Lecture 7: Transcription and Translation

Question 1

What is the stringent response?

Answer 1

The stringent response is a stress response to amino-acid starvation.
• Translation and transcription are strongly linked.
• Therefore, the amount of rRNA produced needs to be linked to amino acid availability.
• Regulation of rRNA is dependent on the relA gene (relaxed).
• RelA mutants do not respond to amino acid regulation.
• RelA encodes for an alarmone (a small intracellular signal) called (p)ppGpp.

Question 2

What is (p)ppGpp?

Answer 2

Also known as guanosine pentaphosphate/tetraphosphate.
• It is a guanosine attached to extra phosphates.
• It is created by adding ATP to GTP for pppGpp or ATP and GDP for ppGpp.
• It has multiple effects, mainly preventing the production of rRNA and tRNA.
• It binds to rRNA promoters and prevents RNA pol from binding.
• pppGpp traps or stabilizes the open or closed conformations as a way to slow elongation.

Question 3

How can mRNA be used to control translation?

Answer 3

Translational regulation can be performed by interfering with the interactions between the ribosome (3’ end of 16S rRNA) and the rbs.
• Secondary structures in mRNA.
• Proteins binding to mRNA.
• RNAs binding to mRNA (antisense and tRNAs).

Question 4

How can secondary structure regulate translation?

Answer 4

Secondary structures can act as blockades for translation. Altering the secondary structures can increase or decrease translation.
• Translation can be repressed by metabolites stabilising a secondary structure which leaves the SD sequence and initiation codon in a base-paired region.
• It can equally be enhanced by metabolites changing this secondary structure to leave the SD sequence and initiation codon in an unpaired region.
• Some mRNA structures can be created by a result of temperature changes (thermosensors), leading to repression of translation.
• Translation can be activated by local mRNA melting which gets rid of the secondary structure covering the SD and AUG.

Question 5

How can non-coding transcripts regulate translation?

Answer 5

Non-coding transcripts can inhibit translation as antisense RNAs.
• Cis-asRNAs have a high level of complementarity with the target.
• Trans-asRNAs have a lower level of complementarity and they may require a chaperone to bind to the target (Hfq).
• asRNA may induce degradation due to the presence of an asRNA-mRNA hybrid.
• asRNA can also stop ribosome binding by binding directly to the sequence required.
• sRNAs can also enhance translation by interacting with the secondary structure.
• RprA, DsrA and ArcZ have a distinct secondary structure that can interact with the rpoS (RNA polymerase σ38) transcript and stop an SD-occluding helix from forming.
• σ38 is involved in the general stress response.