsis thaliana. This finding indicates that a subset of the monocot WHIRLY1 proteins has acquired a specific function as nucleoid compacters by sequence variation in the N-terminal part preceding the conserved WHIRLY domain and that in different groups of higher plants the compaction of nucleoids is mediated by other proteins.

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Dillon, Shane C., and Charles J. Dorman. "Bacterial nucleoid-associated proteins, nucleoid structure and gene expression." Nature Reviews Microbiology 8, no. 3 (February 8, 2010): 185–95. http://dx.doi.org/10.1038/nrmicro2261.

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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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Ragkousi, Katerina, Ann E. Cowan, Margery A. Ross, and Peter Setlow. "Analysis of Nucleoid Morphology during Germination and Outgrowth of Spores of Bacillus Species." Journal of Bacteriology 182, no. 19 (October 1, 2000): 5556–62. http://dx.doi.org/10.1128/jb.182.19.5556-5562.2000.

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ABSTRACT After a few minutes of germination, nucleoids in the great majority of spores of Bacillus subtilis and Bacillus megaterium were ring shaped. The major spore DNA binding proteins, the α/β-type small, acid-soluble proteins (SASP), colocalized to these nucleoid rings early in spore germination, as did the B. megaterium homolog of the major B. subtilis chromosomal protein HBsu. The percentage of ring-shaped nucleoids was decreased in germinated spores with lower levels of α/β-type SASP. As spore outgrowth proceeded, the ring-shaped nucleoids disappeared and the nucleoid became more compact. This change took place after degradation of most of the spores' pool of major α/β-type SASP and was delayed when α/β-type SASP degradation was delayed. Later in spore outgrowth, the shape of the nucleoid reverted to the diffuse lobular shape seen in growing cells.

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6

K Davies, John. "Control of transcription by nucleoid proteins." Microbiology Australia 27, no. 3 (2006): 112. http://dx.doi.org/10.1071/ma06112.

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Although not confined to a membrane-bound organelle such as the eukaryotic nucleus, the chromosome(s) of bacterial cells are compacted into a DNA-protein complex termed the nucleoid. Many different proteins appear to be associated with the nucleoid, but we understand the function of just a few of these.

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Rimsky, Sylvie, and Andrew Travers. "Pervasive regulation of nucleoid structure and function by nucleoid-associated proteins." Current Opinion in Microbiology 14, no. 2 (April 2011): 136–41. http://dx.doi.org/10.1016/j.mib.2011.01.003.

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McLeod, Sarah M., and Reid C. Johnson. "Control of transcription by nucleoid proteins." Current Opinion in Microbiology 4, no. 2 (April 2001): 152–59. http://dx.doi.org/10.1016/s1369-5274(00)00181-8.

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9

Miyakawa, Isamu, Akira Okamuro, Slavomir Kinsky, Katarina Visacka, Lubomir Tomaska, and Jozef Nosek. "Mitochondrial nucleoids from the yeast Candida parapsilosis: expansion of the repertoire of proteins associated with mitochondrial DNA." Microbiology 155, no. 5 (May 1, 2009): 1558–68. http://dx.doi.org/10.1099/mic.0.027474-0.

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Molecules of mitochondrial DNA (mtDNA) are packed into nucleic acid–protein complexes termed mitochondrial nucleoids (mt-nucleoids). In this study, we analysed mt-nucleoids of the yeast Candida parapsilosis, which harbours a linear form of the mitochondrial genome. To identify conserved as well as specific features of mt-nucleoids in this species, we employed two strategies for analysis of their components. First, we investigated the protein composition of mt-nucleoids isolated from C. parapsilosis mitochondria, determined N-terminal amino acid sequences of 14 proteins associated with the mt-nucleoids and identified corresponding genes. Next, we complemented the list of mt-nucleoid components with additional candidates identified in the complete genome sequence of C. parapsilosis as homologues of Saccharomyces cerevisiae mt-nucleoid proteins. Our approach revealed several known mt-nucleoid proteins as well as additional components that expand the repertoire of proteins associated with these cytological structures. In particular, we identified and purified the protein Gcf1, which is abundant in the mt-nucleoids and exhibits structural features in common with the mtDNA packaging protein Abf2 from S. cerevisiae. We demonstrate that Gcf1p co-localizes with mtDNA, has DNA-binding activity in vitro, and is able to stabilize mtDNA in the S. cerevisiae Δabf2 mutant, all of which points to a role in the maintenance of the C. parapsilosis mitochondrial genome. Importantly, in contrast to Abf2p, in silico analysis of Gcf1p predicted the presence of a coiled-coil domain and a single high-mobility group (HMG) box, suggesting that it represents a novel type of mitochondrial HMG protein.

