Attenuation to Control Gene Expression

Bacteria use a variety of strategies to regulate transcription elongation in response to changes in their environment. Several of these regulatory events are classified as transcription attenuation mechanisms, which involve regulated transcription termination to control expression of downstream genes. In most cases, two alternative RNA secondary structures, an antiterminator and an intrinsic terminator, share nucleotides in common such that their formation is mutually exclusive. Thus, the level of expression of the downstream genes depends on the frequency that the antiterminator forms in the nascent transcript. Transcription attenuation mechanisms in general are separated into two categories. The first category involves situations in which the action of a regulatory molecule promotes transcription termination, with the default situation being transcription readthrough. The second category involves situations in which the action of the regulatory molecule promotes transcription readthrough (antitermination), with the default situation being transcription termination. Transcription attenuation controls the expression of several amino acid biosynthetic and catabolic operons. These mechanisms are often controlled by the efficiency of leader peptide synthesis in Gram-negative bacteria, whereas Gram-positive organisms often use RNA binding proteins or tRNA molecules to determine whether the RNA will fold into the antiterminator or terminator structures. Several examples of transcription attenuation also exist in which an antisense RNA is responsible for controlling plasmid copy number. In addition, small metabolites participate in transcription attenuation mechanisms of a wide variety of bacterial genes by binding directly to the nascent transcript.