In addition to regulation of transcription initiation by activators and repressors, expression of many bacterial operons is controlled by regulation of transcriptional elongation in the promoter-proximal region. This mechanism of control was first discovered in studies of trp operon transcription in E. coli (see Figure 5-13). Transcription of the trp operon is repressed by the trp repressor when the concentration of tryptophan in the cytoplasm is high. But the low level of transcription initiation that still occurs is further controlled by a process called attenuation when the concentration of charged tRNA^Trp is sufficient to support a high rate of protein synthesis. The first 140 nt of the trp operon does not encode proteins required for tryptophan biosynthesis, but rather consists of a short peptide “leader sequence,” as diagrammed in Figure 9-7a. Region 1 of this leader sequence contains two successive Trp codons. Region 3 can base-pair with either region 2 or region 4. A ribosome follows closely behind the RNA polymerase, initiating translation of the leader peptide shortly after the 5′ end of the trp leader sequence emerges from the RNA polymerase. When the concentration of tRNA^Trp is sufficient to support a high rate of protein synthesis, the ribosome translates quickly through region 1 into region 2, blocking the ability of region 2 to base-pair with region 3 as it emerges from the surface of the transcribing RNA polymerase (Figure 9-7b, left). Instead, region 3 base-pairs with region 4 as soon as it emerges from the surface of the polymerase, forming a stem-loop (see Figure 5-9a) followed by several uracils, which is a signal for bacterial RNA polymerase to pause transcription and terminate. As a consequence, the remainder of the long trp operon is not transcribed, and the cell does not waste the energy required for tryptophan synthesis, or for the translation of the encoded proteins, when the concentration of tryptophan is high.

362

However, when the concentration of tRNA^Trp is not sufficient to support a high rate of protein synthesis, the ribosome stalls at the two successive Trp codons in region 1 (Figure 9-7b, right). As a consequence, region 2 base-pairs with region 3 as soon as it emerges from the transcribing RNA polymerase. This prevents region 3 from base-pairing with region 4, so the 3–4 hairpin does not form and does not cause RNA polymerase pausing or transcription termination. As a result, the proteins required for tryptophan synthesis are translated by ribosomes that initiate translation at the start codons for each of these proteins in the long polycistronic trp mRNA.

Attenuation of transcription elongation also occurs at some operons and single genes encoding enzymes involved in the biosynthesis of other amino acids and metabolites through the function of riboswitches. Riboswitches are sequences of RNA most commonly found in the 5′ untranslated region of bacterial mRNAs. They fold into complex tertiary structures called aptamers that bind small-molecule metabolites when those metabolites are present at sufficiently high concentrations. In some cases, this binding results in the formation of stem-loop structures that lead to early termination of transcription, as in the Bacillus subtilis xpt-pbuX operon, which encodes enzymes involved in purine synthesis (Figure 9-8). When the concentration of small-molecule metabolites is lower, the metabolites are not bound by the aptamers, and alternative RNA structures form that do not induce transcription termination, allowing transcription of genes encoding enzymes involved in the synthesis of the metabolites. As we will see below, although the mechanism in eukaryotes is different, regulation of promoter-proximal transcriptional pausing and termination has recently been discovered to occur frequently in the regulation of gene expression in multicellular organisms as well.