Nucleotide-dependent DNA Gripping and an End-clamp Mechanism Regulate the Bacteriophage T4 Viral Packaging Motor

Overview

Journal Nat Commun

Specialty Biology

Date 2018 Dec 22

PMID 30575768

Citations 16

Authors

Mariam Ordyan

Istiaq Alam

Marthandan Mahalingam

Venigalla B Rao

Douglas E Smith

Affiliations

Soon will be listed here.

Abstract

ATP-powered viral packaging motors are among the most powerful biomotors known. Motor subunits arranged in a ring repeatedly grip and translocate the DNA to package viral genomes into capsids. Here, we use single DNA manipulation and rapid solution exchange to quantify how nucleotide binding regulates interactions between the bacteriophage T4 motor and DNA substrate. With no nucleotides, there is virtually no gripping and rapid slipping occurs with only minimal friction resisting. In contrast, binding of an ATP analog engages nearly continuous gripping. Occasional slips occur due to dissociation of the analog from a gripping motor subunit, or force-induced rupture of grip, but multiple other analog-bound subunits exert high friction that limits slipping. ADP induces comparably infrequent gripping and variable friction. Independent of nucleotides, slipping arrests when the end of the DNA is about to exit the capsid. This end-clamp mechanism increases the efficiency of packaging by making it essentially irreversible.

Citing Articles

Single-molecule measurements of bacteriophage lambda DNA packaging using purified terminase motor proteins and E. coli integration host factor.

Rawson B, Yang Q, Catalano C, Smith D Sci Rep. 2025; 15(1):7093.

PMID: 40016253 PMC: 11868608. DOI: 10.1038/s41598-024-74915-2.

Crucial Roles of Electricity in Virology.

McCaig C Rev Physiol Biochem Pharmacol. 2025; 187():411-417.

PMID: 39838020 DOI: 10.1007/978-3-031-68827-0_19.

Optical Tweezers to Study Viruses.

Arias-Gonzalez J Subcell Biochem. 2024; 105:359-399.

PMID: 39738952 DOI: 10.1007/978-3-031-65187-8_10.

Methods for Studying Motor-Driven Viral DNA Packaging in Bacteriophages phi29, Lambda, and T4 via Single DNA Molecule Manipulation and Rapid Solution Exchange.

Fizari M, Rawson B, Keller N, delToro D, Smith D Methods Mol Biol. 2024; 2881():293-327.

PMID: 39704950 DOI: 10.1007/978-1-0716-4280-1_15.

Packing up the genome.

Kiss B, Kellermayer M Elife. 2023; 12.

PMID: 38095555 PMC: 10721213. DOI: 10.7554/eLife.94128.

References

Keller N, delToro D, Smith D . Single-Molecule Measurements of Motor-Driven Viral DNA Packaging in Bacteriophages Phi29, Lambda, and T4 with Optical Tweezers. Methods Mol Biol. 2018; 1805:393-422. DOI: 10.1007/978-1-4939-8556-2_20. View

Fuller D, Raymer D, Kottadiel V, Rao V, Smith D . Single phage T4 DNA packaging motors exhibit large force generation, high velocity, and dynamic variability. Proc Natl Acad Sci U S A. 2007; 104(43):16868-73. PMC: 2040459. DOI: 10.1073/pnas.0704008104. View

Sternberg N, Coulby J . Recognition and cleavage of the bacteriophage P1 packaging site (pac). I. Differential processing of the cleaved ends in vivo. J Mol Biol. 1987; 194(3):453-68. DOI: 10.1016/0022-2836(87)90674-7. View

Fuller D, Raymer D, Rickgauer J, Robertson R, Catalano C, Anderson D . Measurements of single DNA molecule packaging dynamics in bacteriophage lambda reveal high forces, high motor processivity, and capsid transformations. J Mol Biol. 2007; 373(5):1113-22. PMC: 3311920. DOI: 10.1016/j.jmb.2007.09.011. View