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10

Zhao, Haiqing. "Self-assembled nucleoid proteins scaffold bacterial DNA." Biophysical Journal 120, no. 5 (March 2021): 754–55. http://dx.doi.org/10.1016/j.bpj.2021.02.001.

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11

SATO, Fumihiko, and Takeshi NAKANO. "Chloroplast DNA Binding Proteins and Chloroplast Nucleoid." Nippon Nōgeikagaku Kaishi 71, no. 11 (1997): 1173–76. http://dx.doi.org/10.1271/nogeikagaku1924.71.1173.

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12

Pfalz, Jeannette, and Thomas Pfannschmidt. "Essential nucleoid proteins in early chloroplast development." Trends in Plant Science 18, no. 4 (April 2013): 186–94. http://dx.doi.org/10.1016/j.tplants.2012.11.003.

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13

Johansson, Jörgen, Carlos Balsalobre, Su-Yan Wang, Jurate Urbonaviciene, Ding Jun Jin, Berit Sondén, and Bernt Eric Uhlin. "Nucleoid Proteins Stimulate Stringently Controlled Bacterial Promoters." Cell 102, no. 4 (August 2000): 475–85. http://dx.doi.org/10.1016/s0092-8674(00)00052-0.

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14

Lee, Sung Ryul, and Jin Han. "Mitochondrial Nucleoid: Shield and Switch of the Mitochondrial Genome." Oxidative Medicine and Cellular Longevity 2017 (2017): 1–15. http://dx.doi.org/10.1155/2017/8060949.

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Mitochondria preserve very complex and distinctively unique machinery to maintain and express the content of mitochondrial DNA (mtDNA). Similar to chromosomes, mtDNA is packaged into discrete mtDNA-protein complexes referred to as a nucleoid. In addition to its role as a mtDNA shield, over 50 nucleoid-associated proteins play roles in mtDNA maintenance and gene expression through either temporary or permanent association with mtDNA or other nucleoid-associated proteins. The number of mtDNA(s) contained within a single nucleoid is a fundamental question but remains a somewhat controversial issue. Disturbance in nucleoid components and mutations in mtDNA were identified as significant in various diseases, including carcinogenesis. Significant interest in the nucleoid structure and its regulation has been stimulated in relation to mitochondrial diseases, which encompass diseases in multicellular organisms and are associated with accumulation of numerous mutations in mtDNA. In this review, mitochondrial nucleoid structure, nucleoid-associated proteins, and their regulatory roles in mitochondrial metabolism are briefly addressed to provide an overview of the emerging research field involving mitochondrial biology.

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15

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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16

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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17

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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18

Dryden, D. T. F., and M. R. Tock. "DNA mimicry by proteins." Biochemical Society Transactions 34, no. 2 (March 20, 2006): 317–19. http://dx.doi.org/10.1042/bst0340317.

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It has been discovered recently, via structural and biophysical analyses, that proteins can mimic DNA structures in order to inhibit proteins that would normally bind to DNA. Mimicry of the phosphate backbone of DNA, the hydrogen-bonding properties of the nucleotide bases and the bending and twisting of the DNA double helix are all present in the mimics discovered to date. These mimics target a range of proteins and enzymes such as DNA restriction enzymes, DNA repair enzymes, DNA gyrase and nucleosomal and nucleoid-associated proteins. The unusual properties of these protein DNA mimics may provide a foundation for the design of targeted inhibitors of DNA-binding proteins.

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19

Murphy, Lizabeth D., Judah L. Rosner, Steven B. Zimmerman, and Dominic Esposito. "Identification of Two New Proteins in Spermidine Nucleoids Isolated from Escherichia coli." Journal of Bacteriology 181, no. 12 (June 15, 1999): 3842–44. http://dx.doi.org/10.1128/jb.181.12.3842-3844.1999.

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ABSTRACT The Escherichia coli nucleoid contains DNA in a condensed but functional form. Analysis of proteins released from isolated spermidine nucleoids after treatment with DNase I reveals significant amounts of two proteins not previously detected in wild-type E. coli. Partial amino-terminal sequencing has identified them as the products of rdgC andyejK. These proteins are strongly conserved in gram-negative bacteria, suggesting that they have important cellular roles.

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20

Itoh, Kie, Yasushi Tamura, Miho Iijima, and Hiromi Sesaki. "Effects of Fcj1-Mos1 and mitochondrial division on aggregation of mitochondrial DNA nucleoids and organelle morphology." Molecular Biology of the Cell 24, no. 12 (June 15, 2013): 1842–51. http://dx.doi.org/10.1091/mbc.e13-03-0125.

