Collado-Vides J
Department of Biology, Massachusetts Institute of Technology, Cambridge 02139.
J Theor Biol. 1991 Feb 7;148(3):401-29. doi: 10.1016/s0022-5193(05)80245-0.
The experimental study of the molecular mechanisms involved in the regulation of operons and other units of genetic information (UGIs) has not been accompanied by a parallel effort in integrative approaches. Following a recently obtained mathematical justification in the search of a grammatical theory of regulation, in this paper it is shown that a syntactic representation of prokaryotic simple UGIs can help the search for general rules governing their organization and regulation. Molecular categories like promoter, operator, structural gene, etc, are the elements for this level of analysis. Based on diverse types of evidence available in the literature, a principle which establishes a strictly successive representation of UGIs regulated at the initiation of transcription is derived. This linear array of categories is not enough for proposing general rules, which can be obtained by identifying groups of these categories as clusters or syntactic categories. It is shown that the notion of syntactic categories is implicitly used in the classical definition of an operon. Based on a hierarchy of biological restrictions for the construction of UGIs, a grammatical principle that defines a hierarchical relation among activator regions, promoters and operators is proposed. These proposals are integrated in a grammar that accounts for simple positively and negatively regulated UGIs.