Sun S, Kondabagil K, Draper B, Alam T, Bowman V, Zhang Z . The structure of the phage T4 DNA packaging motor suggests a mechanism dependent on electrostatic forces. Cell. 2008; 135(7):1251-62. DOI: 10.1016/j.cell.2008.11.015. View

Migliori A, Keller N, Alam T, Mahalingam M, Rao V, Arya G . Evidence for an electrostatic mechanism of force generation by the bacteriophage T4 DNA packaging motor. Nat Commun. 2014; 5:4173. PMC: 4157569. DOI: 10.1038/ncomms5173. View

Keller N, delToro D, Grimes S, Jardine P, Smith D . Repulsive DNA-DNA interactions accelerate viral DNA packaging in phage Phi29. Phys Rev Lett. 2014; 112(24):248101. PMC: 5001848. DOI: 10.1103/PhysRevLett.112.248101. View

Kindt J, Tzlil S, Ben-Shaul A, Gelbart W . DNA packaging and ejection forces in bacteriophage. Proc Natl Acad Sci U S A. 2001; 98(24):13671-4. PMC: 61099. DOI: 10.1073/pnas.241486298. View

Kottadiel V, Rao V, Chemla Y . The dynamic pause-unpackaging state, an off-translocation recovery state of a DNA packaging motor from bacteriophage T4. Proc Natl Acad Sci U S A. 2012; 109(49):20000-5. PMC: 3523870. DOI: 10.1073/pnas.1209214109. View

10.

Harvey S, Petrov A, Devkota B, Boz M . Viral assembly: a molecular modeling perspective. Phys Chem Chem Phys. 2010; 11(45):10553-64. DOI: 10.1039/b912884k. View

11.

Berndsen Z, Keller N, Smith D . Continuous allosteric regulation of a viral packaging motor by a sensor that detects the density and conformation of packaged DNA. Biophys J. 2015; 108(2):315-24. PMC: 4302192. DOI: 10.1016/j.bpj.2014.11.3469. View

12.

Keller N, Grimes S, Jardine P, Smith D . Single DNA molecule jamming and history-dependent dynamics during motor-driven viral packaging. Nat Phys. 2016; 12(8):757-761. PMC: 4982518. DOI: 10.1038/nphys3740. View

13.

Burroughs A, Iyer L, Aravind L . Comparative genomics and evolutionary trajectories of viral ATP dependent DNA-packaging systems. Genome Dyn. 2008; 3:48-65. DOI: 10.1159/000107603. View

14.

Riemer S, Bloomfield V . Packaging of DNA in bacteriophage heads: some considerations on energetics. Biopolymers. 1978; 17(3):785-94. DOI: 10.1002/bip.1978.360170317. View

15.

Chemla Y, Aathavan K, Michaelis J, Grimes S, Jardine P, Anderson D . Mechanism of force generation of a viral DNA packaging motor. Cell. 2005; 122(5):683-92. DOI: 10.1016/j.cell.2005.06.024. View

16.

Purohit P, Inamdar M, Grayson P, Squires T, Kondev J, Phillips R . Forces during bacteriophage DNA packaging and ejection. Biophys J. 2004; 88(2):851-66. PMC: 1305160. DOI: 10.1529/biophysj.104.047134. View

17.

Leffers G, Rao V . Biochemical characterization of an ATPase activity associated with the large packaging subunit gp17 from bacteriophage T4. J Biol Chem. 2000; 275(47):37127-36. DOI: 10.1074/jbc.M003357200. View

18.

Kanamaru S, Kondabagil K, Rossmann M, Rao V . The functional domains of bacteriophage t4 terminase. J Biol Chem. 2004; 279(39):40795-801. DOI: 10.1074/jbc.M403647200. View

19.

Allemand J, Maier B, Smith D . Molecular motors for DNA translocation in prokaryotes. Curr Opin Biotechnol. 2012; 23(4):503-9. PMC: 3381886. DOI: 10.1016/j.copbio.2011.12.023. View

20.

Black L . Old, new, and widely true: The bacteriophage T4 DNA packaging mechanism. Virology. 2015; 479-480:650-6. PMC: 4424107. DOI: 10.1016/j.virol.2015.01.015. View