Control of mini-R1 plasmid replication: a computer simulation

A molecular model for the control of plasmid R1 replication has been proposed by Nordström, Molin and Light (Plasmid 12, 71-90, 1984), involving three genes: repA, copA, copB. RepA codes for a polypeptide whose synthesis is required for initiation; replication is controlled by regulating this synthesis. CopA encodes a small, unstable, untranslated RNA molecule that inhibits translation of the repA message whereas copB produces a protein that inhibits transcription from the repA promoter. We have recast this model into precise mathematical terms and tested it by computer simulation of a synchronous culture in steady-state balanced growth, composed of individual Escherichia coli cells harboring the small, unstable derivative, mini-R1. All single-cell steady-state distributions obtained are independent of initial conditions, and the average values of various plasmid-related variables are similar to those measured experimentally. The relationship between the number of replication events per cell and the copy number at birth, as predicted by the model, mitigates against a sensitive correction mechanism for cells born with other than average copy number and is much closer quantitatively to a nonresponse system, although there is a weak dependence on copy number. The effect of the convergent transcription initiated at the repA and copB promoters on the expression of the copA gene is found to contribute little to the stability of mini-R1 replicons under steady-state growth conditions or to their potential for survival following infection. In fact, the role of the entire CopB control loop is shown to be quite minor, both in steady state and after infection. It is pointed out that genetic manipulations are far more easily performed in silico than in vivo but that results of the kind presented here are very often possible only when simulating individual cells.