Initiation of chromosome replication in bacteria: analysis of an inhibitor control model

Abstract

This article contains an analysis of a version of the well-known inhibitor-dilution model for the control of initiation of chromosome replication in bacteria. According to this model, an unstable inhibitor interacts with an initiation primer in a hit-and-destroy fashion to prevent successful initiation; both constituents are presumed to be RNA species that are synthesized constitutively. The model further postulates that the inhibitor interacts cooperatively with the primer, that the inhibitor gene is removed some distance from the origin of replication, and that an eclipse period exists during which the chromosome origin is not able to reinitiate. This unstable-inhibitor version is characterized by four parameters: the inhibitor half-life, the cooperativity index, the location of the inhibitor gene, and the eclipse period; computer simulations are used to study the effect of each of these on the DNA and interdivision time distributions in exponentially growing steady-state cultures. In neither case was any combination of parameter values found that could provide even moderately satisfactory agreement between the simulation results and experimental data. From the examples furnished and the associated discussion, it appears that there are none-that no combination of parameter values exists that can reasonably be expected to produce a significantly better fit than those tested. We conclude that the model in its present form cannot be a valid description of chromosome replication control in bacteria. It is pointed out that this does not necessarily apply to negative initiation control models in general, or even to all inhibitor-dilution systems, merely to the particular ColEl-like mechanism considered here. Nevertheless, recent experimental results, which can only be understood in terms of a very high degree of initiation synchrony within individual cells, offer strong evidence against stochastic models of this kind for the control of chromosome replication.At any fixed temperature, bacteria in steady-state exponential growth have different average generation times, depending on the composition of the culture medium. Since the duration of chromosome replication and the interval between its termination and the subsequent cell division are both essentially constant, the major contribution to this difference must come from the timing of the initiation event itself (18).The initiation of chromosome replication is thus a critical stage in the cell cycle of bacteria, and despite the considerable experimental data available regarding replication at different growth rates, the precise factors responsible for its control remain largely unknown.Originally it was thought that initiation occurs when a fixed ratio is attained between cell mass and the number of origins of replication, independent of the growth rate (5; In a previous article (16), we presented a detailed quantitative analysis of the initiation structure model originally put forward by Sompayrac and Maal0e (29) and were able to delineate the characteristics that ...

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“…For example, Margalit and Grover combined evidence from experiments and simulations to refute this model. They found that this model cannot reproduce the generation time distributions obtained from experimental data [354– 356].…”

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“…This model inspired formulation of new models for how initiation in E. coli could be controlled. The inhibitor dilution model has later been formally rejected by Margalit and Grover ( 1987 ).…”

New evidence of an old problem: The coupling of genome replication to cell growth in bacteria

“…Yet its structural gene is located near OriC and self controls its expression by the mechanism of autorepression [5]. Second, a sto chastic variant of the "repressor" model, proposed by Margalit and Grover [21] almost 20 years later, poorly presented the experimental data on the distribution of DNA mass in fast dividing E. coli cells, for which a high level of synchrony of DNA replication acts is typ ical. In opposition to that, the "initiator" idea was developed, which was connected with the discovery of DnaA protein as the main regulator of DNA replica tion initiation.…”