Ionic effects on viral DNA packaging and portal motor function in bacteriophage φ29

Abstract

In many viruses, DNA is confined at such high density that its bending rigidity and electrostatic self-repulsion present a strong energy barrier in viral assembly. Therefore, a powerful molecular motor is needed to package the DNA into the viral capsid. Here, we investigate the role of electrostatic repulsion on single DNA packaging dynamics in bacteriophage 29 via optical tweezers measurements. We show that ionic screening strongly affects the packing forces, confirming the importance of electrostatic repulsion. Separately, we find that ions affect the motor function. We separate these effects through constant force measurements and velocity versus load measurements at both low and high capsid filling. Regarding motor function, we find that eliminating free Mg 2؉ blocks initiation of packaging. In contrast, Na ؉ is not required, but it increases the motor velocity by up to 50% at low load. Regarding internal resistance, we find that the internal force was lowest when Mg 2؉ was the dominant ion or with the addition of 1 mM Co 3؉ . Forces resisting DNA confinement were up to Ϸ80% higher with Na ؉ as the dominant counterion, and only Ϸ90% of the genome length could be packaged in this condition. The observed trend of the packing forces is in accord with that predicted by DNA charge-screening theory. However, the forces are up to six times higher than predicted by models that assume coaxial spooling of the DNA and interaction potentials derived from DNA condensation experiments. The forces are also severalfold higher than ejection forces measured with bacteriophage .optical tweezers ͉ single molecule D uring the assembly of many dsDNA viruses, the genome is compacted to near-crystalline density (1). Because the size of viral capsids is on the order of the persistence length of the DNA (Ϸ50 nm), significant DNA bending must occur during packaging (2-7). Moreover, due to the negatively charged phosphate backbone of DNA, a large repulsive electrostatic barrier must be overcome during DNA confinement (2-7). In some cases, more than half of the physically available space inside the capsid is taken up by the viral genome (1, 7).In the case of bacteriophage 29, the 19.3-kbp genome (Ϸ6.5 m in length) is packed inside a prolate icosahedral capsid Ϸ45-nm wide and 54-nm long (8). As with many other dsDNA viruses, DNA is translocated into the preformed precursor capsid (prohead) by an ATP-powered molecular motor (9-11). The 29 motor is situated at a unique vertex of the prohead and consists of a ring of RNA molecules (pRNA) sandwiched between two protein rings: the head-tail connector (gene product 10, gp10) and the packaging ATPase (gp16) (12).Previously, we developed an optical tweezers assay that allowed us to measure the packaging of a single DNA molecule into a single 29 prohead (9). We found that the rate of packaging decreased during capsid filling or when an external force was applied to the DNA substrate. From these measurements, we showed that a large internal force builds during packaging because of DNA confinement ...

Measurements of Single DNA Molecule Packaging Dynamics in Bacteriophage λ Reveal High Forces, High Motor Processivity, and Capsid Transformations

“…5A. The rate is constant during the first 20% of genome packaging, consistent with negligible internal force resisting DNA packaging in this low capsid filling regime, in accord with our findings with ϕ29 in the absence of Na + and theoretical predictions 6,19,21,22,23 . The average rate of 580 bp/s (SD 120 bp/s) is approximately equal to that at 5 pN determined in our velocity vs. load measurements (Fig.…”

“…Since the motor velocity decreases with increasing load (Fig. 3), this decrease in velocity with capsid filling is indicative of a building internal force resisting DNA confinement in the procapsid, as found previously with bacteriophage ϕ29 6,7 . The internal force may be deduced by relating the velocity measured in the velocity vs. filling dataset (Fig.…”

“…We find that the force rises steeply with filling during the latter half of genome packaging, as observed with ϕ29 6, 7 and predicted theoretically 19,21,22,23,24,25 , and reaches 25 ± 6 pN with 90% of the genome length packaged. This force is notably two to three-fold lower than that measured for ϕ29 in a similar ionic condition 6 . However, it is in good agreement with the λ phage DNA ejection force measured by osmotic pressure experiments 35,36 and predicted by theoretical calculations 23,36 .…”

“…We tracked packaging over longer distances by using a force-clamp in which the separation between the two optical traps was varied under feedback control to maintain a small constant load of ~5 pN as the DNA was translocated 6 . The DNA tether length versus time (Fig.…”

“…We recently developed a method to directly measure the packaging of single DNA molecules into single bacteriophage ϕ29 procapsids using optical tweezers 6,7 . We found that the ϕ29 packaging motor translocates DNA processively at rates up to 165 bp/s, exerting forces of at least 80 pN, and that this high force generation is required to overcome large forces resisting dense DNA confinement in the procapsid.…”