Solid-to-fluid–like DNA transition in viruses facilitates infection

Liu, Ting; Sae-Ueng, Udom; Li, Dong; Lander, Gabriel C.; Zuo, Xiaobing; Jönsson, Bengt; Rau, Donald C.; Shefer, Ivetta; Evilevitch, Alex

doi:10.1073/pnas.1321637111

Cited by 56 publications

(142 citation statements)

References 45 publications

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“…The temperature for heat-induced DNA ejection observed here also coincides with previous experiments on phage λ utilizing light scattering to monitor genome release as a function of temperature 18 . Further, by measuring receptor-triggered genome release using isothermal titration calorimetry (ITC), we previously confirmed that DNA ejection from viral capsids does indeed have a measurable exothermic enthalpy component 13; 20 . By inducing genome release with heat treatment, rather than a cellular receptor protein, we probe the overall stability of packaged DNA within virions.…”

Section: Resultsmentioning

confidence: 72%

“…We have recently shown that packaged DNA within wt DNA length λ capsids exhibits a structural transition 13 . This temperature-induced transition results in an abrupt variation in the structure, energy, and mobility (or fluidity) of encapsidated DNA and occurs close to 37 ºC depending on the buffer conditions 13 . Internal pressure was found to influence the temperature at which this DNA transition occurred, with higher pressure resulting in a lower transition temperature.…”

Section: Resultsmentioning

confidence: 99%

“…This resulted in initiation of receptor-triggered DNA ejection occurring more readily from a significantly larger fraction of viruses for temperatures just above the transition. At the same time, below the transition temperature, DNA packaged in the capsid has restricted mobility, which delays or completely prevents its release even when the capsid is opened by receptor molecule 13 . Such restriction on DNA movement within the capsid may also have a role in the heat-induced formation of DNA-filled but non-infectious virions observed above.…”

Section: Resultsmentioning

confidence: 99%

“…More recently, internal genome pressure was confirmed within an Archaeal virus (His1) 10 and a eukaryotic virus (Herpes Simplex virus type 1; HSV-1) 11 . Experimental and theoretical work has investigated the role of internal pressure for receptor-triggered DNA ejection 7; 12; 13; 14; 15; 16; 17 . Here, using differential scanning calorimetry (DSC), we investigate the influence of internal DNA pressure on the thermal stability of viral particles.…”

Section: Introductionmentioning

confidence: 99%

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Influence of Internal DNA Pressure on Stability and Infectivity of Phage λ

Bauer

Evilevitch²

2015

Journal of Molecular Biology

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Viruses must remain infectious while in harsh extracellular environments. An important aspect of viral particle stability for double-stranded DNA viruses is the energetically unfavorable state of the tightly confined DNA chain within the virus capsid creating pressures of tens of atmospheres. Here we study the influence of internal genome pressure on the thermal stability of viral particles. Using differential scanning calorimetry (DSC) to monitor genome loss upon heating, we find that internal pressure destabilizes the virion, resulting in a smaller activation energy barrier to trigger DNA release. These experiments are complemented by plaque assay and electron microscopy measurements to determine the influence of intra-capsid DNA pressure on the rates of viral infectivity loss. At higher temperatures (65 – 75 °C), failure to retain the packaged genome is the dominant mechanism of viral inactivation. Conversely, at lower temperatures (40 – 55 ºC), a separate inactivation mechanism dominates, which results in non-infectious particles that still retain their packaged DNA. Most significantly, both mechanisms of infectivity loss are directly influenced by internal DNA pressure, with higher pressure resulting in a more rapid rate of inactivation at all temperatures.

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Section: Resultsmentioning

confidence: 72%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Influence of Internal DNA Pressure on Stability and Infectivity of Phage λ

Bauer

Evilevitch²

2015

Journal of Molecular Biology

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“…We demonstrate that the solid-to-fluid-like intracapsid DNA transition (Liu et al, 2014), is a determining factor for either rapid synchronized or slow desynchronized ejection dynamics from a phage population. We show that at optimum temperature for infection (i.e.…”

Section: Resultsmentioning

confidence: 99%

The mobility of packaged phage genome controls ejection dynamics

Evilevitch

2018

eLife

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The cell decision between lytic and lysogenic infection is strongly influenced by dynamics of DNA injection into a cell from a phage population, as phages compete for limited resources and progeny. However, what controls the timing of viral DNA ejection events was not understood. This in vitro study reveals that DNA ejection dynamics for phages can be synchronized (occurring within seconds) or desynchronized (displaying minutes-long delays in initiation) based on mobility of encapsidated DNA, which in turn is regulated by environmental factors, such as temperature and extra-cellular ionic conditions. This mechano-regulation of ejection dynamics is suggested to influence viral replication where the cell’s decision between lytic and latent infection is associated with synchronized or desynchronized delayed ejection events from phage population adsorbed to a cell. Our findings are of significant importance for understanding regulatory mechanisms of latency in phage and Herpesviruses, where encapsidated DNA undergoes a similar mechanical transition.

