Collado-Vides J
Centro de Investigación sobre Fijación de Nitrógeno, UNAM, Morelos, Mexico.
Biochimie. 1996;78(5):351-63. doi: 10.1016/0300-9084(96)84767-5.
The organization and integration of large amounts of information on the regulation of gene expression requires new conceptual frameworks to facilitate the discovery of general principles underlying different mechanisms of gene regulation. I have developed a formalism based on generative grammar to explicitly describe pertinent regulatory properties of mechanisms of regulation. The formal proof that justifies the use of generative grammar has been made. We have collected and analyzed an exhaustive database of sigma 70 and sigma 54 promoters in E coli and Salmonella where there is sufficient knowledge on the regulation of these genes. This collection has supported the construction of a grammatical model of the sigma 70 type of promoters. The purpose of this paper is to present some ideas towards the construction of a unified grammar capable of describing regulatory arrays for the sigma 70 and the sigma 54 bacterial promoters. This model is not intended to simply generate the set of binding sites of regulators distributed in a linear array in the DNA. It should also reflect the biological differences on the regulatory mechanisms of these collections, as understood from the analysis that we have done on these collections (Gralla and Collado-Vides, 1996). Based on the biology of these two types of bacterial promoters, a hypothesis is proposed stipulating that in principle it is feasible to activate sigma 70 promoters at a distance, an exclusive property of the sigma 54 class shared with promoters of higher organisms. The model presented assumes this hypothesis is correct. The ideas presented support the beginning of a unique 'universal' grammar for the sigma 70 and sigma 54 promoters. The specification of certain parameters would derive the respective specific sigma 70 and sigma 54 grammatical models.
组织和整合大量关于基因表达调控的信息需要新的概念框架，以促进发现基因调控不同机制背后的一般原则。我已经开发了一种基于生成语法的形式体系，以明确描述调控机制的相关调控特性。已经给出了证明使用生成语法合理性的形式证明。我们收集并分析了大肠杆菌和沙门氏菌中σ70和σ54启动子的详尽数据库，其中对这些基因的调控有足够的了解。这一收集工作支持了σ70型启动子语法模型的构建。本文的目的是提出一些关于构建统一语法的想法，该语法能够描述细菌σ70和σ54启动子的调控阵列。该模型并非旨在简单地生成分布在DNA线性阵列中的调控因子结合位点集。它还应反映这些集合在调控机制上的生物学差异，正如我们对这些集合所做分析（格拉拉和科利亚多 - 维德斯，1996年）所理解的那样。基于这两种细菌启动子的生物学特性，提出了一个假设，即原则上远距离激活σ70启动子是可行的，这是σ54类启动子与高等生物启动子共有的排他性特性。所提出的模型假定这个假设是正确的。所提出的想法支持了为σ70和σ54启动子构建独特“通用”语法的开端。某些参数的设定将推导出各自特定的σ70和σ54语法模型。