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Mitochondrial DNA (mtDNA) is packaged into DNA–protein complexes called nucleoids, which are distributed as many small foci in mitochondria. Nucleoids are crucial for the biogenesis and function of mtDNA. Here, using a yeast genetic screen for components that control nucleoid distribution and size, we identify Fcj1 and Mos1, two evolutionarily conserved mitochondrial proteins that maintain the connection between the cristae and boundary membranes. These two proteins are also important for establishing tubular morphology of mitochondria, as mitochondria lacking Fcj1 and Mos1 form lamellar sheets. We find that nucleoids aggregate, increase in size, and decrease in number in fcj1∆ and mos1∆ cells. In addition, Fcj1 form punctate structures and localized adjacent to nucleoids. Moreover, connecting mitochondria by deleting the DNM1 gene required for organelle division enhances aggregation of mtDNA nucleoids in fcj1∆ and mos1∆ cells, whereas single deletion of DNM1 does not affect nucleoids. Conversely, deleting F1Fo-ATP synthase dimerization factors generates concentric ring-like cristae, restores tubular mitochondrial morphology, and suppresses nucleoid aggregation in these mutants. Our findings suggest an unexpected role of Fcj1-Mos1 and organelle division in maintaining the distribution and size of mtDNA nucleoids.

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Japaridze, Aleksandre, Wayne Yang, Cees Dekker, William Nasser, and Georgi Muskhelishvili. "DNA sequence-directed cooperation between nucleoid-associated proteins." iScience 24, no. 5 (May 2021): 102408. http://dx.doi.org/10.1016/j.isci.2021.102408.

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22

He, J., H. M. Cooper, A. Reyes, M. Di Re, H. Sembongi, T. R. Litwin, J. Gao, et al. "Mitochondrial nucleoid interacting proteins support mitochondrial protein synthesis." Nucleic Acids Research 40, no. 13 (March 27, 2012): 6109–21. http://dx.doi.org/10.1093/nar/gks266.

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23

Dahlke, Katelyn, and Charles E. Sing. "Influence of Nucleoid-Associated Proteins on DNA Supercoiling." Journal of Physical Chemistry B 123, no. 48 (November 11, 2019): 10152–62. http://dx.doi.org/10.1021/acs.jpcb.9b07436.

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Dorman, Charles J., and Niamh Ní Bhriain. "CRISPR-Cas, DNA Supercoiling, and Nucleoid-Associated Proteins." Trends in Microbiology 28, no. 1 (January 2020): 19–27. http://dx.doi.org/10.1016/j.tim.2019.08.004.

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Weber, Michael H. W., Arsen V. Volkov, Ingo Fricke, Mohamed A. Marahiel, and Peter L. Graumann. "Localization of Cold Shock Proteins to Cytosolic Spaces Surrounding Nucleoids in Bacillus subtilis Depends on Active Transcription." Journal of Bacteriology 183, no. 21 (November 1, 2001): 6435–43. http://dx.doi.org/10.1128/jb.183.21.6435-6443.2001.

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ABSTRACT Using immunofluorescence microscopy and a fusion of a cold shock protein (CSP), CspB, to green fluorescent protein (GFP), we showed that in growing cells Bacillus subtilis CSPs specifically localize to cytosolic regions surrounding the nucleoid. The subcellular localization of CSPs is influenced by the structure of the nucleoid. Decondensed chromosomes in smc mutant cells reduced the sizes of the regions in which CSPs localized, while cold shock-induced chromosome compaction was accompanied by an expansion of the space in which CSPs were present. As a control, histone-like protein HBsu localized to the nucleoids, while β-galactosidase and GFP were detectable throughout the cell. After inhibition of translation, CspB-GFP was still present around the nucleoids in a manner similar to that in cold-shocked cells. However, in stationary-phase cells and after inhibition of transcription, CspB was distributed throughout the cell, indicating that specific localization of CspB depends on active transcription and is not due to simple exclusion from the nucleoid. Furthermore, we observed that nucleoids are more condensed and frequently abnormal incspB cspC and cspB cspDdouble-mutant cells. This suggests that the function of CSPs affects chromosome structure, probably through coupling of transcription to translation, which is thought to decondense nucleoids. In addition, we found that cspB cspD and cspB cspC double mutants are defective in sporulation, with a block at or before stage 0. Interestingly, CspB and CspC are depleted from the forespore compartment but not from the mother cell. In toto, our findings suggest that CSPs localize to zones of newly synthesized RNA, coupling transcription with initiation of translation.

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26

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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Miyakawa, Isamu, Hiroshi Sato, Yukari Maruyama, and Tomoko Nakaoka. "Isolation of the mitochondrial nucleoids from yeast Kluyveromyces lactis and analyses of the nucleoid proteins." Journal of General and Applied Microbiology 49, no. 2 (2003): 85–93. http://dx.doi.org/10.2323/jgam.49.85.

