The proposed mechanism of how this mRNA secondary structure and the trp leader peptide could regulate transcription of the trp biosynthetic enzymes includes the following.
*RNAP initiates transcription of the trp promoter.
*RNAP pauses at about nucleotide 90 at a secondary structure (?the first one shown above?).
*Ribosomes engage this nascent mRNA and initiate translation of the leader peptide.
**RNAP is then "released" from its pause and continues transcription.
*When RNAP reaches the region of the potential terminator, whether it continues or not is dependent on the position of the ribosome "trailing behind".
**If the ribosome stalls at the tandem Trp codons, waiting for the appropriate tRNA, region 1 is sequestered within the ribosome and thus cannot base pair with region 2. This means that region 2 and 3 become based paired before region 4 can be transcribed. This forces region 4 when it is made to be single stranded, preventing the formation of the region 3/4 terminator structure. Transcription will then continue.
**If the ribosome translates the leader peptide with no hesitation, it then covers a portion of region 2 preventing it from base pairing with region 3. Then when region 4 is transcribed, it forms a stem and loop with region 3 and transcription is terminated, generating a ca. 140 base transcript.
*This mechanism of control measures the amount of available, charged Trp-tRNA.
The location of ribosomes determines which alternate secondary structures form.