Some ideas towards a grammatical model of the σ54 bacterial promoters

The integration of large amounts of information on the regulation of gene expression requires conceptual frameworks which should facilitate the discovery of general principles underlying different mechanisms of gene regulation. An exhaustive database of σ⁷⁰ and σ⁵⁴ promoters in E. Coli has supported the construction of a grammatical model of the σ⁷⁰ type of promoters. This grammar generates all and only those regulatory arrangements of the collection, as well as new ones which are consistent with the biological principles of the collection. In this paper, some ideas towards a unified model of the σ⁷⁰ and the σ⁵⁴ bacterial promoters are presented. This model should reflect the biological differences on the possible regulatory mechanisms of these collections. The σ⁵⁴ class represents an intermediate step between the 7⁰ promoters and those present in higher organisms. Based on the biology of these bacterial promoters a hypothesis is proposed which stipulates that in principle it is feasible to activate σ⁷⁰ promoters at a distance, an exclusive property of the σ⁵⁴ class shared with promoters from higher organisms. Assuming this hypothesis is correct, some a ideas supporting a unique “universal” grammar for the σ⁷⁰ and σ⁵⁴ promoters are presented