Translation and Initiation Regulation in Biology

Translation Regulation

• Translation is a process where ribosomes synthesize proteins from mRNA. Changes in thermodynamics and kinetics affect the core translational steps.
• Polysome profiling is a method to understand translation, using sucrose gradient to separate components based on density.
• Ribosome profiling quantifies ribosome positions on mRNA, useful to determine efficiency and position of ribosomes.
  • Cyclohexamide is used to freeze translation in cells.

Initiation Regulation

• Initiation is a rate-limiting step; mRNAs have fewer ribosomes than they could potentially handle.

• Bacteria: during starvation, deacylated tRNA binds ribosome, RelA binds ribosome, causing ppGpp generation, which inhibits RNA polymerase, affecting transcription response.

• Eukaryotes:

  • Integrated stress response (ISR): deacylated tRNA binds Gcn2 kinase, which phosphorylates elF2a. This reduces global translation by limiting eIF2B (an exchange factor) and impacts transcription.
  • Global response to amino acid starvation (GCN): GCN4 story utilizes Upstream Open Reading Frames (uORFs) in this process.
  • Viral infections (dsRNA): PRK and PERK (unfolded proteins in ER) phosphorylate elF2a limiting global translation.

• Cap-dependent regulation: 4E-BP and elF4E influence cap-binding, impacting translation initiation.

• Viruses often target the cap-dependent pathway and recruit IRES elements to translate their own genes independently. IRES is a cis element in mRNA. SARS-CoV-2 (COVID) nsp1 inhibits host translation and causes viral RNA translation.

• Bacterial Gene Specific Regulation: Riboswitches regulate translation by binding small molecules.

Bacterial Gene Specific Regulation

• Riboswitches are regulatory mRNA segments responding to small molecules, controlling their translation.
• Riboswitches regulate their own translation based on presence of small molecules

Eukaryotic Gene Specific Regulation

• 5' UTR can block scanning or 3' UTR, often regulates development.
• miRNAs (microRNAs) can influence cap-dependent initiation by binding to 3' UTR.

Elongation Regulation

• Nonsense suppression: tRNA can bind to a stop codon, allowing elongation to continue past termination, suppressing premature termination
• Frameshifting: mRNA can be read out-of-frame. Viruses exploit this to produce proteins.
• Sequence motifs:
  • Selenocysteine & Pyrrolysine: specific sequences/motifs stall/direct ribosome activity in translation.
• Ribosome-mediated quality control mechanisms ensure proper processing of translated RNAs.

This quiz explores the processes of translation and initiation regulation in protein synthesis. It covers methods like polysome profiling and ribosome profiling, as well as the mechanisms of translation initiation in bacteria and eukaryotes. Test your knowledge on these critical aspects of molecular biology.