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Cheng, Xiaoli, Tomotake Kanki, Atsushi Fukuoh, Kippei Ohgaki, Ryu Takeya, Yoshimasa Aoki, Naotaka Hamasaki, and Dongchon Kang. "PDIP38 Associates with Proteins Constituting the Mitochondrial DNA Nucleoid." Journal of Biochemistry 138, no. 6 (December 1, 2005): 673–78. http://dx.doi.org/10.1093/jb/mvi169.

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Yee, Benjamin, Evgeny Sagulenko, and John A. Fuerst. "Making heads or tails of the HU proteins in the planctomycete Gemmata obscuriglobus." Microbiology 157, no. 7 (July 1, 2011): 2012–21. http://dx.doi.org/10.1099/mic.0.047605-0.

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Gemmata obscuriglobus has a highly condensed nucleoid which is implicated in its resistance to radiation. However, the mechanisms by which such compaction is achieved, and the proteins responsible, are still unknown. Here we have examined the genome of G. obscuriglobus for the presence of proteins homologous to those that have been associated with nucleoid condensation. We found two different proteins homologous to the bacterial nucleoid-associated protein HU, one with an N-terminal and one with a C-terminal extension relative to the amino acid sequence of the HU found in Escherichia coli. Sequence analysis revealed that one of these HU homologues represents a novel type with a high number of prolines in its C-terminal extension, whereas the other one has motifs similar to the N terminus of the HU homologue from the radio-resistant bacterium Deinococcus radiodurans. The occurrence of two such HU homologue proteins with these two different terminal extensions in one organism appears to be unique among the Bacteria.

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Ali Azam, Talukder, Akira Iwata, Akiko Nishimura, Susumu Ueda, and Akira Ishihama. "Growth Phase-Dependent Variation in Protein Composition of the Escherichia coli Nucleoid." Journal of Bacteriology 181, no. 20 (October 15, 1999): 6361–70. http://dx.doi.org/10.1128/jb.181.20.6361-6370.1999.

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ABSTRACT The genome DNA of Escherichia coli is associated with about 10 DNA-binding structural proteins, altogether forming the nucleoid. The nucleoid proteins play some functional roles, besides their structural roles, in the global regulation of such essential DNA functions as replication, recombination, and transcription. Using a quantitative Western blot method, we have performed for the first time a systematic determination of the intracellular concentrations of 12 species of the nucleoid protein in E. coli W3110, including CbpA (curved DNA-binding protein A), CbpB (curved DNA-binding protein B, also known as Rob [right origin binding protein]), DnaA (DNA-binding protein A), Dps (DNA-binding protein from starved cells), Fis (factor for inversion stimulation), Hfq (host factor for phage Qβ), H-NS (histone-like nucleoid structuring protein), HU (heat-unstable nucleoid protein), IciA (inhibitor of chromosome initiation A), IHF (integration host factor), Lrp (leucine-responsive regulatory protein), and StpA (suppressor oftd mutant phenotype A). Intracellular protein levels reach a maximum at the growing phase for nine proteins, CbpB (Rob), DnaA, Fis, Hfq, H-NS, HU, IciA, Lrp, and StpA, which may play regulatory roles in DNA replication and/or transcription of the growth-related genes. In descending order, the level of accumulation, calculated in monomers, in growing E. coli cells is Fis, Hfq, HU, StpA, H-NS, IHF*, CbpB (Rob), Dps*, Lrp, DnaA, IciA, and CbpA* (stars represent the stationary-phase proteins). The order of abundance, in descending order, in the early stationary phase is Dps*, IHF*, HU, Hfq, H-NS, StpA, CbpB (Rob), DnaA, Lrp, IciA, CbpA, and Fis, while that in the late stationary phase is Dps*, IHF*, Hfq, HU, CbpA*, StpA, H-NS, CbpB (Rob), DnaA, Lrp, IciA, and Fis. Thus, the major protein components of the nucleoid change from Fis and HU in the growing phase to Dps in the stationary phase. The curved DNA-binding protein, CbpA, appears only in the late stationary phase. These changes in the composition of nucleoid-associated proteins in the stationary phase are accompanied by compaction of the genome DNA and silencing of the genome functions.

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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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Cabrera, Julio E., Cedric Cagliero, Selwyn Quan, Catherine L. Squires, and Ding Jun Jin. "Active Transcription of rRNA Operons Condenses the Nucleoid in Escherichia coli: Examining the Effect of Transcription on Nucleoid Structure in the Absence of Transertion." Journal of Bacteriology 191, no. 13 (April 24, 2009): 4180–85. http://dx.doi.org/10.1128/jb.01707-08.

