Question

One way that tryptophan metabolism in prokaryotes is regulated is “attenuation”. Describe the process of attenuation. Could this process also be found in eukaryotes? Explain.

Answer 1

Attenuation is a mechnaism of control in some bacterial operons which results in premature termination of transcription and is based on the fact that, in bacteria, transcription and translation proceed side by side. Attenuation involves a stop signal that is attenuator, located in the DNA segment that corresponds to the leader sequence of mRNA.
During attenuation, the ribosome becomes delayed in the attenuator region in the mRNA leader. Depend on the metabolic conditions, the attenuator may be stops transcription at that point or allows read-through to the structural gene part of the mRNA and synthesis of the appropriate protein.

Classes of attenuators
Attenuators may be differentiate on basis of changes in RNA structure.

Small-molecule-mediated attenuation {riboswitches}
small molecule mediated attenuation bind molecules such as amino acids, nucleotides, sugars, vitamins, metal ions and other small ligands ; which cause a conformational change in the mRNA. Most of these attenuators are inhibitory and are employed by genes fo transporters ; whose expression is inversely related to the concentration of their corresponding metabolites. Example- Cobalamine biosynthesis, lysin biosynthesis, glycine biosynthesis, etc

T-boxes
These elements are bound by specific uncharged tRNAs and modulate the expression of corresponding aminoacyl-tRNA synthetase operons. incresed levels of non charged tRNA promote the anti-terminator sequence leading to increased concentrations of charged tRNA. These are evaluated by some to be a different family of riboswitches. but are significantly more confusing than the last class of attenuators.

Protein-mediated attenuation
Protein-RNA interactions may stabilize or conserve the formation of an anti-terminator structure.

Ribosome-mediated attenuation
In this phenomenon RNA polymerase is dependent on ribosome activity; if the ribosome pauses due to insufficient charged tRNA then the anti-terminator structure is favoured. The canonical attenuator example of the trp operon uses this mechanism in E. coli.

Mechanism in the trp operon

As follows:-

High level of tryptophan Stem loop transcriptlon complete leader peptide RNA pol ribosome terminatlon signal 4 3 2 mRNA UUUU 3 Trp codons trpL DNA Low level of tryptophan ribosome stalls Alternate incomplete leader peptide stem loop: transcriptlon continues 2 3 RNA pol trp regulated genes 5' Trp codons trpL DNA

• RNAP initiates transcription of the trp promoter.
• RNAP stops at about nucleotide 90 at a secondary structure.
• 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 results that region 2 and 3 become based paired before region 4 can be transcribed. This evaluates 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.

Attenuation in eukaryotes  

Research conducted on microRNA processing showed an evidence of attenuation process in Eukaryotes. After co-transcriptional endonucleolitical cleavage by Drosha 5'->3' exonuclease XRN2 may terminate further transcription by torpedo mechanism.