Hexameric molecular motors: P4 packaging ATPase unravels the mechanism

Abstract

Genome packaging into an empty capsid is an essential step in the assembly of many complex viruses. In double-stranded RNA (dsRNA) bacteriophages of the Cystoviridae family this step is performed by a hexameric helicase P4 which is one of the simplest packaging motors found in nature. Biochemical and structural studies of P4 proteins have led to a surprising finding that these proteins bear mechanistic and structural similarities to a variety of the pervasive RecA/F1-ATPase-like motors that are involved in diverse biological functions. This review describes the role of P4 proteins in assembly, transcription and replication of dsRNA bacteriophages as it has emerged over the past decade while focusing on the most recent structural studies. The P4 mechanism is compared with the models proposed for the related hexameric motors.

Compression of the DNA substrate by a viral packaging motor is supported by removal of intercalating dye during translocation

“…DNA structure | terminase inhibitors N ucleic acid translocation into an empty procapsid is a conserved capsid assembly mechanism found among diverse DNA and RNA viruses (1). High-resolution structures of all of the conserved motor components found among tailed dsDNA bacteriophages have been determined (2)(3)(4)(5).…”

RNA remodeling by hexameric RNA helicases

“…Transient openings of the Rho ring therefore provide the most likely means for entry of the RNA chain into the central channel during the early formation (and activation) of the enzyme-substrate complex. 41 A similar mechanism for RNA entry was also suggested for the ϕ8 P4 hexamer 15 from the detection of open ring states by fast amide hydrogen-deuterium exchanges at subunit interfaces during RNA loading. 42 The second major advantage of a ring-shaped architecture is its high potential for structural and functional modularity.…”

“…5 Preliminary experiments suggest that the ϕ8 P4 helicase does not benefit significantly from the presence of specific RNA packaging sequences (pac sites) 15,49 in the single-stranded loading region of the substrate (our unpublished observations). This is consistent with the previously envisioned separation of tasks in the viral capsid whereby specific recognition of the phage RNAs is provided by binding sites on the major core protein P1 while the hexameric P4 pore provides the mechanical work for packaging.…”

“…47,48 The P4 packaging motors of Pseudomonas phages, however, are pore-like structures by functional necessity and therefore adopt the classical ring-shaped architecture of other viral portals to package RNA genomes into the phage procapsids. 15 They associate with the procapsid major a high stability of the enzyme-substrate complex is not acquired by high affinity for NA which would compromise translocation (threading) capacity. Indeed, there shall be no need to compensate for the loose NA binding states that may arise from the continuous remodeling of the productive NA contacts during translocation since substrate release cannot occur unless the enzyme ring opens or dissociates.…”

“…2A), melting unwanted RNA secondary structures in the process (reviewed in ref. 15 for a detailed review of the structural organization of Pseudomonas phages and role of their P4 packaging motors).…”