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ABSTRACT In Escherichia coli the genome must be compacted ∼1,000-fold to be contained in a cellular structure termed the nucleoid. It is proposed that the structure of the nucleoid is determined by a balance of multiple compaction forces and one major expansion force. The latter is mediated by transertion, a coupling of transcription, translation, and translocation of nascent membrane proteins and/or exported proteins. In supporting this notion, it has been shown consistently that inhibition of transertion by the translation inhibitor chloramphenicol results in nucleoid condensation due to the compaction forces that remain active in the cell. Our previous study showed that during optimal growth, RNA polymerase is concentrated into transcription foci or “factories,” analogous to the eukaryotic nucleolus, indicating that transcription and RNA polymerase distribution affect the nucleoid structure. However, the interpretation of the role of transcription in the structure of the nucleoid is complicated by the fact that transcription is implicated in both compacting forces and the expansion force. In this work, we used a new approach to further examine the effect of transcription, specifically from rRNA operons, on the structure of the nucleoid, when the major expansion force was eliminated. Our results showed that transcription is necessary for the chloramphenicol-induced nucleoid compaction. Further, an active transcription from multiple rRNA operons in chromosome is critical for the compaction of nucleoid induced by inhibition of translation. All together, our data demonstrated that transcription of rRNA operons is a key mechanism affecting genome compaction and nucleoid structure.

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BESSA RAMOS, ESIO, KATHELIJNE WINTRAECKEN, ANS GEERLING, and RENKO DE VRIES. "SYNERGY OF DNA-BENDING NUCLEOID PROTEINS AND MACROMOLECULAR CROWDING IN CONDENSING DNA." Biophysical Reviews and Letters 02, no. 03n04 (October 2007): 259–65. http://dx.doi.org/10.1142/s1793048007000556.

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Many prokaryotic nucleoid proteins bend DNA and form extended helical protein-DNA fibers rather than condensed structures. On the other hand, it is known that such proteins (such as bacterial HU) strongly promote DNA condensation by macromolecular crowding. Using theoretical arguments, we show that this synergy is a simple consequence of the larger diameter and lower net charge density of the protein-DNA filaments as compared to naked DNA, and hence, should be quite general. To illustrate this generality, we use light-scattering to show that the 7kDa basic archaeal nucleoid protein Sso7d from Sulfolobus solfataricus (known to sharply bend DNA) likewise does not significantly condense DNA by itself. However, the resulting protein-DNA fibers are again highly susceptible to crowding-induced condensation. Clearly, if DNA-bending nucleoid proteins fail to condense DNA in dilute solution, this does not mean that they do not contribute to DNA condensation in the context of the crowded living cell.

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Kriel, Nastassja L., James Gallant, Niël van Wyk, Paul van Helden, Samantha L. Sampson, Robin M. Warren, and Monique J. Williams. "Mycobacterial nucleoid associated proteins: An added dimension in gene regulation." Tuberculosis 108 (January 2018): 169–77. http://dx.doi.org/10.1016/j.tube.2017.12.004.

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Reon, Brian J., Khoa H. Nguyen, Gargi Bhattacharyya, and Anne Grove. "Functional comparison of Deinococcus radiodurans Dps proteins suggests distinct in vivo roles." Biochemical Journal 447, no. 3 (October 5, 2012): 381–91. http://dx.doi.org/10.1042/bj20120902.

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Deinococcus radiodurans exhibits extreme resistance to DNA damage and is one of only few bacteria that encode two Dps (DNA protection during starvation) proteins. Dps-1 was shown previously to bind DNA with high affinity and to localize to the D. radiodurans nucleoid. A unique feature of Dps-2 is its predicted signal peptide. In the present paper, we report that Dps-2 assembly into a dodecamer requires the C-terminal extension and, whereas Dps-2 binds DNA with low affinity, it protects against degradation by reactive oxygen species. Consistent with a role for Dps-2 in oxidative stress responses, the Dps-2 promoter is up-regulated by oxidative stress, whereas the Dps-1 promoter is not. Although DAPI (4′,6-diamidino-2-phenylindole) staining of Escherichia coli nucleoids shows that Dps-1 can compact genomic DNA, such nucleoid condensation is absent from cells expressing Dps-2. A fusion of EGFP (enhanced green fluorescent protein) to the Dps-2 signal peptide results in green fluorescence at the perimeter of D. radiodurans cells. The differential response of the Dps-1 and Dps-2 promoters to oxidative stress, the distinct cellular localization of the proteins and the differential ability of Dps-1 and Dps-2 to attenuate hydroxyl radical production suggest distinct functional roles; whereas Dps-1 may function in DNA metabolism, Dps-2 may protect against exogenously derived reactive oxygen species.

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Gorsich, Steven W., and Janet M. Shaw. "Importance of Mitochondrial Dynamics During Meiosis and Sporulation." Molecular Biology of the Cell 15, no. 10 (October 2004): 4369–81. http://dx.doi.org/10.1091/mbc.e03-12-0875.

