Transcription attenuation associated with bacterial repetitive extragenic BIME elements

Transcription attenuation comprises several processes that affect transcrip t elongation and transcription termination, and has an important role in re gulating gene expression. In most cases, transcription attenuation is used as a regulatory mechanism that allows the cell to adjust protein synthesis levels in response to a specific signal. Here, by using a tRNA gene as a tr anscriptional reporter, we characterize a new type of transcription attenua tion mechanism in Escherichia coli that involves bacterial interspersed mos aic elements (BIMEs), the main family of repetitive extragenic elements. Th e transcription termination factor Rho is required for attenuation in assoc iation with BIMEs, thus revealing a new role for Rho as a BIMEs-dependent g lobal regulator of gene expression. By mutational analyses, we identified n ucleotide determinants of BIMEs that are required for attenuation and showe d that this process relies on a sequence-specific mechanism. Our data are c onsistent with a model in which BIMEs provoke a pause in RNA polymerase mov ement and Rho acts ultimately to terminate transcription. BIME-dependent tr anscription attenuation may be used as a means to differentially regulate e xpression of adjacent genes belonging to a single operon. BIMEs are dispers ed in more than 230 operons such that attenuation can simultaneously affect expression of a large number of genes encoding unrelated proteins. This at tenuation phenomenon, together with the known ability of BIMEs to stabilize upstream mRNA, reveals how dispersion of these abundant repetitive element s may affect gene regulation at the genome level. (C) 2001 Academic Press.