The modulation of the rate of transcription initiation is the most common mechanism of gene regulation. However, other stages of transcription also can be targets for regulation. In addition, the process of translation provides other points of intervention for regulating the level of a protein produced in a cell. In Chapter 29, we considered riboswitches that control transcription termination (Section 29.1). Other riboswitches control gene expression by other mechanisms such as the formation of structures that inhibit translation. Additional mechanisms for posttranscriptional gene regulation have been discovered, one of which will be described here.

A means for regulating transcription in bacteria was discovered by Charles Yanofsky and his colleagues as a result of their studies of the tryptophan operon. This operon encodes five enzymes that convert chorismate into tryptophan. Analysis of the 5′ end of trp mRNA revealed the presence of a leader sequence of 162 nucleotides before the initiation codon of the first enzyme. The next striking observation was that bacteria produced a transcript consisting of only the first 130 nucleotides when the tryptophan level was high, but they produced a 7000-nucleotide trp mRNA, including the entire leader sequence, when tryptophan was scarce. Thus, when tryptophan is plentiful and the biosynthetic enzymes are not needed, transcription is abruptly broken off before any mRNA coding for the enzymes is produced. The site of termination is called the attenuator, and this mode of regulation is called attenuation.

Attenuation depends on features at the 5′ end of the mRNA product (Figure 31.20). The first part of the leader sequence encodes a 14-amino-acid leader peptide. Following the open reading frame for the peptide is the attenuator, a region of RNA that is capable of forming several alternative structures. Recall that transcription and translation are tightly coupled in bacteria. Thus, the translation of the trp mRNA begins soon after the ribosome-binding site has been synthesized.

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How does the level of tryptophan alter transcription of the trp operon? An important clue was the finding that the 14-amino-acid leader peptide includes two adjacent tryptophan residues. A ribosome is able to translate the leader region of the mRNA product only in the presence of adequate concentrations of tryptophan. When enough tryptophan is present, a stem-loop structure forms in the attenuator region, which leads to the release of RNA polymerase from the DNA (Figure 31.21). However, when tryptophan is scarce, transcription is terminated less frequently. Little tryptophanyl-tRNA is present, and so the ribosome stalls at the tandem UGG codons encoding tryptophan. This delay leaves the adjacent region of the mRNA exposed as transcription continues. An alternative RNA structure that does not function as a terminator is formed, and transcription continues into and through the coding regions for the enzymes. Thus, attenuation provides an elegant means of sensing the supply of tryptophan required for protein synthesis.

Several other operons for the biosynthesis of amino acids in E. coli also are regulated by attenuator sites. The leader peptide of each contains an abundance of the amino acid residues of the type synthesized by the operon (Figure 31.22). For example, the leader peptide for the phenylalanine operon includes 7 phenylalanine residues among 15 residues. The threonine operon encodes enzymes required for the synthesis of both threonine and isoleucine; the leader peptide contains 8 threonine and 4 isoleucine residues in a 16-residue sequence. The leader peptide for the histidine operon includes 7 histidine residues in a row. In each case, low levels of the corresponding charged tRNA cause the ribosome to stall, trapping the nascent mRNA in a state that can form a structure that allows RNA polymerase to read through the attenuator site. Evolution has apparently converged on this strategy repeatedly as a mechanism for controlling amino acid biosynthesis.

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The examples of prokaryotic gene regulation that we have been describing come from bacteria, as opposed to archaea. The transcriptional apparatus present in archaea shares many features with that found in eukaryotes. This commonality is frequently interpreted to suggest that eukaryotes evolved after a cell fusion event in which a bacterial cell was engulfed by an archaeal cell. Nonetheless, the key principles of gene regulation such as the occurrence of operons and the roles of DNA-binding proteins in directly blocking or stimulating RNA polymerase are the same in bacteria and archaea, perhaps because of similar genome sizes. As we shall see in the next chapter, eukaryotic cells with larger genomes and, often, many distinct cell types, utilize quite different strategies.