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Opposing fission and fusion events maintain the yeast mitochondrial network. Six proteins regulate these membrane dynamics during mitotic growth—Dnm1p, Mdv1p, and Fis1p mediate fission; Fzo1p, Mgm1p, and Ugo1p mediate fusion. Previous studies established that mitochondria fragment and rejoin at distinct stages during meiosis and sporulation, suggesting that mitochondrial fission and fusion are required during this process. Here we report that strains defective for mitochondrial fission alone, or both fission and fusion, complete meiosis and sporulation. However, visualization of mitochondria in sporulating cultures reveals morphological defects associated with the loss of fusion and/or fission proteins. Specifically, mitochondria collapse to one side of the cell and fail to fragment during presporulation. In addition, mitochondria are not inherited equally by newly formed spores, and mitochondrial DNA nucleoid segregation defects give rise to spores lacking nucleoids. This nucleoid inheritance defect is correlated with an increase in petite spore colonies. Unexpectedly, mitochondria fragment in mature tetrads lacking fission proteins. The latter finding suggests either that novel fission machinery operates during sporulation or that mechanical forces generate the mitochondrial fragments observed in mature spores. These results provide evidence of fitness defects caused by fission mutations and reveal new phenotypes associated with fission and fusion mutations.

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Salerno, Paola, Jessica Larsson, Giselda Bucca, Emma Laing, Colin P. Smith, and Klas Flärdh. "One of the Two Genes Encoding Nucleoid-Associated HU Proteins in Streptomyces coelicolor Is Developmentally Regulated and Specifically Involved in Spore Maturation." Journal of Bacteriology 191, no. 21 (August 28, 2009): 6489–500. http://dx.doi.org/10.1128/jb.00709-09.

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ABSTRACT Streptomyces genomes encode two homologs of the nucleoid-associated HU proteins. One of them, here designated HupA, is of a conventional type similar to E. coli HUα and HUβ, while the other, HupS, is a two-domain protein. In addition to the N-terminal part that is similar to that of HU proteins, it has a C-terminal domain that is similar to the alanine- and lysine-rich C termini of eukaryotic linker histones. Such two-domain HU proteins are found only among Actinobacteria. In this phylum some organisms have only a single HU protein of the type with a C-terminal histone H1-like domain (e.g., Hlp in Mycobacterium smegmatis), while others have only a single conventional HU. Yet others, including the streptomycetes, produce both types of HU proteins. We show here that the two HU genes in Streptomyces coelicolor are differentially regulated and that hupS is specifically expressed during sporulation, while hupA is expressed in vegetative hyphae. The developmental upregulation of hupS occurred in sporogenic aerial hyphal compartments and was dependent on the developmental regulators whiA, whiG, and whiI. HupS was found to be nucleoid associated in spores, and a hupS deletion mutant had an average nucleoid size in spores larger than that in the parent strain. The mutant spores were also defective in heat resistance and spore pigmentation, although they possessed apparently normal spore walls and displayed no increased sensitivity to detergents. Overall, the results show that HupS is specifically involved in sporulation and may affect nucleoid architecture and protection in spores of S. coelicolor.

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Errington, Jeffery, Richard A. Daniel, and Dirk-Jan Scheffers. "Cytokinesis in Bacteria." Microbiology and Molecular Biology Reviews 67, no. 1 (March 2003): 52–65. http://dx.doi.org/10.1128/mmbr.67.1.52-65.2003.

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SUMMARY Work on two diverse rod-shaped bacteria, Escherichia coli and Bacillus subtilis, has defined a set of about 10 conserved proteins that are important for cell division in a wide range of eubacteria. These proteins are directed to the division site by the combination of two negative regulatory systems. Nucleoid occlusion is a poorly understood mechanism whereby the nucleoid prevents division in the cylindrical part of the cell, until chromosome segregation has occurred near midcell. The Min proteins prevent division in the nucleoid-free spaces near the cell poles in a manner that is beginning to be understood in cytological and biochemical terms. The hierarchy whereby the essential division proteins assemble at the midcell division site has been worked out for both E. coli and B. subtilis. They can be divided into essentially three classes depending on their position in the hierarchy and, to a certain extent, their subcellular localization. FtsZ is a cytosolic tubulin-like protein that polymerizes into an oligomeric structure that forms the initial ring at midcell. FtsA is another cytosolic protein that is related to actin, but its precise function is unclear. The cytoplasmic proteins are linked to the membrane by putative membrane anchor proteins, such as ZipA of E. coli and possibly EzrA of B. subtilis, which have a single membrane span but a cytoplasmic C-terminal domain. The remaining proteins are either integral membrane proteins or transmembrane proteins with their major domains outside the cell. The functions of most of these proteins are unclear with the exception of at least one penicillin-binding protein, which catalyzes a key step in cell wall synthesis in the division septum.