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Can DNA Organization in the Full Bacteriophage Capsid be modified by changes in Temperature or Ionic Conditions?

Frutos

Leforestier

Degrouard

et al. 2016

European Microscopy Congress 2016: Proceedings

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As revealed initially by X‐ray diffraction and visualized later on by cryoEM in several bacteriophages, the DNA chain confined in the capsid is densely packed and organized locally in such a way that DNA segments form an hexagonal lattice with an average inter‐helix spacing aH close to 26 – 27 Å. The 3D organization of DNA in the capsid or the path followed by the chain remains unknown. DNA is kinetically constrained and undergoes out‐of‐equilibrium conformational dynamics during packaging in the capsid. The structural analysis of full capsids also indicates that there is not a unique deterministic DNA packaging pathway. All consequences of this high confinement on DNA ordering and mobility are not yet well understood. Our aim is here to explore how confinement determines DNA organization in the full capsid and to what extent spermine and temperature may affect this ordering. CryoEM has been used to visualize DNA patterns in individual capsids, Circular Dichroism (CD) to detect possible changes of the conformation of DNA and of its supramolecular chiral organization and Small Angle X‐ray Scattering (SAXS) to detect possible variations of inter‐helix distances, while controlling the conformation of the full capsids. We have compared T5, λ, T7, and Φ29 bacteriophages. This selection let us explore the effect of extreme confinement and compare capsids of different shape (prolate or isometric icosahedron) and size, with or without an internal core. We also compared T5 strains containing the full‐length genome to the mutant T5st0 containing a shorter DNA chain, to detect whether possible effects may be increased or reduced at lower densities. Selected CryoEM views show the overall shape of the phages (Figure 1A) and highlight the local hexagonal DNA lattice seen in top view (domains framed in red in Figure 1B). In the direction normal to the capsid faces, up to 5‐6 layers define the thickness of the domain. Figure 1C presents structure factors recorded for all phages. ‐ First, we did not detect any change of DNA organization as a function of temperature between 20 to 40°C, as opposed to previous results (1, 2). ‐ Second, the presence of spermine (4+) enlarges the size of the hexagonal domains determined by the width of the diffraction peak: from 139 to 156 Å in T5, from 111 to 123 Å in λ, from 111 to 128 Å in T7, and from 96 to 110 Å in Φ29 when 100 mM sp is added in HS buffer (10 mM Tris‐HCl, 100 mM NaCl, 1 mM MgCl2, and 1 mM CaCl2). 4 mM spermine is enough to produce this effect. We interpret this increase of the domain size detected for all phages as an increase of the DNA ordering upon spermine addition in agreement with (3). The addition of spermine, by reducing the repulsive interactions between DNA strands would help the local hexagonal order to expand and slightly move the defects further apart. In this hypothesis, DNA reorganization would require very minor sliding of the DNA chain inside the capsid. The enlargement of the DNA hexagonal domains by spermine does not modify the CD spectrum of the encapsidated DNA that stays close to the typical B‐type spectrum. Our estimations of the DNA concentrations based on SAXS measurements (540 ± 20 mg/ml in T5, 525 ± 20 mg/ml in λ, 575 ± 20 in T7 and 615 ± 50 in Φ29) seem to indicate that the smallest phages (T7 and Φ29) are the most densely packed. The comparison between λ and T7 (both icosahedral, with dimensions and DNA length in the same range) suggest that the presence of an internal core in T7 facilitate DNA organization by wounding part of the chain around it in a toroidal organization, thus reducing the defect lattice required to solve the frustration arising from the confinement of the hexagonal lattice in an icosahedral capsid (4).

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Solid-to-fluid–like DNA transition in viruses facilitates infection

Cited by 56 publications

References 45 publications

Influence of Internal DNA Pressure on Stability and Infectivity of Phage λ

Influence of Internal DNA Pressure on Stability and Infectivity of Phage λ

The mobility of packaged phage genome controls ejection dynamics

Can DNA Organization in the Full Bacteriophage Capsid be modified by changes in Temperature or Ionic Conditions?

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