SpoIIIE pauses when two consecutive subunits are bound to ATPγS.
However, the data shown in this study does not eliminate that five consecutive subunits of SpoIIIE interact with the DNA and step size is one bp.
In Rho and E1, there are 5 consecutive subunits contacting the DNA and the step size is one bp whereas the proposed model of SpoIIIE has two consecutive subunits interacting with DNA.
For example, n=1 (green shaded region) corresponds to a sequentially coordinated ring that pauses whenever a single subunit is bound to ATPγS; n=2 (blue shaded region) corresponds to a sequentially coordinated ring that pauses when two consecutive subunits are both bound to ATPγS, and so on.
We disfavor models where SpoIIIE subunit simultaneously contact more than two consecutive phosphate groups on the DNA backbone, and models where three or more consecutive subunits contact the DNA backbone because such models would require large motor/DNA distortions.
We note that the phage φ12 P4 hexameric pump, which belongs to the RecA-family, also seems to use an escort mechanism for ssRNA translocation into the capsid, although in this case it appears that three consecutive nucleotide-bound subunits contact RNA and cooperate in catalysis (Mancini et al, 2004; Kainov et al, 2008).
To rationalize the results of the MeP experiments, we propose a minimal translocation model in which SpoIIIE subunits fire sequentially around the ring, each subunit translocates 2 bp of DNA per power-stroke, at least two consecutive ATPase subunits contact the backbone of one DNA strand, and each subunit contacts two consecutive backbone phosphates.
In other words, analysis of the pause density indicates that the motor can operate processively with non-consecutive inactive subunits but not with two or more consecutive subunits.
In this model, two consecutive SpoIIIE subunits each contact two adjacent phosphates, and DNA is translocated in 2-bp steps.
Initially we did not consider a E1/Rho-like translocation mechanism as a potential model for SpoIIIE operation because this mechanism requires five consecutive motor subunits to contact five consecutive phosphate groups on the nucleic acid backbone.
