title: Testing a proposed paradigm shift in analysis of phage DNA packaging.
abstract: We argue that a paradigm shift is needed in the analysis of phage DNA packaging. We then test a prediction of the following paradigm shift-engendering hypothesis. The motor of phage DNA packaging has two cycles: (1) the well-known packaging ATPase-driven (type 1) cycle and (2) a proposed back-up, shell expansion/contraction-driven (type 2) cycle that reverses type 1 cycle stalls by expelling accidentally packaged non-DNA molecules. We test the prediction that increasing the cellular concentration of all macromolecules will cause packaging-active capsids to divert to states of hyper-expansion and contraction. We use a directed evolution-derived, 3-site phage T3 mutant, adapted to propagation in concentrated bacterial cytoplasm. We find this prediction correct while discovering novel T3 capsids previously obscure.
authors.affiliation: Department of Biochemistry, The University of Texas Health Science Center , San Antonio, TX, USA.
authors.forename: Philip
authors.initials: P
authors.lastname: Serwer
authors.affiliation: Department of Biochemistry, The University of Texas Health Science Center , San Antonio, TX, USA.
authors.forename: Elena T
authors.initials: ET
authors.lastname: Wright
keywords: bacteriophage assembly; capsid dynamics; electron microscopy; permeability-based fractionation; ultracentrifugation