Grant Matthew A A, Saggioro Chiara, Ferrari Ulisse, Bassetti Bruno, Sclavi Bianca, Cosentino Lagomarsino Marco
BSS Group, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK.
BMC Syst Biol. 2011 Dec 21;5:201. doi: 10.1186/1752-0509-5-201.
In Escherichia coli, overlapping rounds of DNA replication allow the bacteria to double in faster times than the time required to copy the genome. The precise timing of initiation of DNA replication is determined by a regulatory circuit that depends on the binding of a critical number of ATP-bound DnaA proteins at the origin of replication, resulting in the melting of the DNA and the assembly of the replication complex. The synthesis of DnaA in the cell is controlled by a growth-rate dependent, negatively autoregulated gene found near the origin of replication. Both the regulatory and initiation activity of DnaA depend on its nucleotide bound state and its availability.
In order to investigate the contributions of the different regulatory processes to the timing of initiation of DNA replication at varying growth rates, we formulate a minimal quantitative model of the initiator circuit that includes the key ingredients known to regulate the activity of the DnaA protein. This model describes the average-cell oscillations in DnaA-ATP/DNA during the cell cycle, for varying growth rates. We evaluate the conditions under which this ratio attains the same threshold value at the time of initiation, independently of the growth rate.
We find that a quantitative description of replication initiation by DnaA must rely on the dependency of the basic parameters on growth rate, in order to account for the timing of initiation of DNA replication at different cell doubling times. We isolate two main possible scenarios for this, depending on the roles of DnaA autoregulation and DnaA ATP-hydrolysis regulatory process. One possibility is that the basal rate of regulatory inactivation by ATP hydrolysis must vary with growth rate. Alternatively, some parameters defining promoter activity need to be a function of the growth rate. In either case, the basal rate of gene expression needs to increase with the growth rate, in accordance with the known characteristics of the dnaA promoter. Furthermore, both inactivation and autorepression reduce the amplitude of the cell-cycle oscillations of DnaA-ATP/DNA.
在大肠杆菌中，多轮重叠的DNA复制使得细菌能够在比复制基因组所需时间更短的时间内实现数量翻倍。DNA复制起始的精确时间由一个调控回路决定，该回路依赖于关键数量的与ATP结合的DnaA蛋白在复制起点的结合，从而导致DNA解链并组装复制复合体。细胞中DnaA的合成由一个位于复制起点附近的、依赖生长速率且负向自调控的基因控制。DnaA的调控和起始活性均取决于其核苷酸结合状态及其可利用性。
为了研究不同调控过程对不同生长速率下DNA复制起始时间的贡献，我们构建了一个起始子回路的最小定量模型，该模型包含了已知调控DnaA蛋白活性的关键要素。该模型描述了在不同生长速率下，细胞周期中DnaA-ATP/DNA在平均细胞中的振荡情况。我们评估了该比率在起始时达到相同阈值的条件，而与生长速率无关。
我们发现，为了解释不同细胞倍增时间下DNA复制起始的时间，对DnaA介导的复制起始进行定量描述必须依赖于基本参数对生长速率的依赖性。我们为此分离出两种主要的可能情况，这取决于DnaA自调控和DnaA ATP水解调控过程的作用。一种可能性是，ATP水解导致的调控失活的基础速率必须随生长速率而变化。或者，一些定义启动子活性的参数需要是生长速率的函数。在任何一种情况下，基因表达的基础速率都需要根据dnaA启动子的已知特性随生长速率增加。此外，失活和自抑制都会降低DnaA-ATP/DNA细胞周期振荡的幅度。
