Towards a unified grammatical model of sigma 70 and sigma 54 bacterial promoters

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.