Bacterial protein HU dictates the morphology of DNA condensates produced by crowding agents and polyamines

Sarkar, Tumpa; Vitoc, Iulia; Mukerji, Ishita; Hud, Nicholas V.

doi:10.1093/nar/gkl1093

Cited by 32 publications

(20 citation statements)

References 76 publications

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“…In bacterial cytoplasm, cellular DNA is compacted by several factors. The most important of these are: macromolecular crowding, 26 DNA-binding proteins (such as HU and H-NS proteins) 49,50 and polyamines. 51 The cryo-EM images in Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Furthermore, it was shown that even at such low HU concentrations as ≤ 1 HU dimer per 225 bp DNA, HU still plays an architectural role in guiding DNA condensation in the cell's crowding conditions resulting in more ordered DNA condensates. 50 The observed combined effect of molecular crowding and DNA-binding agent on the extent of DNA ejection from capsids might also be relevant in the case of eukaryotic cell infection. Although during infection of a eukaryotic cell the whole viral capsid enters the cell, it is still not fully understood how the genome of double-stranded DNA viruses is released from the capsid, especially in those cases where the capsid does not disassemble during infection (as in the case of herpes simplex virus type 1).…”

Section: Resultsmentioning

confidence: 99%

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Osmotic Pressure: Resisting or Promoting DNA Ejection from Phage?

Jeembaeva

Castelnovo

Larsson

et al. 2008

Journal of Molecular Biology

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Recent in vitro experiments have shown that DNA ejection from bacteriophage can be partially stopped by surrounding osmotic pressure when ejected DNA is digested by DNase I in the course of ejection. In this work, we argue by a combination of experimental techniques (osmotic suppression without DNase I monitored by UV absorbance, pulse-field electrophoresis, and cryo-transmission electron microscopy visualization) and simple scaling modeling that intact genome (i.e., undigested) ejection in a crowded environment is, on the contrary, enhanced or eventually complete with the help of a pulling force resulting from DNA condensation induced by the osmotic stress itself. This demonstrates that in vivo, the osmotically stressed cell cytoplasm will promote phage DNA ejection rather than resist it. The further addition of DNA-binding proteins under crowding conditions is shown to enhance the extent of ejection. We also found some optimal crowding conditions for which DNA content remaining in the capsid upon ejection is maximum, which correlates well with the optimal conditions of maximum DNA packaging efficiency into viral capsids observed almost 20 years ago. Biological consequences of this finding are discussed.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Osmotic Pressure: Resisting or Promoting DNA Ejection from Phage?

Jeembaeva

Castelnovo

Larsson

et al. 2008

Journal of Molecular Biology

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“…The spatial distribution of DNA-binding protein HU, which is the most abundant NAP 67,68 , was investigated in fixed C. crescentus cells usin g photoinduced blinking of the HU2–eYFP fusion protein 69 . HU is typically present as a heterodimer, consisting of HU1 and HU2 in C. crescentus (or HU1α and HUβ in E. coli ), that nonspecifically binds to both double-stranded and single-stranded DNA 67,68 .…”

Section: Nucleoid Organization and Partitioningmentioning

confidence: 99%

Exploring bacterial cell biology with single-molecule tracking and super-resolution imaging

2013

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The ability to detect single molecules in live bacterial cells enables us to probe biological events one molecule at a time and thereby gain knowledge of the activities of intracellular molecules that remain obscure in conventional ensemble-averaged measurements. Single-molecule fluorescence tracking and super-resolution imaging are thus providing a new window into bacterial cells and facilitating the elucidation of cellular processes at an unprecedented level of sensitivity, specificity and spatial resolution. In this Review, we consider what these technologies have taught us about the bacterial cytoskeleton, nucleoid organization and the dynamic processes of transcription and translation, and we also highlight the methodological improvements that are needed to address a number of experimental challenges in the field.

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“…4) incorporate a regular serpentine-like fold of the sort thought to nucleate the rodlike condensates formed in the presence of HU. 27 …”

Section: Hu Positioning In Open and Closed Moleculesmentioning

confidence: 99%

Effects of the Nucleoid Protein HU on the Structure, Flexibility, and Ring-Closure Properties of DNA Deduced from Monte Carlo Simulations

Czapla

Swigon

Olson

2008

Journal of Molecular Biology

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The histone-like HU (heat unstable) protein plays a key role in the organization and regulation of the Escherichia coli genome. The nonspecific nature of HU binding to DNA complicates analysis of the mechanism by which the protein contributes to the looping of DNA. Conventional models of the looping of HU-bound duplexes attribute the changes in biophysical properties of DNA brought about by the random binding of protein to changes in the effective parameters of an ideal helical wormlike chain. Here, we introduce a novel Monte Carlo approach to study the effects of nonspecific HU binding on the configurational properties of DNA directly. We randomly decorated segments of an ideal double-helical DNA with HU molecules that induce the bends and other structural distortions of the double helix find in currently available X-ray structures. We find that the presence of HU at levels approximating those found in the cell reduces the persistence length by roughly threefold compared with that of naked DNA. The binding of protein has particularly striking effects on the cyclization properties of short duplexes, altering the dependence of ring closure on chain length in a way that cannot be mimicked by a simple wormlike model and accumulating at higher-than-expected levels on successfully closed chains. Moreover, the uptake of protein on small minicircles depends on chain length, taking advantage of the HU-induced deformations of DNA structure to facilitate ligation. Circular duplexes with bound HU show much greater propensity than protein-free DNA to exist as negatively supercoiled topoisomers, suggesting a potential role of HU in organizing the bacterial nucleoid. The local bending and undertwisting of DNA by HU, in combination with the number of bound proteins, provide a structural rationale for the condensation of DNA and the observed expression levels of reporter genes in vivo.

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Bacterial protein HU dictates the morphology of DNA condensates produced by crowding agents and polyamines

Cited by 32 publications

References 76 publications

Osmotic Pressure: Resisting or Promoting DNA Ejection from Phage?

Osmotic Pressure: Resisting or Promoting DNA Ejection from Phage?

Exploring bacterial cell biology with single-molecule tracking and super-resolution imaging

Effects of the Nucleoid Protein HU on the Structure, Flexibility, and Ring-Closure Properties of DNA Deduced from Monte Carlo Simulations

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