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Morikawa, Kazuya, Yuri Ushijima, Ryosuke L. Ohniwa, Masatoshi Miyakoshi, and Kunio Takeyasu. "What Happens in the Staphylococcal Nucleoid under Oxidative Stress?" Microorganisms 7, no. 12 (November 29, 2019): 631. http://dx.doi.org/10.3390/microorganisms7120631.

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The evolutionary success of Staphylococcus aureus as an opportunistic human pathogen is largely attributed to its prominent abilities to cope with a variety of stresses and host bactericidal factors. Reactive oxygen species are important weapons in the host arsenal that inactivate phagocytosed pathogens, but S. aureus can survive in phagosomes and escape from phagocytic cells to establish infections. Molecular genetic analyses combined with atomic force microscopy have revealed that the MrgA protein (part of the Dps family of proteins) is induced specifically in response to oxidative stress and converts the nucleoid from the fibrous to the clogged state. This review collates a series of evidences on the staphylococcal nucleoid dynamics under oxidative stress, which is functionally and physically distinct from compacted Escherichia coli nucleoid under stationary phase. In addition, potential new roles of nucleoid clogging in the staphylococcal life cycle will be proposed.

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Vingadassalon, Audrey, Philippe Bouloc, and Sylvie Rimsky. "Removing nucleic acids from nucleoid-Associated proteins purified by affinity column." Journal of Biological Methods 3, no. 1 (January 30, 2016): 35. http://dx.doi.org/10.14440/jbm.2016.98.

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Yan, Jie. "DNA binding by bacterial nucleoid proteins and the DNA overstretching transition." Physics of Life Reviews 7, no. 3 (September 2010): 342–43. http://dx.doi.org/10.1016/j.plrev.2010.06.003.

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Shintani, Masaki, Chiho Suzuki-Minakuchi, and Hideaki Nojiri. "Nucleoid-associated proteins encoded on plasmids: Occurrence and mode of function." Plasmid 80 (July 2015): 32–44. http://dx.doi.org/10.1016/j.plasmid.2015.04.008.

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de Vries, Renko. "DNA condensation in bacteria: Interplay between macromolecular crowding and nucleoid proteins." Biochimie 92, no. 12 (December 2010): 1715–21. http://dx.doi.org/10.1016/j.biochi.2010.06.024.

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Dorman, Charles J. "Function of Nucleoid-Associated Proteins in Chromosome Structuring and Transcriptional Regulation." Journal of Molecular Microbiology and Biotechnology 24, no. 5-6 (2014): 316–31. http://dx.doi.org/10.1159/000368850.

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Kivisaar, Maia. "Mutation and Recombination Rates Vary Across Bacterial Chromosome." Microorganisms 8, no. 1 (December 21, 2019): 25. http://dx.doi.org/10.3390/microorganisms8010025.

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Bacteria evolve as a result of mutations and acquisition of foreign DNA by recombination processes. A growing body of evidence suggests that mutation and recombination rates are not constant across the bacterial chromosome. Bacterial chromosomal DNA is organized into a compact nucleoid structure which is established by binding of the nucleoid-associated proteins (NAPs) and other proteins. This review gives an overview of recent findings indicating that the mutagenic and recombination processes in bacteria vary at different chromosomal positions. Involvement of NAPs and other possible mechanisms in these regional differences are discussed. Variations in mutation and recombination rates across the bacterial chromosome may have implications in the evolution of bacteria.

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Busch, Karin B., Axel Kowald, and Johannes N. Spelbrink. "Quality matters: how does mitochondrial network dynamics and quality control impact on mtDNA integrity?" Philosophical Transactions of the Royal Society B: Biological Sciences 369, no. 1646 (July 5, 2014): 20130442. http://dx.doi.org/10.1098/rstb.2013.0442.

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Mammalian mtDNA encodes for 13 core proteins of oxidative phosphorylation. Mitochondrial DNA mutations and deletions cause severe myopathies and neuromuscular diseases. Thus, the integrity of mtDNA is pivotal for cell survival and health of the organism. We here discuss the possible impact of mitochondrial fusion and fission on mtDNA maintenance as well as positive and negative selection processes. Our focus is centred on the important question of how the quality of mtDNA nucleoids can be assured when selection and mitochondrial quality control works on functional and physiological phenotypes constituted by oxidative phosphorylation proteins. The organelle control theory suggests a link between phenotype and nucleoid genotype. This is discussed in the light of new results presented here showing that mitochondrial transcription factor A/nucleoids are restricted in their intramitochondrial mobility and probably have a limited sphere of influence. Together with recent published work on mitochondrial and mtDNA heteroplasmy dynamics, these data suggest first, that single mitochondria might well be internally heterogeneous and second, that nucleoid genotypes might be linked to local phenotypes (although the link might often be leaky). We discuss how random or site-specific mitochondrial fission can isolate dysfunctional parts and enable their elimination by mitophagy, stressing the importance of fission in the process of mtDNA quality control. The role of fusion is more multifaceted and less understood in this context, but the mixing and equilibration of matrix content might be one of its important functions.

