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One of the secondary structures contains one hairpin produced by the base pairing of regions 1 and 2 and another hairpin produced by the base pairing of regions 3 and 4. Notice that a string of uracil nucleotides follows the 3+4 hairpin. Not coincidentally, the structure of a bacterial intrinsic terminator (Chapter 13) includes a hairpin followed by a string of uracil nucleotides; this secondary structure in the 5' UTR of the trp operon is indeed a terminator and is called an attenuator. When cellular levels of tryptophan are high, regions 3 and 4 of the 5' UTR base pair, producing the attenuator structure; this base pairing causes transcription to be terminated before the trp structural genes can be transcribed.

The alternative secondary structure of the 5' UTR is produced by the base pairing of regions 2 and 3 (see Figure 16.15b). This base pairing also produces a hairpin, but this hairpin is not followed by a string of uracil nucleotides; so this structure does not function as a terminator. When cellular levels of tryptophan are low, regions 2 and 3 base pair, and transcription of the trp structural genes is not terminated. RNA polymerase continues past the 5' UTR into the coding section of the structural genes, and the enzymes that synthesize tryptophan are produced. Because it prevents the termination of transcription, the 2+3 structure is called an antiterminator.

To summarize, the 5' UTR of the trp operon can fold into one of two structures. When tryptophan is high, the 3+ 4 structure forms, transcription is terminated within the 5' UTR, and no additional tryptophan is synthesized. When tryptophan is low, the 2+ 3 structure forms, transcription continues through the structural genes, and tryptophan is synthesized. The critical question, then, is, Why does the 3+ 4 structure arise when tryptophan is high and the 2+ 3 structure when tryptophan is low?

To answer this question, we must take a closer look at the nucleotide sequence of the 5' UTR. At the 5' end, upstream of region 1, is a ribosome-binding site. Region 1 actually encodes a small protein (see Figure 16.15b). Within the coding sequence for this protein are two UGG codons, which specify the amino acid tryptophan; so tryp-tophan is required for the translation of this 5' UTR sequence. The protein encoded by the 5' UTR has not been isolated and is presumed to be unstable; its only apparent function is to control attenuation. Although it was stated in Chapter 14 that a 5' UTR is not translated into a protein, the 5' UTR of operons subject to attenuation are exceptions to this rule.

The formation of hairpins in the 5' UTR of the trp operon is controlled by the interplay of transcription and translation that takes place near the 5' end of the mRNA. Recall that, in prokaryotic cells, transcription and translation are coupled: while transcription is taking place at the 3' end of the mRNA, translation is initiated at the 5' end. The precise timing and interaction of these two processes in the 5' UTR determine whether attenuation occurs.

Transcription when tryptophan levels are high Let's first consider what happens when intracellular levels of tryp-tophan are high. RNA polymerase begins transcribing the DNA, producing region 1 of the 5' UTR (< Figure 16.16a). Following RNA polymerase closely, a ribosome binds to the 5' UTR (at the Shine-Dalgarno sequence, see Chapter 14) and begins to translate the coding region. Meanwhile, RNA polymerase is transcribing region 2 (Figure 16.16b). Region 2 is complementary to region 1 but, because the ribosome is translating region 1, the nucleotides in regions 1 and 2 cannot base pair. As RNA polymerase begins to transcribe region 3, the ribosome is continuing to translate region 1 (Figure 16.16c). When the ribosome reaches the two UGG tryptophan codons, it doesn't slow or stall, because tryptophan is abundant and tRNAs charged with tryptophan are readily available. This point is critical to note: because tryptophan is abundant, translation can keep up with transcription.

As it moves past region 1 to the stop codon, the ribosome partly covers region 2; (Figure 16.16d); meanwhile, RNA polymerase completes the transcription of region 3. Although regions 2 and 3 are complementary, region 2 is partly covered by the ribosome; so it can't base pair with 3.

RNA polymerase continues to move along the DNA, eventually transcribing regions 4 of the 5' UTR. Region 4 is complementary to region 3, and, because region 3 cannot base pair with region 2, it pairs with region 4. The pairing of regions 3 and 4 (see Figure 16.16d) produces the attenuator—a hairpin followed by a string of uracil nucleotides— and transcription terminates just beyond region 4. The structural genes are not transcribed, no tryptophan-producing enzymes are translated, and no additional tryp-tophan is synthesized.

Transcription when tryptophan levels are low What happens when tryptophan levels are low? Once again, RNA polymerase begins transcribing region 1 of the 5' UTR (< Figure 16.16e), and the ribosome binds to the 5' end of the 5' UTR and begins to translate region 1 while RNA poly-merase continues transcribing region 2 (Figure 16.16f). When the ribosome reaches the UGG tryptophan codons, it stalls (Figure 16.16g) because the level of tryptophan is low, and tRNAs charged with tryptophan are scarce or even unavailable. The ribosome sits at the tryptophan codons, awaiting the arrival of a tRNA charged with tryptophan. Stalling of the ribosome does not, however, hinder transcription; RNA polymerase continues to move along the DNA, and transcription gets ahead of translation.

Because the ribosome is stalled at the tryptophan codons in region 1, region 2 is not covered by the ribosome when region 3 has been transcribed. Therefore, nucleotides in region 2 and region 3 base pair, forming the 2+ 3 hairpin (< Figure 16.16h). This hairpin does not cause termination, and so transcription continues. Because region 3 is already paired with region 2, the 3 + 4 hairpin (the attenuator)

When tryptophan is high

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