The bacterial nucleoid: A highly organized and dynamic structure

Thanbichler, Martin; Wang, Sherry; Shapiro, Lucy

doi:10.1002/jcb.20519

Cited by 115 publications

(101 citation statements)

References 170 publications

(168 reference statements)

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“…These approaches were limited by either the resolution or by possible preparation artifacts. Hence, the organization of the nucleoid inside bacterial cells is still elusive and a matter of an ongoing debate 25,26 .…”

Section: Manuscript Textmentioning

confidence: 99%

Binding-Activated Localization Microscopy of DNA Structures

et al. 2011

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Many nucleic acid stains show a strong fluorescence enhancement upon binding to doublestranded DNA. Here we exploit this property to perform superresolution microscopy based on the localization of individual binding events. The dynamic labeling scheme and the optimization of fluorophore brightness yielded a resolution of 14 nm (fwhm) and a spatial sampling of 1/nm. We illustrate our approach with two different DNA-binding dyes and apply it to visualize the organization of the bacterial chromosome in fixed Escherichia coli cells. In general, the principle of binding-activated localization microscopy (BALM) can be extended to other dyes and targets such as protein structures.

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Section: Manuscript Textmentioning

confidence: 99%

Binding-Activated Localization Microscopy of DNA Structures

et al. 2011

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“…This difference is, in part, due to a lack of functional redundancy in Gram-positive bacteria, while E. coli expresses a wide variety of NAPs, including H-NS, Fis, Dps and IHF (Thanbichler et al, 2005). Yet, even with a wide variety of functional NAP homologues, E. coli cells lacking HU do exhibit a variety of growth defects.…”

Section: Introductionmentioning

confidence: 99%

The nucleoid-associated protein HUβ affects global gene expression in Porphyromonas gingivalis

et al. 2013

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HU is a non-sequence-specific DNA-binding protein and one of the most abundant nucleoidassociated proteins in the bacterial cell. Like Escherichia coli, the genome of Porphyromonas gingivalis is predicted to encode both the HUa (PG1258) and the HUb (PG0121) subunit. We have previously reported that PG0121 encodes a non-specific DNA-binding protein and that PG0121 is co-transcribed with the K-antigen capsule synthesis operon. We also reported that deletion of PG0121 resulted in downregulation of capsule operon expression and produced a P. gingivalis strain that is phenotypically deficient in surface polysaccharide production. Here, we show through complementation experiments in an E. coli MG1655 hupAB double mutant strain that PG0121 encodes a functional HU homologue. Microarray and quantitative RT-PCR analysis were used to further investigate global transcriptional regulation by HUb using comparative expression profiling of the PG0121 (HUb) mutant strain to the parent strain, W83. Our analysis determined that expression of genes encoding proteins involved in a variety of biological functions, including iron acquisition, cell division and translation, as well as a number of predicted nucleoid associated proteins were altered in the PG0121 mutant. Phenotypic and quantitative real-time-PCR (qRT-PCR) analyses determined that under iron-limiting growth conditions, cell division and viability were defective in the PG0121 mutant. Collectively, our studies show that PG0121 does indeed encode a functional HU homologue, and HUb has global regulatory functions in P. gingivalis; it affects not only production of capsular polysaccharides but also expression of genes involved in basic functions, such as cell wall synthesis, cell division and iron uptake. INTRODUCTIONPorphyromonas gingivalis is a Gram-negative obligate anaerobe belonging to the family Bacteroidaceae that persists as a natural member of the human oral microbiota. A shift in the microbial community leading to outgrowth of this anaerobe is directly linked to periodontitis, a chronic inflammatory disease that leads to destruction of the tissues supporting the gums and ultimately, exfoliation of the teeth (Choil et al., 1990;Dzink et al., 1988;Grossi et al., 1994;Lamont & Jenkinson, 2000;Moore et al., 1991). This commensal can colonize, invade and multiply within gingival epithelial cells, as well as penetrate into deeper epithelial cell layers, potentially releasing the whole organism and/or virulence factors into the bloodstream (reviewed by Yilmaz, 2008). In addition to its ability to cause disease in the oral cavity, there are data indicating a role in systemic disease, including its ability to invade vascular endothelial cells (Dorn et al., 2000(Dorn et al., , 2002Jandik et al., 2008) and to cause aggregation of platelets (Pham et al., 2002). For many pathogenic bacteria, surface polysaccharides play a key role in immune modulation et al., 1996). HU typically acts as an accessory protein in virtually all types of nucleoprotein-mediated processes (reviewed by...

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“…Studies of chromosome organization in bacterial cells show that the chromosome is an exquisitely organized and dynamic structure (reviewed recently in Thanbichler et al, 2005). Chromosome segregation in bacteria does not occur all at once but in sequential phases (Lau et al, 2003;Viollier et al, 2004;Bates and Kleckner, 2005;Nielsen et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

Chromosome segregation control by Escherichia coli ObgE GTPase

Foti

Persky²,

Ferullo

et al. 2007

Molecular Microbiology

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SummaryEscherichia coli cells depleted of the conserved GTPase, ObgE, show early chromosome-partitioning defects and accumulate replicated chromosomes in which the terminus regions are colocalized. Cells lacking ObgE continue to initiate replication, with a normal ratio of the origin to terminus. Localization of the SeqA DNA binding protein, normally seen as punctate foci, however, was disturbed. Depletion of ObgE also results in cell filamentation, with polyploid DNA content. Depletion of ObgE did not cause lethality, and cells recovered fully after expression of ObgE was restored. We propose a model in which ObgE is required to license chromosome segregation and subsequent cell cycle events.

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The bacterial nucleoid: A highly organized and dynamic structure

Cited by 115 publications

References 170 publications

Binding-Activated Localization Microscopy of DNA Structures

Binding-Activated Localization Microscopy of DNA Structures

The nucleoid-associated protein HUβ affects global gene expression in Porphyromonas gingivalis

Chromosome segregation control by Escherichia coli ObgE GTPase

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