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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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Dias, Rita S. "Role of Protein Self-Association on DNA Condensation and Nucleoid Stability in a Bacterial Cell Model." Polymers 11, no. 7 (June 29, 2019): 1102. http://dx.doi.org/10.3390/polym11071102.

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Bacterial cells do not have a nuclear membrane that encompasses and isolates the genetic material. In addition, they do not possess histone proteins, which are responsible for the first levels of genome condensation in eukaryotes. Instead, there is a number of more or less specific nucleoid-associated proteins that induce DNA bridging, wrapping and bending. Many of these proteins self-assemble into oligomers. The crowded environment of cells is also believed to contribute to DNA condensation due to excluded volume effects. Ribosomes are protein-RNA complexes found in large concentrations in the cytosol of cells. They are overall negatively charged and some DNA-binding proteins have been reported to also bind to ribosomes. Here the effect of protein self-association on DNA condensation and stability of DNA-protein complexes is explored using Monte Carlo simulations and a simple coarse-grained model. The DNA-binding proteins are described as positively charged dimers with the same linear charge density as the DNA, described using a bead and spring model. The crowding molecules are simply described as hard-spheres with varying charge density. It was found that applying a weak attractive potential between protein dimers leads to their association in the vicinity of the DNA (but not in its absence), which greatly enhances the condensation of the model DNA. The presence of neutral crowding agents does not affect the DNA conformation in the presence or absence of protein dimers. For weakly self-associating proteins, the presence of negatively charged crowding particles induces the dissociation of the DNA-protein complex due to the partition of the proteins between the DNA and the crowders. Protein dimers with stronger association potentials, on the other hand, stabilize the nucleoid, even in the presence of highly charged crowders. The interactions between protein dimers and crowding agents are not completely prevented and a few crowding molecules typically bind to the nucleoid.

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Qian, Zhong, Victor B. Zhurkin, and Sankar Adhya. "DNA–RNA interactions are critical for chromosome condensation inEscherichia coli." Proceedings of the National Academy of Sciences 114, no. 46 (October 30, 2017): 12225–30. http://dx.doi.org/10.1073/pnas.1711285114.

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Bacterial chromosome (nucleoid) conformation dictates faithful regulation of gene transcription. The conformation is condition-dependent and is guided by several nucleoid-associated proteins (NAPs) and at least one nucleoid-associated noncoding RNA, naRNA4. Here we investigated the molecular mechanism of how naRNA4 and the major NAP, HU, acting together organize the chromosome structure by establishing multiple DNA–DNA contacts (DNA condensation). We demonstrate that naRNA4 uniquely acts by forming complexes that may not involve long stretches of DNA–RNA hybrid. Also, uncommonly, HU, a chromosome-associated protein that is essential in the DNA–RNA interactions, is not present in the final complex. Thus, HU plays a catalytic (chaperone) role in the naRNA4-mediated DNA condensation process.

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Qin, L., A. M. Erkelens, F. Ben Bdira, and R. T. Dame. "The architects of bacterial DNA bridges: a structurally and functionally conserved family of proteins." Open Biology 9, no. 12 (December 2019): 190223. http://dx.doi.org/10.1098/rsob.190223.

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Every organism across the tree of life compacts and organizes its genome with architectural chromatin proteins. While eukaryotes and archaea express histone proteins, the organization of bacterial chromosomes is dependent on nucleoid-associated proteins. In Escherichia coli and other proteobacteria, the histone-like nucleoid structuring protein (H-NS) acts as a global genome organizer and gene regulator. Functional analogues of H-NS have been found in other bacterial species: MvaT in Pseudomonas species, Lsr2 in actinomycetes and Rok in Bacillus species. These proteins complement hns − phenotypes and have similar DNA-binding properties, despite their lack of sequence homology. In this review, we focus on the structural and functional characteristics of these four architectural proteins. They are able to bridge DNA duplexes, which is key to genome compaction, gene regulation and their response to changing conditions in the environment. Structurally the domain organization and charge distribution of these proteins are conserved, which we suggest is at the basis of their conserved environment responsive behaviour. These observations could be used to find and validate new members of this protein family and to predict their response to environmental changes.

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Journal articles on the topic 'Nucleoid Proteins'

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