Model of gene expression regulation in bacteria via formation of RNA secondary structures

A model was proposed for the classical attenuating mRNA regulation of gene expression via transcription termination. The model is based on the concept of secondary structure macrostates in the RNA regulatory region between the ribosome and RNA polymerase, utilizes resonant equations for estimating the deceleration of RNA polymerase by a set of hairpins located in this RNA region, and takes into account views on the initiation and elongation of transcription and translation. Special attention was paid to selecting the model parameters. To test the model, computations were performed to estimate, in particular, the probability of translation termination as dependent on the charged tRNA concentration and the amino acid concentration for several regulatory regions of the bacterial genome (as exemplified by trpE of Streptomyces spp., Bradyrhizobium japonicum, and Escherichia coli). Analysis was performed with different values of three parameters isolated as major ones. The resulting dependences agreed with the available experimental data, including those characterizing an enzymatic activity as dependent on the amino acid concentration in a culture (e.g., the anthranylate synthase activity as dependent on the tryptophan concentration in S. venezuelae). The following possible application was proposed for the model. Attenuating regulation is usually predicted on the basis of multiple sequence alignment, which requires several sequences. With the model, an individual sequence can be analyzed with proper parameters to generate a concentration-enzymatic activity curve. The curve characteristic of attenuation or its absence provides an additional argument for the presence or absence of attenuation.