Gene expression regulation in bacteria allows the organism to adapt quickly to environmental changes. A fundamental control system governs the production of essential building blocks, such as the amino acid tryptophan. The cell employs the Tryptophan Repressor protein (TrpR) to manage this synthesis. TrpR ensures that the necessary enzymes are only produced when tryptophan is scarce, conserving the cell’s energy and resources.
The trp Operon and the TrpR Protein
Bacteria utilize an operon to coordinate the expression of genes involved in a single metabolic pathway. The trp operon in Escherichia coli is a cluster of five structural genes (trpE, trpD, trpc, trpB, and trpA) whose protein products are the enzymes required to synthesize tryptophan. These genes are transcribed together as a single messenger RNA molecule, allowing their production to be controlled simultaneously.
Upstream of these structural genes are regulatory DNA sequences, including the promoter, which is the binding site for the enzyme RNA polymerase that initiates transcription. Immediately following the promoter is the operator region, which serves as the recognition site for the TrpR protein. The default state of the trp operon is “on,” meaning that when tryptophan is absent, RNA polymerase can freely bind to the promoter and begin transcribing the genes.
The TrpR protein, encoded by a separate gene (trpR), is always present inside the cell. It exists naturally as an inactive homodimer, a protein made of two identical subunits. In this inactive state, TrpR has a low affinity for the operator DNA sequence and cannot bind effectively, allowing the cell to continue producing tryptophan.
Tryptophan as the Corepressor Signal
The regulatory mechanism hinges on the intracellular concentration of tryptophan. When the cell has produced or absorbed sufficient tryptophan, the excess acts as a specific signaling molecule. This negative feedback means the end product controls the activity of the pathway’s beginning.
Tryptophan performs this signaling role by acting as a corepressor, a molecule required to activate a repressor protein. It is the molecular trigger that transforms the inactive TrpR protein into its active, DNA-binding form. High levels of free tryptophan signal to TrpR that the synthesis pathway should be shut down to conserve cellular resources.
How TrpR Changes Shape to Bind DNA
The core of the repression mechanism is the physical change that occurs when tryptophan molecules meet the TrpR protein. The inactive TrpR homodimer must bind two molecules of L-tryptophan, one for each subunit, to become fully activated. This binding occurs at specific sites on the repressor protein distant from its DNA-binding region.
The binding of the corepressor causes a precise structural reorganization of the protein, known as an allosteric change. In its inactive form (the apo-repressor), the DNA-binding domains are not correctly spaced to fit the operator DNA geometry. The allosteric change alters the protein’s three-dimensional shape, specifically repositioning the two DNA-binding domains, which consist of a helix-turn-helix motif on each subunit.
This newly shaped, active complex (the holo-repressor) has a structure where the helix-turn-helix motifs fit snugly into two consecutive major grooves of the operator DNA sequence. The presence of tryptophan stabilizes this active conformation, increasing the protein’s affinity for the operator DNA by a factor of thousands. Without the corepressor to lock the protein into this precise shape, TrpR cannot bind the operator DNA with high affinity.
The Result of Repression
Once the activated TrpR-tryptophan complex binds tightly to the operator region, the final stage of repression is achieved. The operator sequence is strategically located so that the bound repressor physically overlaps with the promoter region. This physical obstruction prevents RNA polymerase from accessing the promoter and initiating the transcription of the structural genes.
By blocking RNA polymerase, the cell turns off the synthesis of tryptophan enzymes. This halt in production allows the bacterium to conserve energy and metabolic precursors when the amino acid is abundant. When cellular tryptophan levels drop, the corepressor molecules dissociate from TrpR, causing the repressor to revert to its inactive shape and release the operator, switching the operon back on.