Regulation of the Escherichia coli secA gene is mediated by two distinct RNA structural conformations

Expression from the secA gene, encoding a key component of the general secr etory pathway of Escherichia coli, is influenced by the secretion status of the cell, autogenous translational repression, and translational coupling to the upstream gene, X. SecA binds to its mRNA in a region overlapping its ribosome binding site, thus competing with ribosomes that would initiate s ecA translation. Mapping of the geneX-secA mRNA secondary structure has dem onstrated that the RNA can adopt two distinct conformations in solution. Th e first conformation arises from the base-pairing of the secA Shine-Dalgarn o (SD) sequence with the geneX terminus. The second conformation, in which the secA SD sequence is no longer paired with the geneX terminus, contains a GC-rich stem upstream of the secA SD sequence. The presence of this GC-ri ch stem is supported by structure mapping of a mutant RNA containing a dele tion in the geneX terminus. The former structure appears to be involved in translational coupling by directly linking the geneX and secA sequences, wh ere geneX translation activates secA translational initiation through the u npairing and unmasking of the secA SD sequence. As indicated by SecA-RNA bi nding assays, the latter structure is probably involved in SecA binding and translational repression of the secA gene. The stabilizing effect of magne sium ions toward occlusion of the secA SD sequence supports the presence of RNA tertiary structure in this regulatory domain.