Tryptophan Operon
Ashutosh Upadhye Ashutosh Upadhye
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 Published On Aug 27, 2021

The trp operon is an operon—a group of genes that is used, or transcribed, together—that codes for the components for production of tryptophan. The trp operon is present in many bacteria, but was first characterized in Escherichia coli. The operon is regulated so that, when tryptophan is present in the environment, the genes for tryptophan synthesis are not expressed. It was an important experimental system for learning about gene regulation, and is commonly used to teach gene regulation.

Trp operon contains five structural genes: trpE, trpD, trpC, trpB, and trpA, which encode enzymatic parts of the pathway. It also contains a repressive regulator gene called trpR. trpR has a promoter where RNA polymerase binds and synthesizes mRNA for a regulatory protein. The protein that is synthesized by trpR then binds to the operator which then causes the transcription to be blocked. In the trp operon, tryptophan binds to the repressor protein effectively blocking gene transcription. In this situation, repression is that of RNA polymerase transcribing the genes in the operon. Also unlike the lac operon, the trp operon contains a leader peptide and an attenuator sequence which allows for graded regulation.
It is an example of repressible negative regulation of gene expression. Within the operon's regulatory sequence, the operator is bound to the repressor protein in the presence of tryptophan (thereby preventing transcription) and is liberated in tryptophan's absence (thereby allowing transcription).
Trp operon contains five structural genes. Their roles are:

TrpE (P00895): Anthranilate synthase produces anthranilate.
TrpD (P00904): Cooperates with TrpE.
TrpC (P00909): Phosphoribosylanthranilate isomerase domain first turns N-(5-phospho-β-D-ribosyl)anthranilate into 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate. The Indole-3-glycerol-phosphate synthase on the same protein then turns the product into (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate.
TrpA (P0A877), TrpB (P0A879): two subunits of tryptophan synthetase. Combines TrpC's product with serine to produce tryptophan.
Repression
The operon operates by a negative repressible feedback mechanism. The repressor for the trp operon is produced upstream by the trpR gene, which is constitutively expressed at a low level. Synthesized trpR monomers associate into dimers. When tryptophan is present, these tryptophan repressor dimers bind to tryptophan, causing a change in the repressor conformation, allowing the repressor to bind to the operator. This prevents RNA polymerase from binding to and transcribing the operon, so tryptophan is not produced from its precursor. When tryptophan is not present, the repressor is in its inactive conformation and cannot bind the operator region, so transcription is not inhibited by the repressor.
Attenuation
Attenuation is a second mechanism of negative feedback in the trp operon. The repression system targets the intracellular trp concentration whereas the attenuation responds to the concentration of charged tRNAtrp.
Thus, the trpR repressor decreases gene expression by altering the initiation of transcription, while attenuation does so by altering the process of transcription that's already in progress.[2] While the TrpR repressor decreases transcription by a factor of 70, attenuation can further decrease it by a factor of 10, thus allowing accumulated repression of about 700-fold.
Attenuation is made possible by the fact that in prokaryotes (which have no nucleus), the ribosomes begin translating the mRNA while RNA polymerase is still transcribing the DNA sequence. This allows the process of translation to affect transcription of the operon directly.At the beginning of the transcribed genes of the trp operon is a sequence of at least 130 nucleotides termed the leader transcript.
This transcript includes four short sequences designated 1–4, each of which is partially complementary to the next one. Thus, three distinct secondary structures (hairpins) can form: 1–2, 2–3 or 3–4. The hybridization of sequences 1 and 2 to form the 1–2 structure is rare because the RNA polymerase waits for a ribosome to attach before continuing transcription past sequence 1, however if the 1–2 hairpin were to form it would prevent the formation of the 2–3 structure (but not 3–4). The formation of a hairpin loop between sequences 2–3 prevents the formation of hairpin loops between both 1–2 and 3–4. The 3–4 structure is a transcription termination sequence (abundant in G/C and immediately followed by several uracil residues), once it forms RNA polymerase will disassociate from the DNA and transcription of the structural genes of the operon can not occur (see below for a more detailed explanation). The functional importance of the 2nd hairpin for the transcriptional termination is illustrated by the reduced transcription termination frequency observed in experiments destabilizing the central G+C pairing of this hairpin.

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