Quantitative Study of the Chiral Organization of the Phage Genome Induced by the Packaging Motor

Abstract

Molecular motors that translocate DNA are ubiquitous in nature. During morphogenesis of double-stranded DNA bacteriophages, a molecular motor drives the viral genome inside a protein capsid. Several models have been proposed for the three-dimensional geometry of the packaged genome, but very little is known of the signature of the molecular packaging motor. For instance, biophysical experiments show that in some systems, DNA rotates during the packaging reaction, but most current biophysical models fail to incorporate this property. Furthermore, studies including rotation mechanisms have reached contradictory conclusions. In this study, we compare the geometrical signatures imposed by different possible mechanisms for the packaging motors: rotation, revolution, and rotation with revolution. We used a previously proposed kinetic Monte Carlo model of the motor, combined with Brownian dynamics simulations of DNA to simulate deterministic and stochastic motor models. We find that rotation is necessary for the accumulation of DNA writhe and for the chiral organization of the genome. We observe that although in the initial steps of the packaging reaction, the torsional strain of the genome is released by rotation of the molecule, in the later stages, it is released by the accumulation of writhe. We suggest that the molecular motor plays a key role in determining the final structure of the encapsidated genome in bacteriophages.

Chromonic liquid crystals and packing configurations of bacteriophage viruses

“…Furthermore, the ability to increase d plays a main role in genome delivery, as a mechanism fostering the solid-to-liquid transition, relevant to a successful infection [12]. A second shortcoming is neglecting possible defects that naturally occur in hexagonal chromonic lattices as well as ignoring the role of chirality [27,28]. These may affect the genome’s delivery process leading to potential jamming .…”

Effects of Model Shape, Volume, and Softness of the Capsid for DNA Packaging of phi29

“…10 It has been found that the phi29 packaging motor negatively twists DNA during filling at a rate of ∼60°per helical turn, 34,35 and it has been considered by some as an important feature in determining the final packaged configuration of the viral genome. 36 defects such as kinks and bubbles often localized at certain sequences in AT-rich regions while allowing the rest of the chain to relax to B form. 37−39 In this contribution, we have performed model simulations of DNA packaging in the phi29 capsid capturing some features of the DNA representation, the filling process, and the protein capsid geometry.…”

“…In particular, phage phi29 is among the smallest double-stranded DNA phages and possesses a double-stranded DNA genome of 19,282 base pairs (bp) confined within a prolate capsid with icosahedral features ( T = 3, Q = 5) and external dimensions of the prolate head of 42 nm × 54 nm . It has been found that the phi29 packaging motor negatively twists DNA during filling at a rate of ∼60° per helical turn, , and it has been considered by some as an important feature in determining the final packaged configuration of the viral genome . DNA under negative torsional stress tends to relieve the stress by spontaneously forming defects such as kinks and bubbles often localized at certain sequences in AT-rich regions while allowing the rest of the chain to relax to B form. − …”