A transformational-grammar approach to the study of the regulation of gene expression

An important problem in biology is the lack of a set of common principles unifying biological knowledge. We propose generative grammar for constructing an integrative paradigm for the understanding of genome organization and the regulation of gene expression. Linguistic terms in molecular biology are defined. A genetic syntactic structure is defined as being equivalent to a sentence. The hypotheses for the grammar of genome structure are: (i) the "grammaticality" of the linguistic approach studies the "regulability" of genome structures; (ii) the "regulability" of genetic structures is independent from their specific biochemical meaning and (iii) the dynamics of regulation is implicit in the genome structure. A general structure is presented for the grammar; the application of phase-structure rules is justified by the existence of lexical categories. Transformational rules are utilized to represent loops of regulation. Negative inducible, positive repressible, positive inducible and negative repressible alternative mechanisms of regulation are represented, by four transformational rules, and the application of these rules is established by two principles. Finally, this approach is compared to other linguistic applications in molecular biology.