trp
Operon Regulation
The gene products of the lactose operon (see here) are not needed unless lactose is also present to be consumed. A different situation is encountered with genes whose products catalyze biosynthesis. Because biosynthesis consumes energy, it is to the cell's advantage to use the preformed product (i.e., an amino acid), if it is available. Therefore, the regulatory goal is to repress gene activity, by turning off the synthesis of enzymes in the pathway when the end product is available.
trp Operon - The trp operon consists of five adjacent structural genes whose transcription is controlled from a common promoter - operator regulatory region (Figure 26.33). Regulation of the E. coli trp operon, which controls the five reactions from chorismic acid to tryptophan (see Figure 21.14), demonstrates the following two ways of accomplishing this shutdown:
1. A repressor design in which binding of a small-molecule ligand activates the repressor, rather than inactivating it, and
2. Early termination of transcription by attenuation.
At low tryptophan concentration the repressor-operator interaction is the principal regulatory mechanism, whereas the effects of attenuation are more significant at moderate to high tryptophan levels.
trp Repressor
- The trp repressor, a 58-kilodalton protein encoded by
the nonadjacent trpR gene, binds tryptophan. The trp
repressor-tryptophan complex binds to the trp operator and
blocks transcription. When intracellular tryptophan levels decrease,
the ligand-protein complex dissociates and the free trp repressor
leaves the operator, so that transcription is activated. The crystal
structure of the trp repressor - DNA complex shows a helix-turn-helix
motif (Figure 28.23),
comparable to that seen with the 
cI,
Cro, and lac
repressors.
Attenuation - Attenuation is the early termination of trp operon transcription (131 nucleotides from the 5' end of the trpL sequence) under conditions of tryptophan abundance (Figure 26.33). Four oligonucleotide sequences in the trp leader region are capable of base-pairing to form stem-loop structures in the RNA transcript (Figure 26.35). In the most stable conformation (Figure 26.36a) (when tryptophan levels are high), region 1 pairs with 2, and region 3 pairs with 4, to give two stem - loops. The 3-4 structure, being followed by eight U's, is an efficient transcription terminator, because it resembles the factor-independent terminator structure shown in Figure 26.15. When this happens, the structural genes are not transcribed, so tryptophan is not synthesized.
Low tryptophan levels - When tryptophan levels are low (Figure 26.36a), cells need to turn on the trp operon. In this case, formation of the 3-4 stem-loop is inhibited, and termination does not occur at the attenuation site. Region 1 contains two tryptophan codons (see Figure 26.35). In prokaryotes, translation is coupled to transcription, so a ribosome can begin translating a message from its 5' end while the message is still being synthesized at its 3' end. When tryptophan levels are low, the ribosome stalls when it reaches the two tryptophan codons, because there is insufficient tryptophanyl-tRNA to translate them. The bulky ribosome on the mRNA prevents region 1 from base-pairing with 2, leaving region 2 free to base-pair with 3. Because region 3 is unavailable to base-pair with 4, the 3-4 stem-loop transcriptional terminator cannot form, and the entire message is synthesized. Conversely, when tryptophan is abundant (Figure 26.36c), the ribosome does not stall, thereby occluding region 2 and allowing the 3 - 4 stem - loop structure to form, which leads to transcription termination on the 3' side of 3 - 4.
Other Systems - Other attenuation-controlled operons of "stalling sequences" include operons for synthesis of leucine, with four adjacent leucine codons in the leader sequence, and of histidine, with seven. In Bacillus subtilis, synthesis of tyrosyl-tRNA synthetase is activated by an antitermination mechanism that allows transcription to proceed past a potential termination site in a leader region. By contrast, termination proceeds efficiently when most of the appropriate tRNA is charged with tyrosine, and there is no need to synthesize more of the aminoacyl-tRNA synthetase (Figure 26.37).
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